TY  - JOUR
AU  - Breberina, Luka
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6502
AB  - The influences of π−π interactions in phycocyanin proteins and their
environmental preferences were analyzed. The observations indicate that the
majority of the aromatic residues in phycocyanin proteins are involved in π−π
interactions. Phenylalanine (Phe) and tyrosine (Tyr) residues were found to be
involved in π–π interactions much more frequently than tryptophan (Trp) or
histidine (His). Similarly, the Phe−Phe and Tyr−Tyr π–π interacting pair had
the highest frequency of occurrence. In addition to π-π interactions, the aromatic
residues also form π-networks in phycocyanins. The π–π interactions are
most favourable at the pair distance range of 5.5–7 Å, with a clear preference
for T-shaped ring arrangements. Using ab initio calculations, we observed that
most of the π−π interactions possess energy from 0 to −10 kJ mol-1. Stabilization
centres for these proteins showed that all residues found in π−π interactions
are important in locating one or more such centres. π−π interacting residues
are evolutionary conserved. The results obtained from this study will be
beneficial in further understanding the structural stability and eventual development
of protein engineering of phycocyanins.
AB  - Анализирани су утицаји π−π интеракција у протеинима фикоцијанинима и њихове
преференције ка окружењу. Запажања показују да је већина ароматичних остатака у
протеинима фикоцијанинима укључена у π−π интеракције. Утврђено је да су остаци фенилаланина (Phe) и тирозина (Tyr) много чешће укључени у π–π интеракције него триптофана (Trp) или хистидина (His). Слично томе, интерагујући π–π парови Phe−Phe и Tyr−Tyr имали су највећу учесталост појављивања. Додатно, ароматични остаци такође
стварају π-мреже у фикоцијанинима. π–π интеракције су најповољније у распону дистанци парова од 5,5–7 Å, с јасном склоношћу за распоред прстенова у облику слова Т. Користећи ab initio прорачуне, приметили смо да већина π−π интеракција има енергију у распону од 0 до −10 kJ mol-1. Стабилизациони центри ових протеина показали су да су сви остаци пронађени у π−π интеракцијама важни у лоцирању једног или више таквих центара. π−π интеракциони остаци су еволутивно конзервирани. Резултати добивени овом студијом биће од користи у даљем разумевању структурне стабилности и евентуалном развоју протеинског инжењеринга фикоцијанина.
PB  - Belgrade : Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - On the importance of π–π interactions in structural stability of phycocyanins
T1  - О значају π−π интеракција у структурној стабилности фикоцијанина
VL  - 88
IS  - 5
SP  - 481
EP  - 494
DO  - 10.2298/JSC221201008B
ER  - 

@article{
author = "Breberina, Luka and Nikolić, Milan and Stojanović, Srđan and Zlatović, Mario",
year = "2023",
abstract = "The influences of π−π interactions in phycocyanin proteins and their
environmental preferences were analyzed. The observations indicate that the
majority of the aromatic residues in phycocyanin proteins are involved in π−π
interactions. Phenylalanine (Phe) and tyrosine (Tyr) residues were found to be
involved in π–π interactions much more frequently than tryptophan (Trp) or
histidine (His). Similarly, the Phe−Phe and Tyr−Tyr π–π interacting pair had
the highest frequency of occurrence. In addition to π-π interactions, the aromatic
residues also form π-networks in phycocyanins. The π–π interactions are
most favourable at the pair distance range of 5.5–7 Å, with a clear preference
for T-shaped ring arrangements. Using ab initio calculations, we observed that
most of the π−π interactions possess energy from 0 to −10 kJ mol-1. Stabilization
centres for these proteins showed that all residues found in π−π interactions
are important in locating one or more such centres. π−π interacting residues
are evolutionary conserved. The results obtained from this study will be
beneficial in further understanding the structural stability and eventual development
of protein engineering of phycocyanins., Анализирани су утицаји π−π интеракција у протеинима фикоцијанинима и њихове
преференције ка окружењу. Запажања показују да је већина ароматичних остатака у
протеинима фикоцијанинима укључена у π−π интеракције. Утврђено је да су остаци фенилаланина (Phe) и тирозина (Tyr) много чешће укључени у π–π интеракције него триптофана (Trp) или хистидина (His). Слично томе, интерагујући π–π парови Phe−Phe и Tyr−Tyr имали су највећу учесталост појављивања. Додатно, ароматични остаци такође
стварају π-мреже у фикоцијанинима. π–π интеракције су најповољније у распону дистанци парова од 5,5–7 Å, с јасном склоношћу за распоред прстенова у облику слова Т. Користећи ab initio прорачуне, приметили смо да већина π−π интеракција има енергију у распону од 0 до −10 kJ mol-1. Стабилизациони центри ових протеина показали су да су сви остаци пронађени у π−π интеракцијама важни у лоцирању једног или више таквих центара. π−π интеракциони остаци су еволутивно конзервирани. Резултати добивени овом студијом биће од користи у даљем разумевању структурне стабилности и евентуалном развоју протеинског инжењеринга фикоцијанина.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "On the importance of π–π interactions in structural stability of phycocyanins, О значају π−π интеракција у структурној стабилности фикоцијанина",
volume = "88",
number = "5",
pages = "481-494",
doi = "10.2298/JSC221201008B"
}

Breberina, L., Nikolić, M., Stojanović, S.,& Zlatović, M.. (2023). On the importance of π–π interactions in structural stability of phycocyanins. in Journal of the Serbian Chemical Society
Belgrade : Serbian Chemical Society., 88(5), 481-494.
https://doi.org/10.2298/JSC221201008B

Breberina L, Nikolić M, Stojanović S, Zlatović M. On the importance of π–π interactions in structural stability of phycocyanins. in Journal of the Serbian Chemical Society. 2023;88(5):481-494.
doi:10.2298/JSC221201008B .

Breberina, Luka, Nikolić, Milan, Stojanović, Srđan, Zlatović, Mario, "On the importance of π–π interactions in structural stability of phycocyanins" in Journal of the Serbian Chemical Society, 88, no. 5 (2023):481-494,
https://doi.org/10.2298/JSC221201008B . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6503
AB  - In the present work, the influences of π–π interactions in superoxide
dismutase (SOD) active centers were analyzed. The majority of the aromatic
residues are involved in π–π interactions. Predominant type of interacting pairs
is His–His and His–Trp pairs. In addition to π–π interactions, π residues also
form π-networks in SOD proteins. The π–π interactions are most favorable at
the pair distance range of 5–7 Å. We observed that most of the π–π interactions
shows stabilization energies in the range from −4.2 to −12.6 kJ mol-1, while the
metal assisted π–π interactions showed an energy in the range from −83.7 to
−334.7 kJ mol-1. Most of the π–π interacting residues were evolutionary conserved
and thus probably important in maintaining the structural stability of
proteins through these interactions. A high percentage of these residues could
be considered as stabilization centers, contributing to the net stability of SOD
proteins.
AB  - У овом раду анализирани су утицаји π–π интеракција у активним центрима супероксид-дисмутазе (SOD). Већина ароматичних остатака је укључена у π–π интеракције. 
Парови His–His и His–Trp су доминантни тип парова у интеракцији. Поред π–π интеракција, π остаци такође формирају π-мреже у SOD протеинима. π–π интерагујући парови
су најповољнији у опсегу дистанци од 5–7 Å. Приметили смо да већина π–π интеракција
има енергију у опсегу од −4,2 до −12,6 kJ mol-1, док су π–π интеракције уз асистенцију
метала показале енергију у опсегу −83,7 до −334,7 kJ mol-1. Већина π–π интерагујућих
остатака били су еволутивно конзервирани и могли би бити важни у одржавању структурне стабилности кроз ове интеракције. Висок проценат ових остатака може се сматрати стабилизационим центрима који доприносе нето стабилности SOD протеина.
PB  - Belgrade : Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - π–π interactions in structural stability: Role in superoxide dismutases
T1  - Испитивање улоге катјон–π интеракција у активним центрима супероксид-дисмутаза
VL  - 88
IS  - 3
SP  - 223
EP  - 235
DO  - 10.2298/JSC220404052S
ER  - 

@article{
author = "Stojanović, Srđan and Zlatović, Mario",
year = "2023",
abstract = "In the present work, the influences of π–π interactions in superoxide
dismutase (SOD) active centers were analyzed. The majority of the aromatic
residues are involved in π–π interactions. Predominant type of interacting pairs
is His–His and His–Trp pairs. In addition to π–π interactions, π residues also
form π-networks in SOD proteins. The π–π interactions are most favorable at
the pair distance range of 5–7 Å. We observed that most of the π–π interactions
shows stabilization energies in the range from −4.2 to −12.6 kJ mol-1, while the
metal assisted π–π interactions showed an energy in the range from −83.7 to
−334.7 kJ mol-1. Most of the π–π interacting residues were evolutionary conserved
and thus probably important in maintaining the structural stability of
proteins through these interactions. A high percentage of these residues could
be considered as stabilization centers, contributing to the net stability of SOD
proteins., У овом раду анализирани су утицаји π–π интеракција у активним центрима супероксид-дисмутазе (SOD). Већина ароматичних остатака је укључена у π–π интеракције. 
Парови His–His и His–Trp су доминантни тип парова у интеракцији. Поред π–π интеракција, π остаци такође формирају π-мреже у SOD протеинима. π–π интерагујући парови
су најповољнији у опсегу дистанци од 5–7 Å. Приметили смо да већина π–π интеракција
има енергију у опсегу од −4,2 до −12,6 kJ mol-1, док су π–π интеракције уз асистенцију
метала показале енергију у опсегу −83,7 до −334,7 kJ mol-1. Већина π–π интерагујућих
остатака били су еволутивно конзервирани и могли би бити важни у одржавању структурне стабилности кроз ове интеракције. Висок проценат ових остатака може се сматрати стабилизационим центрима који доприносе нето стабилности SOD протеина.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "π–π interactions in structural stability: Role in superoxide dismutases, Испитивање улоге катјон–π интеракција у активним центрима супероксид-дисмутаза",
volume = "88",
number = "3",
pages = "223-235",
doi = "10.2298/JSC220404052S"
}

Stojanović, S.,& Zlatović, M.. (2023). π–π interactions in structural stability: Role in superoxide dismutases. in Journal of the Serbian Chemical Society
Belgrade : Serbian Chemical Society., 88(3), 223-235.
https://doi.org/10.2298/JSC220404052S

Stojanović S, Zlatović M. π–π interactions in structural stability: Role in superoxide dismutases. in Journal of the Serbian Chemical Society. 2023;88(3):223-235.
doi:10.2298/JSC220404052S .

Stojanović, Srđan, Zlatović, Mario, "π–π interactions in structural stability: Role in superoxide dismutases" in Journal of the Serbian Chemical Society, 88, no. 3 (2023):223-235,
https://doi.org/10.2298/JSC220404052S . .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Nikolić, Milan R.
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5330
AB  - The influences of cation−π interactions in phycocyanin proteins and their environmental preferences were analyzed. The number of interactions formed by arginine showed to be higher than those formed by the lysine in the cationic group, while histidine is comparatively higher than phenylalanine and N-terminal residue in the π group. Arg−Tyr and Arg−Phe interacting pairs are predominant among the various pairs analyzed. Cation−π interactions are distance-dependent and can be realized above a wider area above the π ring. We analyzed the energy contribution resulting from cation−π interactions using ab initio calculations. The energy contribution resulting from the most frequent cation−π interactions was in the lower range of strong hydrogen bonds. The results showed that, while most of their interaction energies lay ranged from − 2 to − 8 kcal/mol, those energies could be up to −12− 12 kcal/mol. Stabilization centers for these proteins showed that all residues found in cation−π interactions are important in locating one or more of such centers. In the cation–π interacting residues, 54% of the amino acid residues involved in these interactions might be conserved in phycocyanins. From this study, we infer that cation−π forming residues play an important role in the stability of the multiply commercially used phycocyanin proteins and could help structural biologists and medicinal chemists to design better and safer drugs.
PB  - Elsevier
T2  - Computational Biology and Chemistry
T1  - Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study
VL  - 100
IS  - 107752
DO  - 10.1016/j.compbiolchem.2022.107752
ER  - 

@article{
author = "Breberina, Luka M. and Nikolić, Milan R. and Stojanović, Srđan and Zlatović, Mario",
year = "2022",
abstract = "The influences of cation−π interactions in phycocyanin proteins and their environmental preferences were analyzed. The number of interactions formed by arginine showed to be higher than those formed by the lysine in the cationic group, while histidine is comparatively higher than phenylalanine and N-terminal residue in the π group. Arg−Tyr and Arg−Phe interacting pairs are predominant among the various pairs analyzed. Cation−π interactions are distance-dependent and can be realized above a wider area above the π ring. We analyzed the energy contribution resulting from cation−π interactions using ab initio calculations. The energy contribution resulting from the most frequent cation−π interactions was in the lower range of strong hydrogen bonds. The results showed that, while most of their interaction energies lay ranged from − 2 to − 8 kcal/mol, those energies could be up to −12− 12 kcal/mol. Stabilization centers for these proteins showed that all residues found in cation−π interactions are important in locating one or more of such centers. In the cation–π interacting residues, 54% of the amino acid residues involved in these interactions might be conserved in phycocyanins. From this study, we infer that cation−π forming residues play an important role in the stability of the multiply commercially used phycocyanin proteins and could help structural biologists and medicinal chemists to design better and safer drugs.",
publisher = "Elsevier",
journal = "Computational Biology and Chemistry",
title = "Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study",
volume = "100",
number = "107752",
doi = "10.1016/j.compbiolchem.2022.107752"
}

Breberina, L. M., Nikolić, M. R., Stojanović, S.,& Zlatović, M.. (2022). Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study. in Computational Biology and Chemistry
Elsevier., 100(107752).
https://doi.org/10.1016/j.compbiolchem.2022.107752

Breberina LM, Nikolić MR, Stojanović S, Zlatović M. Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study. in Computational Biology and Chemistry. 2022;100(107752).
doi:10.1016/j.compbiolchem.2022.107752 .

Breberina, Luka M., Nikolić, Milan R., Stojanović, Srđan, Zlatović, Mario, "Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study" in Computational Biology and Chemistry, 100, no. 107752 (2022),
https://doi.org/10.1016/j.compbiolchem.2022.107752 . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5013
AB  - In this study, we have analysed the influence of cation–π interactions on stability and properties of superoxide dismutase (SOD) active centres. The number of interactions formed by arginine is higher than by lysine in the cat­ionic group, while those formed by histidine are comparatively higher in the π group. The energy contribution resulting from most frequent cation–π interact­ions was in the lower range of strong hydrogen bonds. The cation–π interact­ions involving transition metal ions as cation have energy more negative than –418.4 kJ mol-1. The stabilization centres for these proteins showed that all the residues involved in cation–π interactions were important in locating one or more of such centres. The majority of the residues involved in cation–p inter­actions were evolutionarily conserved and might have a significant contribution towards the stability of SOD proteins. The results presented in this work can be very useful for understanding the contribution of cation–π interactions to the stability of SOD active centres.
AB  - У овој студији смо анализирали утицај катјон–π интеракција на стабилност и особине активних центара супероксид-дисмутазе (SOD). Број интеракција које формира аргинин је већи од лизина у групи катјона, док је хистидин сразмерно већи у π групи. Енергетски допринос који је резултат најчешћих катјон–π интеракција био је у доњемопсегу јаких водоничних веза. Катјон–π интеракције које укључују јоне прелазних метала као катјон имају енергију негативнију од –418,4 kJ mol-1. Стабилизациони центри ових протеина показали су да су сви остаци укључени у катјон–π интеракције важни у распоређивању једног или више таквих центара. Већина остатака који су укључени у катјон–π интеракције су еволуцијски конзервирани и могли би имати значајан допринос стабилности SOD протеина. Резултати представљени у овом раду могу бити веома корисни за разумевање доприноса катјон–π интеракција стабилности активних центара SOD.
PB  - Serbian Chemical Society
T2  - The Journal of the Serbian Chemical Society
T1  - Investigations on the role of cation–pi interactions in active centres of superoxide dismutase
T1  - Испитивање улоге катјон–π интеракција у активним центрима супероксид-дисмутаза
VL  - 87
IS  - 4
SP  - 465
EP  - 477
DO  - 10.2298/JSC220109013S
ER  - 

@article{
author = "Stojanović, Srđan and Zlatović, Mario",
year = "2022",
abstract = "In this study, we have analysed the influence of cation–π interactions on stability and properties of superoxide dismutase (SOD) active centres. The number of interactions formed by arginine is higher than by lysine in the cat­ionic group, while those formed by histidine are comparatively higher in the π group. The energy contribution resulting from most frequent cation–π interact­ions was in the lower range of strong hydrogen bonds. The cation–π interact­ions involving transition metal ions as cation have energy more negative than –418.4 kJ mol-1. The stabilization centres for these proteins showed that all the residues involved in cation–π interactions were important in locating one or more of such centres. The majority of the residues involved in cation–p inter­actions were evolutionarily conserved and might have a significant contribution towards the stability of SOD proteins. The results presented in this work can be very useful for understanding the contribution of cation–π interactions to the stability of SOD active centres., У овој студији смо анализирали утицај катјон–π интеракција на стабилност и особине активних центара супероксид-дисмутазе (SOD). Број интеракција које формира аргинин је већи од лизина у групи катјона, док је хистидин сразмерно већи у π групи. Енергетски допринос који је резултат најчешћих катјон–π интеракција био је у доњемопсегу јаких водоничних веза. Катјон–π интеракције које укључују јоне прелазних метала као катјон имају енергију негативнију од –418,4 kJ mol-1. Стабилизациони центри ових протеина показали су да су сви остаци укључени у катјон–π интеракције важни у распоређивању једног или више таквих центара. Већина остатака који су укључени у катјон–π интеракције су еволуцијски конзервирани и могли би имати значајан допринос стабилности SOD протеина. Резултати представљени у овом раду могу бити веома корисни за разумевање доприноса катјон–π интеракција стабилности активних центара SOD.",
publisher = "Serbian Chemical Society",
journal = "The Journal of the Serbian Chemical Society",
title = "Investigations on the role of cation–pi interactions in active centres of superoxide dismutase, Испитивање улоге катјон–π интеракција у активним центрима супероксид-дисмутаза",
volume = "87",
number = "4",
pages = "465-477",
doi = "10.2298/JSC220109013S"
}

Stojanović, S.,& Zlatović, M.. (2022). Investigations on the role of cation–pi interactions in active centres of superoxide dismutase. in The Journal of the Serbian Chemical Society
Serbian Chemical Society., 87(4), 465-477.
https://doi.org/10.2298/JSC220109013S

Stojanović S, Zlatović M. Investigations on the role of cation–pi interactions in active centres of superoxide dismutase. in The Journal of the Serbian Chemical Society. 2022;87(4):465-477.
doi:10.2298/JSC220109013S .

Stojanović, Srđan, Zlatović, Mario, "Investigations on the role of cation–pi interactions in active centres of superoxide dismutase" in The Journal of the Serbian Chemical Society, 87, no. 4 (2022):465-477,
https://doi.org/10.2298/JSC220109013S . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Petrović, Zoran Z.
AU  - Zlatović, Mario
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4761
AB  - PaiIn this work, the influence of amide–π interactions on stability and properties of superoxide dismutase (SOD) active centres was analysed. In the data set of 43 proteins, 5017 amide–π interactions were observed, and every active centre formed averagely about 117 interactions. Most of the interactions belonged to the backbone of proteins. The analysis of the geometry of the amide–π interactions revealed two preferred structures, parallel-displaced and T-shaped structure. The aim of this study was to investigate the energy contribution resulting the from amide–π interactions, which were in the lower range of strong hydrogen bonds. The conservation patterns in the present study indicate that more than half of the residues involved in these interactions are evolutionarily conserved. The stabilization centres for these proteins showed that all residues involved in amide–π interactions were of use in locating one or more of such centres. The results presented in this work can be very useful for the understanding of contribution of amide–π interaction to the stability of SOD active centres.
AB  - У овом раду је анализиран утицај амид–π интеракција на стабилност и особине
активног центра супероксид-дисмутазe (SOD). Примећено је 5017 амид–π интеракција у
сету података од 43 протеина, где, просечно, сваки активни центар формира 117 интер-
акција. Већина интеракција је укључена у основни ланац протеина. Анализа геометрије
амид–π интеракција открива две приоритетне структуре, паралелно-измештен (parallel-
-displaced) и Т-облик (T-shaped) структуре. Ова студија има за циљ истраживање допри-
носа енергије амид–π интеракција чије јачине су у доњем рангу јаких водоничних веза.
Преглед конзервираности показује да је више од половине остатака укључених у ове
интеракције еволутивно конзервирано. Стабилизациони центри ових протеина показују
да су сви остаци који чине амид–_интеракције важни у распоређивању једног или више
таквих центара. Свеукупно, резултати у овом раду ће бити врло корисни за разумевање
доприноса амид–π интеракција када се анализира стабилност активних центара SOD.
PB  - Belgrade : Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - Amide–π interactions in active centres of superoxide dismutase
T1  - Amid-–π interakcije u aktivnom centru superoksid-dismutaza
VL  - 86
VL  - 9
SP  - 781
EP  - 793
DO  - 10.2298/JSC210321042S
ER  - 

@article{
author = "Stojanović, Srđan and Petrović, Zoran Z. and Zlatović, Mario",
year = "2021",
abstract = "PaiIn this work, the influence of amide–π interactions on stability and properties of superoxide dismutase (SOD) active centres was analysed. In the data set of 43 proteins, 5017 amide–π interactions were observed, and every active centre formed averagely about 117 interactions. Most of the interactions belonged to the backbone of proteins. The analysis of the geometry of the amide–π interactions revealed two preferred structures, parallel-displaced and T-shaped structure. The aim of this study was to investigate the energy contribution resulting the from amide–π interactions, which were in the lower range of strong hydrogen bonds. The conservation patterns in the present study indicate that more than half of the residues involved in these interactions are evolutionarily conserved. The stabilization centres for these proteins showed that all residues involved in amide–π interactions were of use in locating one or more of such centres. The results presented in this work can be very useful for the understanding of contribution of amide–π interaction to the stability of SOD active centres., У овом раду је анализиран утицај амид–π интеракција на стабилност и особине
активног центра супероксид-дисмутазe (SOD). Примећено је 5017 амид–π интеракција у
сету података од 43 протеина, где, просечно, сваки активни центар формира 117 интер-
акција. Већина интеракција је укључена у основни ланац протеина. Анализа геометрије
амид–π интеракција открива две приоритетне структуре, паралелно-измештен (parallel-
-displaced) и Т-облик (T-shaped) структуре. Ова студија има за циљ истраживање допри-
носа енергије амид–π интеракција чије јачине су у доњем рангу јаких водоничних веза.
Преглед конзервираности показује да је више од половине остатака укључених у ове
интеракције еволутивно конзервирано. Стабилизациони центри ових протеина показују
да су сви остаци који чине амид–_интеракције важни у распоређивању једног или више
таквих центара. Свеукупно, резултати у овом раду ће бити врло корисни за разумевање
доприноса амид–π интеракција када се анализира стабилност активних центара SOD.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "Amide–π interactions in active centres of superoxide dismutase, Amid-–π interakcije u aktivnom centru superoksid-dismutaza",
volume = "86, 9",
pages = "781-793",
doi = "10.2298/JSC210321042S"
}

Stojanović, S., Petrović, Z. Z.,& Zlatović, M.. (2021). Amide–π interactions in active centres of superoxide dismutase. in Journal of the Serbian Chemical Society
Belgrade : Serbian Chemical Society., 86, 781-793.
https://doi.org/10.2298/JSC210321042S

Stojanović S, Petrović ZZ, Zlatović M. Amide–π interactions in active centres of superoxide dismutase. in Journal of the Serbian Chemical Society. 2021;86:781-793.
doi:10.2298/JSC210321042S .

Stojanović, Srđan, Petrović, Zoran Z., Zlatović, Mario, "Amide–π interactions in active centres of superoxide dismutase" in Journal of the Serbian Chemical Society, 86 (2021):781-793,
https://doi.org/10.2298/JSC210321042S . .

TY  - CONF
AU  - Breberina, Luka
AU  - Stojanović, Srđan
AU  - Nikolić, Milan
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6504
AB  - We investigated 321 possible anion-π interactions in a data set consisting of different
subunit interfaces in 20 phycocyanins PDB structures. We observed that phycocyanobilin
tetrapyrrole chromophore is capable of forming anion-π interactions only as an anion. It
was found that Tyr is the most common aromatic donor. Although presented in the
examined set of interfaces, Trp does not take part in anion-π interactions. Asp-Tyr is the
most common anion-π pair, while Glu-His pair does not exist in our data set. Distance
examination revealed that anion-π interactions between amino acid residues appear in the
range of 3-7 Å, with the average value around 5 Å. The angle between carboxylate and
aromatic ring points preference toward higher values, with a peak at 90° and average value
around 66°. Interestingly, much less represented anion-π contacts including chromophore
show higher values of distance and lower values of this angle. Ab initio calculations
revealed that interaction energies lay in the range from +0.3 to −14 kcal mol−1, with
generally much higher values for anion-π interaction pairs between amino acid residues
compared to the chromophore including interactions. The most common (>50%) anion-π
residue in the stabilization protein centers is Phe, while Glu and His are not presented at
all. Anion-π interacting residues have high average conservation score of 7.7, which is
especially pronounced for anion residues. The highest conservation score is observed for
Asp and the lowest for Phe. Anion-π interacting residues show a preference for buried
regions. Almost half of the residues involved in anion-π interactions are also part of hotspot
regions, but only Asp, Phe, and Tyr. Further, in approximately one-fifth of anion-π
interaction pairs, both of the residues come from the same hot-spot region and these are
exclusively Asp-Tyr contacts. To conclude, a high percentage of anion-π interacting pairs
in stabilization centers, their high presence in hot-spot regions and high conservation score,
together with the favorable energy profile, imply that these interactions might have a
significant role in the stability of phycocyanin oligomers.
PB  - Belgrade : Serbian Biochemical Society
C3  - Proceedings - Serbian Biochemical Society Ninth Conference with international participation, “Diversity in Biochemistry”, 14-16.11.2019. Belgrade, Serbia
T1  - Anion-π interactions in phycocyanin interfaces: a computational analysis
SP  - 80
EP  - 81
UR  - https://hdl.handle.net/21.15107/rcub_cer_6504
ER  - 

@conference{
author = "Breberina, Luka and Stojanović, Srđan and Nikolić, Milan",
year = "2019",
abstract = "We investigated 321 possible anion-π interactions in a data set consisting of different
subunit interfaces in 20 phycocyanins PDB structures. We observed that phycocyanobilin
tetrapyrrole chromophore is capable of forming anion-π interactions only as an anion. It
was found that Tyr is the most common aromatic donor. Although presented in the
examined set of interfaces, Trp does not take part in anion-π interactions. Asp-Tyr is the
most common anion-π pair, while Glu-His pair does not exist in our data set. Distance
examination revealed that anion-π interactions between amino acid residues appear in the
range of 3-7 Å, with the average value around 5 Å. The angle between carboxylate and
aromatic ring points preference toward higher values, with a peak at 90° and average value
around 66°. Interestingly, much less represented anion-π contacts including chromophore
show higher values of distance and lower values of this angle. Ab initio calculations
revealed that interaction energies lay in the range from +0.3 to −14 kcal mol−1, with
generally much higher values for anion-π interaction pairs between amino acid residues
compared to the chromophore including interactions. The most common (>50%) anion-π
residue in the stabilization protein centers is Phe, while Glu and His are not presented at
all. Anion-π interacting residues have high average conservation score of 7.7, which is
especially pronounced for anion residues. The highest conservation score is observed for
Asp and the lowest for Phe. Anion-π interacting residues show a preference for buried
regions. Almost half of the residues involved in anion-π interactions are also part of hotspot
regions, but only Asp, Phe, and Tyr. Further, in approximately one-fifth of anion-π
interaction pairs, both of the residues come from the same hot-spot region and these are
exclusively Asp-Tyr contacts. To conclude, a high percentage of anion-π interacting pairs
in stabilization centers, their high presence in hot-spot regions and high conservation score,
together with the favorable energy profile, imply that these interactions might have a
significant role in the stability of phycocyanin oligomers.",
publisher = "Belgrade : Serbian Biochemical Society",
journal = "Proceedings - Serbian Biochemical Society Ninth Conference with international participation, “Diversity in Biochemistry”, 14-16.11.2019. Belgrade, Serbia",
title = "Anion-π interactions in phycocyanin interfaces: a computational analysis",
pages = "80-81",
url = "https://hdl.handle.net/21.15107/rcub_cer_6504"
}

Breberina, L., Stojanović, S.,& Nikolić, M.. (2019). Anion-π interactions in phycocyanin interfaces: a computational analysis. in Proceedings - Serbian Biochemical Society Ninth Conference with international participation, “Diversity in Biochemistry”, 14-16.11.2019. Belgrade, Serbia
Belgrade : Serbian Biochemical Society., 80-81.
https://hdl.handle.net/21.15107/rcub_cer_6504

Breberina L, Stojanović S, Nikolić M. Anion-π interactions in phycocyanin interfaces: a computational analysis. in Proceedings - Serbian Biochemical Society Ninth Conference with international participation, “Diversity in Biochemistry”, 14-16.11.2019. Belgrade, Serbia. 2019;:80-81.
https://hdl.handle.net/21.15107/rcub_cer_6504 .

Breberina, Luka, Stojanović, Srđan, Nikolić, Milan, "Anion-π interactions in phycocyanin interfaces: a computational analysis" in Proceedings - Serbian Biochemical Society Ninth Conference with international participation, “Diversity in Biochemistry”, 14-16.11.2019. Belgrade, Serbia (2019):80-81,
https://hdl.handle.net/21.15107/rcub_cer_6504 .

TY  - JOUR
AU  - Breberina, Luka
AU  - Zlatović, Mario
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3233
AB  - Protein‐protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non‐redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter‐atomic non‐covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard‐size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water‐bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein‐protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non‐covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein‐bioactive compound interactions.
PB  - Wiley
T2  - Molecular Informatics
T1  - Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces
VL  - 38
IS  - 11-12
SP  - 1800145
DO  - 10.1002/minf.201800145
ER  - 

@article{
author = "Breberina, Luka and Zlatović, Mario and Nikolić, Milan and Stojanović, Srđan",
year = "2019",
abstract = "Protein‐protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non‐redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter‐atomic non‐covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call “standard‐size” interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water‐bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein‐protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than −16 kJ mol−1, while most of them have energy in the range from −6 to −14 kJ mol−1. The non‐covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein‐bioactive compound interactions.",
publisher = "Wiley",
journal = "Molecular Informatics",
title = "Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces",
volume = "38",
number = "11-12",
pages = "1800145",
doi = "10.1002/minf.201800145"
}

Breberina, L., Zlatović, M., Nikolić, M.,& Stojanović, S.. (2019). Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics
Wiley., 38(11-12), 1800145.
https://doi.org/10.1002/minf.201800145

Breberina L, Zlatović M, Nikolić M, Stojanović S. Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces. in Molecular Informatics. 2019;38(11-12):1800145.
doi:10.1002/minf.201800145 .

Breberina, Luka, Zlatović, Mario, Nikolić, Milan, Stojanović, Srđan, "Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces" in Molecular Informatics, 38, no. 11-12 (2019):1800145,
https://doi.org/10.1002/minf.201800145 . .

TY  - JOUR
AU  - Ribić, Vesna
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2457
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins.
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 

@article{
author = "Ribić, Vesna and Stojanović, Srđan and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins.",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}

Ribić, V., Stojanović, S.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050

Ribić V, Stojanović S, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .

Ribić, Vesna, Stojanović, Srđan, Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .

TY  - JOUR
AU  - Ribić, Vesna
AU  - Stojanović, Srđan
AU  - Zlatović, Mario
PY  - 2018
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/3151
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3140
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 

@article{
author = "Ribić, Vesna and Stojanović, Srđan and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}

Ribić, V., Stojanović, S.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050

Ribić V, Stojanović S, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .

Ribić, Vesna, Stojanović, Srđan, Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .

TY  - CONF
AU  - Breberina, Luka
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3544
AB  - Phycocyanins (C-phycocyanin and allophycocyanin) are stable water-soluble trimers (αβ)3 or hexamers (αβ)6, containing dark-blue covalently attached phycocyanobilin chromophore with variety of pharmacological properties. Molecular forces (non-covalent interactions) responsible for the observed differences in thermal and chemical stability of different phycocyanin complexes are not completely understood 1. In this study, we used the manually curated non-redundant dataset of 118 interfaces from 20 X-ray phycocyanin structures (PDB ID codes: 1all, 1b33, 1kn1, 2vjt, 3dbj, 4f0u, 4po5,4rmp, 1cpc, 1gh0, 1f99, 1jbo, 1phn, 2bv8, 2vml, 3o18, 4l1e, 4lm6, 4lms, 4yjj) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (http://caps.ncbs.res.in/ppcheck). For our dataset, the mean interface area was 1088 Å2 and there were on average 59 residues per interface. Most of the individual interface parameters are clustered at the middle of the range which we call “standard-size” interfaces. Our observations indicate that there is relatively high composition (51%) of hydrophobic residues at the phycocyanin interfaces; most frequent amino acids in interfaces are Ala (11.4%), Leu (10.0%), Arg (9.5%) and Thr (8.3%). The analysis shows that about 42% of the total hydrogen bonds in the interfaces under consideration are involved in the formation of multiple hydrogen bonds; 52.8% of total number of hydrogen bonds is formed by water (as donor or acceptor; Figure 1); the
hydrogen bonds across the interfaces are predominantly the O–N type; the largest numbers are side chain–side chain hydrogen bonds (55.9%) between the phycocyanin interfaces; most of hydrogen bonds possess distances in the region 2.8–4.2 Å, indicating their moderate and weak strength. The mean number of hydrophobic interactions per interface is 13.6 (max 30); the hydrophobic side chains make larger number of these interactions than side chains of charged and the hydrophilic amino acid. On average, there are about 3 salt bridges per interface in phycocyanin interfaces (max 7); less than one-tenth of the salt bridges in our database are networked, to form several triads, and the remaining are isolated ones. Most salt bridges (~80%) contain at least one hydrogen bond between the atoms in their side-chain charged groups; there is no preferred combination of donors and acceptors. The stability of a non-covalent complex is usually related to the complexation energy, which is proportional to the strength of the interactions involved. Analysis shows that hydrogen bond energies contribute to about 88% to the total energy. Van der Waals and electrostatic energy contributes to 9.3% and 1.9% on average in these complexes, respectively. Thus, hydrogen bonds contribute maximally towards the stability of protein–protein complexes. Results show the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than -16 kJ/mol, while most of them have energy in the range from 6 to 14 kJ/mol. The non-covalent interacting residues in phycocyanin protein interfaces were found to be highly conserved (ConSurfserver: http://consurf.tau.ac.il/2016/); salt bridge forming residues have average conservation scores 7.3; for those involved in hydrogen bonds is 7.0; the amino acid residues forming hydrophobic interactions and water-bridged hydrogen bonds both have average conservation scores of 5.9 (on scale 1–9). Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein–bioactive compound interactions.
PB  - Serbian Biochemical Society
C3  - Serbian Biochemical Society Eighth Conference with international participation, “Coordination in Biochemistry and Life”, University of Novi Sad – Rectorate Hall, 16.11.2018. Novi Sad, Serbia
T1  - Computational analysis of non-covalent interactions in phycocyanin subunit interfaces
SP  - 119
EP  - 120
UR  - https://hdl.handle.net/21.15107/rcub_cer_3544
ER  - 

@conference{
author = "Breberina, Luka and Nikolić, Milan and Stojanović, Srđan",
year = "2018",
abstract = "Phycocyanins (C-phycocyanin and allophycocyanin) are stable water-soluble trimers (αβ)3 or hexamers (αβ)6, containing dark-blue covalently attached phycocyanobilin chromophore with variety of pharmacological properties. Molecular forces (non-covalent interactions) responsible for the observed differences in thermal and chemical stability of different phycocyanin complexes are not completely understood 1. In this study, we used the manually curated non-redundant dataset of 118 interfaces from 20 X-ray phycocyanin structures (PDB ID codes: 1all, 1b33, 1kn1, 2vjt, 3dbj, 4f0u, 4po5,4rmp, 1cpc, 1gh0, 1f99, 1jbo, 1phn, 2bv8, 2vml, 3o18, 4l1e, 4lm6, 4lms, 4yjj) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (http://caps.ncbs.res.in/ppcheck). For our dataset, the mean interface area was 1088 Å2 and there were on average 59 residues per interface. Most of the individual interface parameters are clustered at the middle of the range which we call “standard-size” interfaces. Our observations indicate that there is relatively high composition (51%) of hydrophobic residues at the phycocyanin interfaces; most frequent amino acids in interfaces are Ala (11.4%), Leu (10.0%), Arg (9.5%) and Thr (8.3%). The analysis shows that about 42% of the total hydrogen bonds in the interfaces under consideration are involved in the formation of multiple hydrogen bonds; 52.8% of total number of hydrogen bonds is formed by water (as donor or acceptor; Figure 1); the
hydrogen bonds across the interfaces are predominantly the O–N type; the largest numbers are side chain–side chain hydrogen bonds (55.9%) between the phycocyanin interfaces; most of hydrogen bonds possess distances in the region 2.8–4.2 Å, indicating their moderate and weak strength. The mean number of hydrophobic interactions per interface is 13.6 (max 30); the hydrophobic side chains make larger number of these interactions than side chains of charged and the hydrophilic amino acid. On average, there are about 3 salt bridges per interface in phycocyanin interfaces (max 7); less than one-tenth of the salt bridges in our database are networked, to form several triads, and the remaining are isolated ones. Most salt bridges (~80%) contain at least one hydrogen bond between the atoms in their side-chain charged groups; there is no preferred combination of donors and acceptors. The stability of a non-covalent complex is usually related to the complexation energy, which is proportional to the strength of the interactions involved. Analysis shows that hydrogen bond energies contribute to about 88% to the total energy. Van der Waals and electrostatic energy contributes to 9.3% and 1.9% on average in these complexes, respectively. Thus, hydrogen bonds contribute maximally towards the stability of protein–protein complexes. Results show the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than -16 kJ/mol, while most of them have energy in the range from 6 to 14 kJ/mol. The non-covalent interacting residues in phycocyanin protein interfaces were found to be highly conserved (ConSurfserver: http://consurf.tau.ac.il/2016/); salt bridge forming residues have average conservation scores 7.3; for those involved in hydrogen bonds is 7.0; the amino acid residues forming hydrophobic interactions and water-bridged hydrogen bonds both have average conservation scores of 5.9 (on scale 1–9). Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein–bioactive compound interactions.",
publisher = "Serbian Biochemical Society",
journal = "Serbian Biochemical Society Eighth Conference with international participation, “Coordination in Biochemistry and Life”, University of Novi Sad – Rectorate Hall, 16.11.2018. Novi Sad, Serbia",
title = "Computational analysis of non-covalent interactions in phycocyanin subunit interfaces",
pages = "119-120",
url = "https://hdl.handle.net/21.15107/rcub_cer_3544"
}

Breberina, L., Nikolić, M.,& Stojanović, S.. (2018). Computational analysis of non-covalent interactions in phycocyanin subunit interfaces. in Serbian Biochemical Society Eighth Conference with international participation, “Coordination in Biochemistry and Life”, University of Novi Sad – Rectorate Hall, 16.11.2018. Novi Sad, Serbia
Serbian Biochemical Society., 119-120.
https://hdl.handle.net/21.15107/rcub_cer_3544

Breberina L, Nikolić M, Stojanović S. Computational analysis of non-covalent interactions in phycocyanin subunit interfaces. in Serbian Biochemical Society Eighth Conference with international participation, “Coordination in Biochemistry and Life”, University of Novi Sad – Rectorate Hall, 16.11.2018. Novi Sad, Serbia. 2018;:119-120.
https://hdl.handle.net/21.15107/rcub_cer_3544 .

Breberina, Luka, Nikolić, Milan, Stojanović, Srđan, "Computational analysis of non-covalent interactions in phycocyanin subunit interfaces" in Serbian Biochemical Society Eighth Conference with international participation, “Coordination in Biochemistry and Life”, University of Novi Sad – Rectorate Hall, 16.11.2018. Novi Sad, Serbia (2018):119-120,
https://hdl.handle.net/21.15107/rcub_cer_3544 .

TY  - JOUR
AU  - Borozan, Sunčica
AU  - Zlatović, Mario
AU  - Stojanović, Srđan
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2007
AB  - We analyzed the potential influence of anion-pi interactions on the stability of complexes of proteins and halogen-containing non-natural amino acids. Anion-pi interactions are distance and orientation dependent and our ab initio calculations showed that their energy can be lower than -8 kcal mol(-1), while most of their interaction energies lie in the range from -1 to -4 kcal mol(-1). About 20 % of these interactions were found to be repulsive. We have observed that Tyr has the highest occurrence among the aromatic residues involved in anion-pi interactions, while His made the least contribution. Furthermore, our study showed that 67 % of total interactions in the dataset are multiple anion-pi interactions. Most of the amino acid residues involved in anion-pi interactions tend to be buried in the solvent-excluded environment. The majority of the anion-pi interacting residues are located in regions with helical secondary structure. Analysis of stabilization centers for these complexes showed that all of the six residues capable of anion-pi interactions are important in locating one or more of such centers. We found that anion-pi interacting residues are sometimes involved in simultaneous interactions with halogens as well. With all that in mind, we can conclude that the anion-pi interactions can show significant influence on molecular organization and on the structural stability of the complexes of proteins and halogen-containing non-natural amino acids. Their influence should not be neglected in supramolecular chemistry and crystal engineering fields as well.
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - Anion-pi interactions in complexes of proteins and halogen-containing amino acids
VL  - 21
IS  - 3
SP  - 357
EP  - 368
DO  - 10.1007/s00775-016-1346-y
ER  - 

@article{
author = "Borozan, Sunčica and Zlatović, Mario and Stojanović, Srđan",
year = "2016",
abstract = "We analyzed the potential influence of anion-pi interactions on the stability of complexes of proteins and halogen-containing non-natural amino acids. Anion-pi interactions are distance and orientation dependent and our ab initio calculations showed that their energy can be lower than -8 kcal mol(-1), while most of their interaction energies lie in the range from -1 to -4 kcal mol(-1). About 20 % of these interactions were found to be repulsive. We have observed that Tyr has the highest occurrence among the aromatic residues involved in anion-pi interactions, while His made the least contribution. Furthermore, our study showed that 67 % of total interactions in the dataset are multiple anion-pi interactions. Most of the amino acid residues involved in anion-pi interactions tend to be buried in the solvent-excluded environment. The majority of the anion-pi interacting residues are located in regions with helical secondary structure. Analysis of stabilization centers for these complexes showed that all of the six residues capable of anion-pi interactions are important in locating one or more of such centers. We found that anion-pi interacting residues are sometimes involved in simultaneous interactions with halogens as well. With all that in mind, we can conclude that the anion-pi interactions can show significant influence on molecular organization and on the structural stability of the complexes of proteins and halogen-containing non-natural amino acids. Their influence should not be neglected in supramolecular chemistry and crystal engineering fields as well.",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "Anion-pi interactions in complexes of proteins and halogen-containing amino acids",
volume = "21",
number = "3",
pages = "357-368",
doi = "10.1007/s00775-016-1346-y"
}

Borozan, S., Zlatović, M.,& Stojanović, S.. (2016). Anion-pi interactions in complexes of proteins and halogen-containing amino acids. in Journal of Biological Inorganic Chemistry
Springer, New York., 21(3), 357-368.
https://doi.org/10.1007/s00775-016-1346-y

Borozan S, Zlatović M, Stojanović S. Anion-pi interactions in complexes of proteins and halogen-containing amino acids. in Journal of Biological Inorganic Chemistry. 2016;21(3):357-368.
doi:10.1007/s00775-016-1346-y .

Borozan, Sunčica, Zlatović, Mario, Stojanović, Srđan, "Anion-pi interactions in complexes of proteins and halogen-containing amino acids" in Journal of Biological Inorganic Chemistry, 21, no. 3 (2016):357-368,
https://doi.org/10.1007/s00775-016-1346-y . .

TY  - JOUR
AU  - Radakovic, M.
AU  - Davitkov, D.
AU  - Borozan, Sunčica
AU  - Stojanović, Srđan
AU  - Stevanović, Jevrosima
AU  - Krstic, V.
AU  - Stanimirovic, Z.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1947
AB  - The aim of this study was to determine the concentrations of oxidative stress parameters and DNA damage in horses infected by Theileria equi. Initial screening of 110 horses with duplex PCR enabled the selection of 30 infected horses with T. equi and 30 free of infection (control). Specimens from the 60 horses were further analysed by determining the following oxidative stress parameters: extent of haemolysis (EH), plasma free haemoglobin (PHb), catalase (CAT), Cu,Zn superoxide dismutase (SOD1), paraoxonase (PON1), nitrite (NO2-), total nitrate and nitrite (NOx), malondialdehyde (MDA) and free thiol groups (-SH). In addition, relative distribution of lactate dehydrogenase (LDH1-LDH5) activity and the DNA-damaging effects of T. equi infection were evaluated. Compared to control horses, horses infected with T. equi had significantly higher SOD1 activities (P  LT  0.05) and PHb (P  LT  0.01), NO2- (P  LT  0.001), NOx (P  LT  0.05) and MDA concentrations (P  LT  0.001), and significantly-lower EH (P  LT  0.001), CAT (P  LT  0.01) and PON1 (P  LT  0.001) activities, and thiol group concentrations (P  LT  0.05). The comet assay demonstrated significantly increased DNA damage in T. equi infected cells compared to non-infected cells (P  LT  0.001). Infected horses had significantly increased LDH5 isoenzyme activities (P  LT  0.05). There was higher production of ROS/RNS in T. equi-infected horses, which resulted in changes in osmotic fragility, damage to lipids, proteins and DNA, haemolysis and hepatocellular damage. Oxidative stress in horses naturally infected with T equi could contribute to the pathogenesis of the infection.
PB  - Elsevier Sci Ltd, Oxford
T2  - Veterinary Journal
T1  - Oxidative stress and DNA damage in horses naturally infected with Theileria equi
VL  - 217
SP  - 112
EP  - 118
DO  - 10.1016/j.tvjl.2016.10.003
ER  - 

@article{
author = "Radakovic, M. and Davitkov, D. and Borozan, Sunčica and Stojanović, Srđan and Stevanović, Jevrosima and Krstic, V. and Stanimirovic, Z.",
year = "2016",
abstract = "The aim of this study was to determine the concentrations of oxidative stress parameters and DNA damage in horses infected by Theileria equi. Initial screening of 110 horses with duplex PCR enabled the selection of 30 infected horses with T. equi and 30 free of infection (control). Specimens from the 60 horses were further analysed by determining the following oxidative stress parameters: extent of haemolysis (EH), plasma free haemoglobin (PHb), catalase (CAT), Cu,Zn superoxide dismutase (SOD1), paraoxonase (PON1), nitrite (NO2-), total nitrate and nitrite (NOx), malondialdehyde (MDA) and free thiol groups (-SH). In addition, relative distribution of lactate dehydrogenase (LDH1-LDH5) activity and the DNA-damaging effects of T. equi infection were evaluated. Compared to control horses, horses infected with T. equi had significantly higher SOD1 activities (P  LT  0.05) and PHb (P  LT  0.01), NO2- (P  LT  0.001), NOx (P  LT  0.05) and MDA concentrations (P  LT  0.001), and significantly-lower EH (P  LT  0.001), CAT (P  LT  0.01) and PON1 (P  LT  0.001) activities, and thiol group concentrations (P  LT  0.05). The comet assay demonstrated significantly increased DNA damage in T. equi infected cells compared to non-infected cells (P  LT  0.001). Infected horses had significantly increased LDH5 isoenzyme activities (P  LT  0.05). There was higher production of ROS/RNS in T. equi-infected horses, which resulted in changes in osmotic fragility, damage to lipids, proteins and DNA, haemolysis and hepatocellular damage. Oxidative stress in horses naturally infected with T equi could contribute to the pathogenesis of the infection.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Veterinary Journal",
title = "Oxidative stress and DNA damage in horses naturally infected with Theileria equi",
volume = "217",
pages = "112-118",
doi = "10.1016/j.tvjl.2016.10.003"
}

Radakovic, M., Davitkov, D., Borozan, S., Stojanović, S., Stevanović, J., Krstic, V.,& Stanimirovic, Z.. (2016). Oxidative stress and DNA damage in horses naturally infected with Theileria equi. in Veterinary Journal
Elsevier Sci Ltd, Oxford., 217, 112-118.
https://doi.org/10.1016/j.tvjl.2016.10.003

Radakovic M, Davitkov D, Borozan S, Stojanović S, Stevanović J, Krstic V, Stanimirovic Z. Oxidative stress and DNA damage in horses naturally infected with Theileria equi. in Veterinary Journal. 2016;217:112-118.
doi:10.1016/j.tvjl.2016.10.003 .

Radakovic, M., Davitkov, D., Borozan, Sunčica, Stojanović, Srđan, Stevanović, Jevrosima, Krstic, V., Stanimirovic, Z., "Oxidative stress and DNA damage in horses naturally infected with Theileria equi" in Veterinary Journal, 217 (2016):112-118,
https://doi.org/10.1016/j.tvjl.2016.10.003 . .

TY  - JOUR
AU  - Radakovic, M.
AU  - Davitkov, D.
AU  - Borozan, Sunčica
AU  - Stojanović, Srđan
AU  - Stevanović, Jevrosima
AU  - Krstic, V.
AU  - Stanimirovic, Z.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4383
AB  - The aim of this study was to determine the concentrations of oxidative stress parameters and DNA damage in horses infected by Theileria equi. Initial screening of 110 horses with duplex PCR enabled the selection of 30 infected horses with T. equi and 30 free of infection (control). Specimens from the 60 horses were further analysed by determining the following oxidative stress parameters: extent of haemolysis (EH), plasma free haemoglobin (PHb), catalase (CAT), Cu,Zn superoxide dismutase (SOD1), paraoxonase (PON1), nitrite (NO2-), total nitrate and nitrite (NOx), malondialdehyde (MDA) and free thiol groups (-SH). In addition, relative distribution of lactate dehydrogenase (LDH1-LDH5) activity and the DNA-damaging effects of T. equi infection were evaluated. Compared to control horses, horses infected with T. equi had significantly higher SOD1 activities (P  LT  0.05) and PHb (P  LT  0.01), NO2- (P  LT  0.001), NOx (P  LT  0.05) and MDA concentrations (P  LT  0.001), and significantly-lower EH (P  LT  0.001), CAT (P  LT  0.01) and PON1 (P  LT  0.001) activities, and thiol group concentrations (P  LT  0.05). The comet assay demonstrated significantly increased DNA damage in T. equi infected cells compared to non-infected cells (P  LT  0.001). Infected horses had significantly increased LDH5 isoenzyme activities (P  LT  0.05). There was higher production of ROS/RNS in T. equi-infected horses, which resulted in changes in osmotic fragility, damage to lipids, proteins and DNA, haemolysis and hepatocellular damage. Oxidative stress in horses naturally infected with T equi could contribute to the pathogenesis of the infection.
PB  - Elsevier
T2  - Veterinary Journal
T1  - Oxidative stress and DNA damage in horses naturally infected with Theileria equi
VL  - 217
SP  - 112
EP  - 118
DO  - 10.1016/j.tvjl.2016.10.003
ER  - 

@article{
author = "Radakovic, M. and Davitkov, D. and Borozan, Sunčica and Stojanović, Srđan and Stevanović, Jevrosima and Krstic, V. and Stanimirovic, Z.",
year = "2016",
abstract = "The aim of this study was to determine the concentrations of oxidative stress parameters and DNA damage in horses infected by Theileria equi. Initial screening of 110 horses with duplex PCR enabled the selection of 30 infected horses with T. equi and 30 free of infection (control). Specimens from the 60 horses were further analysed by determining the following oxidative stress parameters: extent of haemolysis (EH), plasma free haemoglobin (PHb), catalase (CAT), Cu,Zn superoxide dismutase (SOD1), paraoxonase (PON1), nitrite (NO2-), total nitrate and nitrite (NOx), malondialdehyde (MDA) and free thiol groups (-SH). In addition, relative distribution of lactate dehydrogenase (LDH1-LDH5) activity and the DNA-damaging effects of T. equi infection were evaluated. Compared to control horses, horses infected with T. equi had significantly higher SOD1 activities (P  LT  0.05) and PHb (P  LT  0.01), NO2- (P  LT  0.001), NOx (P  LT  0.05) and MDA concentrations (P  LT  0.001), and significantly-lower EH (P  LT  0.001), CAT (P  LT  0.01) and PON1 (P  LT  0.001) activities, and thiol group concentrations (P  LT  0.05). The comet assay demonstrated significantly increased DNA damage in T. equi infected cells compared to non-infected cells (P  LT  0.001). Infected horses had significantly increased LDH5 isoenzyme activities (P  LT  0.05). There was higher production of ROS/RNS in T. equi-infected horses, which resulted in changes in osmotic fragility, damage to lipids, proteins and DNA, haemolysis and hepatocellular damage. Oxidative stress in horses naturally infected with T equi could contribute to the pathogenesis of the infection.",
publisher = "Elsevier",
journal = "Veterinary Journal",
title = "Oxidative stress and DNA damage in horses naturally infected with Theileria equi",
volume = "217",
pages = "112-118",
doi = "10.1016/j.tvjl.2016.10.003"
}

Radakovic, M., Davitkov, D., Borozan, S., Stojanović, S., Stevanović, J., Krstic, V.,& Stanimirovic, Z.. (2016). Oxidative stress and DNA damage in horses naturally infected with Theileria equi. in Veterinary Journal
Elsevier., 217, 112-118.
https://doi.org/10.1016/j.tvjl.2016.10.003

Radakovic M, Davitkov D, Borozan S, Stojanović S, Stevanović J, Krstic V, Stanimirovic Z. Oxidative stress and DNA damage in horses naturally infected with Theileria equi. in Veterinary Journal. 2016;217:112-118.
doi:10.1016/j.tvjl.2016.10.003 .

Radakovic, M., Davitkov, D., Borozan, Sunčica, Stojanović, Srđan, Stevanović, Jevrosima, Krstic, V., Stanimirovic, Z., "Oxidative stress and DNA damage in horses naturally infected with Theileria equi" in Veterinary Journal, 217 (2016):112-118,
https://doi.org/10.1016/j.tvjl.2016.10.003 . .

TY  - JOUR
AU  - Zlatović, Mario
AU  - Borozan, Sunčica
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1811
AB  - In this work, we have analyzed the influence of anion-pi interactions on the stability of high resolution protein-porphyrin complex crystal structures. The anion-pi interactions are distance and orientation dependent. Results of ab initio calculations of stabilization energies showed that they lie mostly in the range from -2 to -4 kcal mol(-1) with some of the anion-pi interactions having stabilization energies of up to -16 kcal mol(-1). In the anionic group, the numbers of anion-pi interactions involving Asp and Glu are similar, while His is more often involved in these interactions than other aromatic residues. Furthermore, our study showed that in the dataset used about 70% of the investigated anion-pi interactions are in fact multiple anion-pi interactions. Our results suggest that interacting residues are predominantly located in buried and partially buried regions. The secondary structure of the anion-pi interaction involving residues shows that most of the interacting residues preferred to be in helix conformations. Significant numbers of aromatic residues involved in anion-pi interactions have one or more stabilization centers, providing additional stability to the protein-porphyrin complexes. The conservation patterns indicate that more than half of the residues involved in these interactions are evolutionarily conserved, indicating that the contribution of the anion-pi interaction is an important factor for the structural stability of the investigated protein-porphyrin complexes.
PB  - Royal Soc Chemistry, Cambridge
T2  - RSC Advances
T1  - Anion-pi interactions in protein-porphyrin complexes
VL  - 5
IS  - 48
SP  - 38361
EP  - 38372
DO  - 10.1039/c5ra03373j
ER  - 

@article{
author = "Zlatović, Mario and Borozan, Sunčica and Nikolić, Milan and Stojanović, Srđan",
year = "2015",
abstract = "In this work, we have analyzed the influence of anion-pi interactions on the stability of high resolution protein-porphyrin complex crystal structures. The anion-pi interactions are distance and orientation dependent. Results of ab initio calculations of stabilization energies showed that they lie mostly in the range from -2 to -4 kcal mol(-1) with some of the anion-pi interactions having stabilization energies of up to -16 kcal mol(-1). In the anionic group, the numbers of anion-pi interactions involving Asp and Glu are similar, while His is more often involved in these interactions than other aromatic residues. Furthermore, our study showed that in the dataset used about 70% of the investigated anion-pi interactions are in fact multiple anion-pi interactions. Our results suggest that interacting residues are predominantly located in buried and partially buried regions. The secondary structure of the anion-pi interaction involving residues shows that most of the interacting residues preferred to be in helix conformations. Significant numbers of aromatic residues involved in anion-pi interactions have one or more stabilization centers, providing additional stability to the protein-porphyrin complexes. The conservation patterns indicate that more than half of the residues involved in these interactions are evolutionarily conserved, indicating that the contribution of the anion-pi interaction is an important factor for the structural stability of the investigated protein-porphyrin complexes.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "RSC Advances",
title = "Anion-pi interactions in protein-porphyrin complexes",
volume = "5",
number = "48",
pages = "38361-38372",
doi = "10.1039/c5ra03373j"
}

Zlatović, M., Borozan, S., Nikolić, M.,& Stojanović, S.. (2015). Anion-pi interactions in protein-porphyrin complexes. in RSC Advances
Royal Soc Chemistry, Cambridge., 5(48), 38361-38372.
https://doi.org/10.1039/c5ra03373j

Zlatović M, Borozan S, Nikolić M, Stojanović S. Anion-pi interactions in protein-porphyrin complexes. in RSC Advances. 2015;5(48):38361-38372.
doi:10.1039/c5ra03373j .

Zlatović, Mario, Borozan, Sunčica, Nikolić, Milan, Stojanović, Srđan, "Anion-pi interactions in protein-porphyrin complexes" in RSC Advances, 5, no. 48 (2015):38361-38372,
https://doi.org/10.1039/c5ra03373j . .

TY  - JOUR
AU  - Mucic, Ivana D
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1630
AB  - In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation-pi residues shows that Arg and Lys preferred to be in strand. Among the pi residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. More than 50 % of the cation-pi interacting residues are highly conserved. It is likely that the cation-pi interactions contribute significantly to the overall stability of Sm/LSm proteins.
PB  - Springer Wien, Wien
T2  - Protoplasma
T1  - Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies
VL  - 252
IS  - 4
SP  - 947
EP  - 958
DO  - 10.1007/s00709-014-0727-8
ER  - 

@article{
author = "Mucic, Ivana D and Nikolić, Milan and Stojanović, Srđan",
year = "2015",
abstract = "In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation-pi residues shows that Arg and Lys preferred to be in strand. Among the pi residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. More than 50 % of the cation-pi interacting residues are highly conserved. It is likely that the cation-pi interactions contribute significantly to the overall stability of Sm/LSm proteins.",
publisher = "Springer Wien, Wien",
journal = "Protoplasma",
title = "Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies",
volume = "252",
number = "4",
pages = "947-958",
doi = "10.1007/s00709-014-0727-8"
}

Mucic, I. D., Nikolić, M.,& Stojanović, S.. (2015). Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies. in Protoplasma
Springer Wien, Wien., 252(4), 947-958.
https://doi.org/10.1007/s00709-014-0727-8

Mucic ID, Nikolić M, Stojanović S. Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies. in Protoplasma. 2015;252(4):947-958.
doi:10.1007/s00709-014-0727-8 .

Mucic, Ivana D, Nikolić, Milan, Stojanović, Srđan, "Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies" in Protoplasma, 252, no. 4 (2015):947-958,
https://doi.org/10.1007/s00709-014-0727-8 . .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Milčić, Miloš
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1693
AB  - We have analyzed the influence of anion-pi interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-pi interactions than Asp. Phe has the highest occurrence in these interactions than the other two pi residues. Among the anion-pi residue pairs, Glu-Phe residue pair showed the maximum number of anion-pi. We have found hot-spot residues forming anion-pi interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-pi interacting residues identified in the dataset were involved in the formation of multiple anion-pi interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-pi interaction energies are distance and orientation dependent. It was found that anion-pi interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-pi interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same pi-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-pi interaction to the stability of Sm/LSm proteins.
PB  - Springer, New York
T2  - Journal of Biological Inorganic Chemistry
T1  - Contribution of anion-pi interactions to the stability of Sm/LSm proteins
VL  - 20
IS  - 3
SP  - 475
EP  - 485
DO  - 10.1007/s00775-014-1227-1
ER  - 

@article{
author = "Breberina, Luka M. and Milčić, Miloš and Nikolić, Milan and Stojanović, Srđan",
year = "2015",
abstract = "We have analyzed the influence of anion-pi interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-pi interactions than Asp. Phe has the highest occurrence in these interactions than the other two pi residues. Among the anion-pi residue pairs, Glu-Phe residue pair showed the maximum number of anion-pi. We have found hot-spot residues forming anion-pi interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-pi interacting residues identified in the dataset were involved in the formation of multiple anion-pi interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-pi interaction energies are distance and orientation dependent. It was found that anion-pi interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-pi interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same pi-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-pi interaction to the stability of Sm/LSm proteins.",
publisher = "Springer, New York",
journal = "Journal of Biological Inorganic Chemistry",
title = "Contribution of anion-pi interactions to the stability of Sm/LSm proteins",
volume = "20",
number = "3",
pages = "475-485",
doi = "10.1007/s00775-014-1227-1"
}

Breberina, L. M., Milčić, M., Nikolić, M.,& Stojanović, S.. (2015). Contribution of anion-pi interactions to the stability of Sm/LSm proteins. in Journal of Biological Inorganic Chemistry
Springer, New York., 20(3), 475-485.
https://doi.org/10.1007/s00775-014-1227-1

Breberina LM, Milčić M, Nikolić M, Stojanović S. Contribution of anion-pi interactions to the stability of Sm/LSm proteins. in Journal of Biological Inorganic Chemistry. 2015;20(3):475-485.
doi:10.1007/s00775-014-1227-1 .

Breberina, Luka M., Milčić, Miloš, Nikolić, Milan, Stojanović, Srđan, "Contribution of anion-pi interactions to the stability of Sm/LSm proteins" in Journal of Biological Inorganic Chemistry, 20, no. 3 (2015):475-485,
https://doi.org/10.1007/s00775-014-1227-1 . .

TY  - JOUR
AU  - Cabarkapa, Andrea
AU  - Borozan, Sunčica
AU  - Živković, Lada
AU  - Milanovic-Cabarkapa, Mirjana
AU  - Stojanović, Srđan
AU  - Bajic, Vladan
AU  - Spremo-Potparević, Biljana
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1706
AB  - The aim of this study was to determine oxidative alterations leading to cellular dysfunctions in Pb-exposed subjects by evaluating damage to all major classes of biomolecules in the cell, lipid peroxidation, protein and DNA damage and determine relationships between parameters of Pb toxicity and specific biomarkers of oxidative damage.Analysis was conducted of smelter workers with high blood Pb and urine aminolevulinic acid levels and slightly elevated values of coproporphyrin and erythrocyte protoporphyrin IX. Significant decreases of thiol groups and increases in carbonyl groups as protein degradation end products, and of nitrite were detected. Elevated rates of lipid peroxidation and rises in the activities of the antioxidant enzymes Cu-Zn superoxide dismutase and catalase were also observed. Both enzymes showed positive correlations with the blood lead levels and urine coproporphyrin, while thiol groups correlated negatively with the same indices. The genotoxic potential of lead was manifested through an increased number of DNA-damaged cells. Increased activities of serum lactate dehydrogenase isoenzymes indicated cellular damage in the lungs, kidneys, and liver. These lead-induced impairments should be taken into consideration in the assessment of Pb-related health hazards.
PB  - Taylor & Francis Ltd, Abingdon
T2  - Toxicological and Environmental Chemistry
T1  - Implications of oxidative stress in occupational exposure to lead on a cellular level
VL  - 97
IS  - 6
SP  - 799
EP  - 813
DO  - 10.1080/02772248.2015.1060973
ER  - 

@article{
author = "Cabarkapa, Andrea and Borozan, Sunčica and Živković, Lada and Milanovic-Cabarkapa, Mirjana and Stojanović, Srđan and Bajic, Vladan and Spremo-Potparević, Biljana",
year = "2015",
abstract = "The aim of this study was to determine oxidative alterations leading to cellular dysfunctions in Pb-exposed subjects by evaluating damage to all major classes of biomolecules in the cell, lipid peroxidation, protein and DNA damage and determine relationships between parameters of Pb toxicity and specific biomarkers of oxidative damage.Analysis was conducted of smelter workers with high blood Pb and urine aminolevulinic acid levels and slightly elevated values of coproporphyrin and erythrocyte protoporphyrin IX. Significant decreases of thiol groups and increases in carbonyl groups as protein degradation end products, and of nitrite were detected. Elevated rates of lipid peroxidation and rises in the activities of the antioxidant enzymes Cu-Zn superoxide dismutase and catalase were also observed. Both enzymes showed positive correlations with the blood lead levels and urine coproporphyrin, while thiol groups correlated negatively with the same indices. The genotoxic potential of lead was manifested through an increased number of DNA-damaged cells. Increased activities of serum lactate dehydrogenase isoenzymes indicated cellular damage in the lungs, kidneys, and liver. These lead-induced impairments should be taken into consideration in the assessment of Pb-related health hazards.",
publisher = "Taylor & Francis Ltd, Abingdon",
journal = "Toxicological and Environmental Chemistry",
title = "Implications of oxidative stress in occupational exposure to lead on a cellular level",
volume = "97",
number = "6",
pages = "799-813",
doi = "10.1080/02772248.2015.1060973"
}

Cabarkapa, A., Borozan, S., Živković, L., Milanovic-Cabarkapa, M., Stojanović, S., Bajic, V.,& Spremo-Potparević, B.. (2015). Implications of oxidative stress in occupational exposure to lead on a cellular level. in Toxicological and Environmental Chemistry
Taylor & Francis Ltd, Abingdon., 97(6), 799-813.
https://doi.org/10.1080/02772248.2015.1060973

Cabarkapa A, Borozan S, Živković L, Milanovic-Cabarkapa M, Stojanović S, Bajic V, Spremo-Potparević B. Implications of oxidative stress in occupational exposure to lead on a cellular level. in Toxicological and Environmental Chemistry. 2015;97(6):799-813.
doi:10.1080/02772248.2015.1060973 .

Cabarkapa, Andrea, Borozan, Sunčica, Živković, Lada, Milanovic-Cabarkapa, Mirjana, Stojanović, Srđan, Bajic, Vladan, Spremo-Potparević, Biljana, "Implications of oxidative stress in occupational exposure to lead on a cellular level" in Toxicological and Environmental Chemistry, 97, no. 6 (2015):799-813,
https://doi.org/10.1080/02772248.2015.1060973 . .

TY  - JOUR
AU  - Cabarkapa, A
AU  - Borozan, Sunčica
AU  - Zivkovic, L
AU  - Stojanović, Srđan
AU  - Milanovic-Cabarkapa, M
AU  - Bajic, V
AU  - Spremo-Potparević, Biljana
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1800
AB  - Lead induced oxidative cellular damage and long-term persistence of associated adverse effects increases risk of late-onset diseases. CaNa(2)EDTA chelation is known to remove contaminating metals and to reduce free radical production. The objective was to investigate the impact of chelation therapy on modulation of lead induced cellular damage, restoration of altered enzyme activities and lipid homeostasis in peripheral blood of workers exposed to lead, by comparing the selected biomarkers obtained prior and after five-day CaNa(2)EDTA chelation intervention. The group of smelting factory workers diagnosed with lead intoxication and current lead exposure 5.8 +/- 1.2 years were administered five-day CaNa(2)EDTA chelation. Elevated baseline activity of antioxidant enzymes Cu, Zn-SOD and CAT as well as depleted thiols and increased protein degradation products-carbonyl groups and nitrites, pointing to Pb induced oxidative damage, were restored toward normal values following the treatment. Lead showed inhibitor potency on both RBC AChE and BChE in exposed workers, and chelation re-established the activity of BChE, while RBC AChE remained unaffected. Also, genotoxic effect of lead detected in peripheral blood lymphocytes was significantly decreased after therapy, exhibiting 18.9% DNA damage reduction. Administration of chelation reversed the depressed activity of serum PON 1 and significantly decreased lipid peroxidation detected by the post-chelation reduction of MDA levels. Lactate dehydrogenase LDF1-5 isoenzymes levels showed evident but no significant trend of restoring toward normal control values following chelation. CaNa(2)EDTA chelation ameliorates the alterations linked with Pb mediated oxidative stress, indicating possible benefits in reducing health risks associated with increased oxidative damage in lead exposed populations.
PB  - Elsevier Ireland Ltd, Clare
T2  - Chemico-Biological Interactions
T1  - CaNa(2)EDTA chelation attenuates cell damage in workers exposed to lead-a pilot study
VL  - 242
SP  - 171
EP  - 178
DO  - 10.1016/j.cbi.2015.10.002
ER  - 

@article{
author = "Cabarkapa, A and Borozan, Sunčica and Zivkovic, L and Stojanović, Srđan and Milanovic-Cabarkapa, M and Bajic, V and Spremo-Potparević, Biljana",
year = "2015",
abstract = "Lead induced oxidative cellular damage and long-term persistence of associated adverse effects increases risk of late-onset diseases. CaNa(2)EDTA chelation is known to remove contaminating metals and to reduce free radical production. The objective was to investigate the impact of chelation therapy on modulation of lead induced cellular damage, restoration of altered enzyme activities and lipid homeostasis in peripheral blood of workers exposed to lead, by comparing the selected biomarkers obtained prior and after five-day CaNa(2)EDTA chelation intervention. The group of smelting factory workers diagnosed with lead intoxication and current lead exposure 5.8 +/- 1.2 years were administered five-day CaNa(2)EDTA chelation. Elevated baseline activity of antioxidant enzymes Cu, Zn-SOD and CAT as well as depleted thiols and increased protein degradation products-carbonyl groups and nitrites, pointing to Pb induced oxidative damage, were restored toward normal values following the treatment. Lead showed inhibitor potency on both RBC AChE and BChE in exposed workers, and chelation re-established the activity of BChE, while RBC AChE remained unaffected. Also, genotoxic effect of lead detected in peripheral blood lymphocytes was significantly decreased after therapy, exhibiting 18.9% DNA damage reduction. Administration of chelation reversed the depressed activity of serum PON 1 and significantly decreased lipid peroxidation detected by the post-chelation reduction of MDA levels. Lactate dehydrogenase LDF1-5 isoenzymes levels showed evident but no significant trend of restoring toward normal control values following chelation. CaNa(2)EDTA chelation ameliorates the alterations linked with Pb mediated oxidative stress, indicating possible benefits in reducing health risks associated with increased oxidative damage in lead exposed populations.",
publisher = "Elsevier Ireland Ltd, Clare",
journal = "Chemico-Biological Interactions",
title = "CaNa(2)EDTA chelation attenuates cell damage in workers exposed to lead-a pilot study",
volume = "242",
pages = "171-178",
doi = "10.1016/j.cbi.2015.10.002"
}

Cabarkapa, A., Borozan, S., Zivkovic, L., Stojanović, S., Milanovic-Cabarkapa, M., Bajic, V.,& Spremo-Potparević, B.. (2015). CaNa(2)EDTA chelation attenuates cell damage in workers exposed to lead-a pilot study. in Chemico-Biological Interactions
Elsevier Ireland Ltd, Clare., 242, 171-178.
https://doi.org/10.1016/j.cbi.2015.10.002

Cabarkapa A, Borozan S, Zivkovic L, Stojanović S, Milanovic-Cabarkapa M, Bajic V, Spremo-Potparević B. CaNa(2)EDTA chelation attenuates cell damage in workers exposed to lead-a pilot study. in Chemico-Biological Interactions. 2015;242:171-178.
doi:10.1016/j.cbi.2015.10.002 .

Cabarkapa, A, Borozan, Sunčica, Zivkovic, L, Stojanović, Srđan, Milanovic-Cabarkapa, M, Bajic, V, Spremo-Potparević, Biljana, "CaNa(2)EDTA chelation attenuates cell damage in workers exposed to lead-a pilot study" in Chemico-Biological Interactions, 242 (2015):171-178,
https://doi.org/10.1016/j.cbi.2015.10.002 . .

TY  - JOUR
AU  - Čabarkapa, Andrea
AU  - Borozan, Sunčica
AU  - Živković, Lada
AU  - Milanović-Čabarkapa, Mirjana
AU  - Stojanović, Srđan
AU  - Bajić, Vladan
AU  - Spremo-Potparević, Biljana
PY  - 2015
UR  - http://farfar.pharmacy.bg.ac.rs/handle/123456789/2440
UR  - http://farfar.pharmacy.bg.ac.rs/handle/123456789/3428
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3121
AB  - The aim of this study was to determine oxidative alterations leading to cellular dysfunctions in Pb-exposed subjects by evaluating damage to all major classes of biomolecules in the cell, lipid peroxidation, protein and DNA damage and determine relationships between parameters of Pb toxicity and specific biomarkers of oxidative damage.Analysis was conducted of smelter workers with high blood Pb and urine aminolevulinic acid levels and slightly elevated values of coproporphyrin and erythrocyte protoporphyrin IX. Significant decreases of thiol groups and increases in carbonyl groups as protein degradation end products, and of nitrite were detected. Elevated rates of lipid peroxidation and rises in the activities of the antioxidant enzymes Cu-Zn superoxide dismutase and catalase were also observed. Both enzymes showed positive correlations with the blood lead levels and urine coproporphyrin, while thiol groups correlated negatively with the same indices. The genotoxic potential of lead was manifested through an increased number of DNA-damaged cells. Increased activities of serum lactate dehydrogenase isoenzymes indicated cellular damage in the lungs, kidneys, and liver. These lead-induced impairments should be taken into consideration in the assessment of Pb-related health hazards.
PB  - Taylor & Francis Ltd, Abingdon
T2  - Toxicology
T1  - Implications of oxidative stress in occupational exposure to lead on a cellular level
VL  - 97
IS  - 6
SP  - 799
EP  - 813
DO  - 10.1080/02772248.2015.1060973
ER  - 

@article{
author = "Čabarkapa, Andrea and Borozan, Sunčica and Živković, Lada and Milanović-Čabarkapa, Mirjana and Stojanović, Srđan and Bajić, Vladan and Spremo-Potparević, Biljana",
year = "2015",
abstract = "The aim of this study was to determine oxidative alterations leading to cellular dysfunctions in Pb-exposed subjects by evaluating damage to all major classes of biomolecules in the cell, lipid peroxidation, protein and DNA damage and determine relationships between parameters of Pb toxicity and specific biomarkers of oxidative damage.Analysis was conducted of smelter workers with high blood Pb and urine aminolevulinic acid levels and slightly elevated values of coproporphyrin and erythrocyte protoporphyrin IX. Significant decreases of thiol groups and increases in carbonyl groups as protein degradation end products, and of nitrite were detected. Elevated rates of lipid peroxidation and rises in the activities of the antioxidant enzymes Cu-Zn superoxide dismutase and catalase were also observed. Both enzymes showed positive correlations with the blood lead levels and urine coproporphyrin, while thiol groups correlated negatively with the same indices. The genotoxic potential of lead was manifested through an increased number of DNA-damaged cells. Increased activities of serum lactate dehydrogenase isoenzymes indicated cellular damage in the lungs, kidneys, and liver. These lead-induced impairments should be taken into consideration in the assessment of Pb-related health hazards.",
publisher = "Taylor & Francis Ltd, Abingdon",
journal = "Toxicology",
title = "Implications of oxidative stress in occupational exposure to lead on a cellular level",
volume = "97",
number = "6",
pages = "799-813",
doi = "10.1080/02772248.2015.1060973"
}

Čabarkapa, A., Borozan, S., Živković, L., Milanović-Čabarkapa, M., Stojanović, S., Bajić, V.,& Spremo-Potparević, B.. (2015). Implications of oxidative stress in occupational exposure to lead on a cellular level. in Toxicology
Taylor & Francis Ltd, Abingdon., 97(6), 799-813.
https://doi.org/10.1080/02772248.2015.1060973

Čabarkapa A, Borozan S, Živković L, Milanović-Čabarkapa M, Stojanović S, Bajić V, Spremo-Potparević B. Implications of oxidative stress in occupational exposure to lead on a cellular level. in Toxicology. 2015;97(6):799-813.
doi:10.1080/02772248.2015.1060973 .

Čabarkapa, Andrea, Borozan, Sunčica, Živković, Lada, Milanović-Čabarkapa, Mirjana, Stojanović, Srđan, Bajić, Vladan, Spremo-Potparević, Biljana, "Implications of oxidative stress in occupational exposure to lead on a cellular level" in Toxicology, 97, no. 6 (2015):799-813,
https://doi.org/10.1080/02772248.2015.1060973 . .

TY  - CONF
AU  - Borozan, Sunčica
AU  - Bošnjak, Ivan
AU  - Katić-Radivojević, Sofija
AU  - Jović, Slavoljub
AU  - Krstić, Milena
AU  - Stojanović, Srđan
PY  - 2014
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6510
AB  - Infectious larvae of equine parasites: Strongylidae and
Ascaridae may induce direct as well as indirect damage, during their
migration within the host. The aim of this study was to evaluate changes in hematological
and biochemical parameters in naturally infected horses, with
the above mentioned parasites.
PB  - International Society for Infectious Diseases
C3  - International Meeting on Emerging Diseases and Surveillance, IMED, October 31- November 3, 2014, Vienna, Austria
T1  - Horses naturally infected with Strongylidae and Ascaridae: Evaluation of hematological and some biochemical parameters
SP  - 160
EP  - 160
UR  - https://hdl.handle.net/21.15107/rcub_cer_6510
ER  - 

@conference{
author = "Borozan, Sunčica and Bošnjak, Ivan and Katić-Radivojević, Sofija and Jović, Slavoljub and Krstić, Milena and Stojanović, Srđan",
year = "2014",
abstract = "Infectious larvae of equine parasites: Strongylidae and
Ascaridae may induce direct as well as indirect damage, during their
migration within the host. The aim of this study was to evaluate changes in hematological
and biochemical parameters in naturally infected horses, with
the above mentioned parasites.",
publisher = "International Society for Infectious Diseases",
journal = "International Meeting on Emerging Diseases and Surveillance, IMED, October 31- November 3, 2014, Vienna, Austria",
title = "Horses naturally infected with Strongylidae and Ascaridae: Evaluation of hematological and some biochemical parameters",
pages = "160-160",
url = "https://hdl.handle.net/21.15107/rcub_cer_6510"
}

Borozan, S., Bošnjak, I., Katić-Radivojević, S., Jović, S., Krstić, M.,& Stojanović, S.. (2014). Horses naturally infected with Strongylidae and Ascaridae: Evaluation of hematological and some biochemical parameters. in International Meeting on Emerging Diseases and Surveillance, IMED, October 31- November 3, 2014, Vienna, Austria
International Society for Infectious Diseases., 160-160.
https://hdl.handle.net/21.15107/rcub_cer_6510

Borozan S, Bošnjak I, Katić-Radivojević S, Jović S, Krstić M, Stojanović S. Horses naturally infected with Strongylidae and Ascaridae: Evaluation of hematological and some biochemical parameters. in International Meeting on Emerging Diseases and Surveillance, IMED, October 31- November 3, 2014, Vienna, Austria. 2014;:160-160.
https://hdl.handle.net/21.15107/rcub_cer_6510 .

Borozan, Sunčica, Bošnjak, Ivan, Katić-Radivojević, Sofija, Jović, Slavoljub, Krstić, Milena, Stojanović, Srđan, "Horses naturally infected with Strongylidae and Ascaridae: Evaluation of hematological and some biochemical parameters" in International Meeting on Emerging Diseases and Surveillance, IMED, October 31- November 3, 2014, Vienna, Austria (2014):160-160,
https://hdl.handle.net/21.15107/rcub_cer_6510 .

TY  - JOUR
AU  - Breberina, Luka M.
AU  - Nikolić, Milan
AU  - Stojanović, Srđan
PY  - 2014
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1468
AB  - In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins.
AB  - U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.
PB  - Univerzitet u Nišu
T2  - Facta universitatis - series: Physics, Chemistry and Technology
T1  - Aromatic π-networks in Sm/LSm protein interfaces
T1  - Aromatična π-mreža u interfejsima Sm/LSm proteina
VL  - 12
IS  - 1
SP  - 27
EP  - 39
DO  - 10.2298/FUPCT1401027B
ER  - 

@article{
author = "Breberina, Luka M. and Nikolić, Milan and Stojanović, Srđan",
year = "2014",
abstract = "In this work, we have analyzed the influence of π-π interactions on stability and properties of Sm/LSm assemblies. The residues were found to be involved in π-π interactions much more frequently than Tyr or His. Similarly, the Phe-Phe π-π interacting pair had the highest frequency of occurrence. Furthermore, a significant number of π-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 Å. 3π and 7π-networks were found to frequently have plane-plane angles less than 60º. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the π-π interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins., U ovom radu smo analizirali uticaj π-π interakcija na stabilnost i osobine Sm/LSm proteinskih agregata. Ostatak fenilalanina znatno češće uzima učešće u π-π interakcijama u odnosu na His i Tyr. Slično, Phe-Phe π-π interagujući parovi su najučestaliji. Prepoznat je značajan broj π-mreža u interfejsima Sm/LSm proteinima. U većini slučajeva, rastojanje između interagujućih parova aminokiselina bilo je u opsegu 5-6 Å. Za 3π i 7π-mreže, prsten-prsten uglovi manji od 60º su bili učestaliji. Razmatrajući delove Sm/LSm proteina dostupne rastvaraču, može se zaključiti da se svi interagujući parovi nalaze u unutrašnjim regionima. Pored toga, većina π-π interagujućih aminokiselinskih ostataka je evoluciono konzervativan i nalazi se u regionima sa nabranom strukturom. Veliki broj ovih ostataka se može smatrati stabilizacionim centrima, koji (značajno) doprinose ukupnoj stabilnost Sm/LSm proteina.",
publisher = "Univerzitet u Nišu",
journal = "Facta universitatis - series: Physics, Chemistry and Technology",
title = "Aromatic π-networks in Sm/LSm protein interfaces, Aromatična π-mreža u interfejsima Sm/LSm proteina",
volume = "12",
number = "1",
pages = "27-39",
doi = "10.2298/FUPCT1401027B"
}

Breberina, L. M., Nikolić, M.,& Stojanović, S.. (2014). Aromatic π-networks in Sm/LSm protein interfaces. in Facta universitatis - series: Physics, Chemistry and Technology
Univerzitet u Nišu., 12(1), 27-39.
https://doi.org/10.2298/FUPCT1401027B

Breberina LM, Nikolić M, Stojanović S. Aromatic π-networks in Sm/LSm protein interfaces. in Facta universitatis - series: Physics, Chemistry and Technology. 2014;12(1):27-39.
doi:10.2298/FUPCT1401027B .

Breberina, Luka M., Nikolić, Milan, Stojanović, Srđan, "Aromatic π-networks in Sm/LSm protein interfaces" in Facta universitatis - series: Physics, Chemistry and Technology, 12, no. 1 (2014):27-39,
https://doi.org/10.2298/FUPCT1401027B . .

TY  - JOUR
AU  - Dimitrijević, Blagoje P.
AU  - Borozan, Sunčica
AU  - Jović, Slavoljub
AU  - Bacić, Dragan
AU  - Katić-Radivojević, Sofija
AU  - Stojanović, Srđan
AU  - Savić, Mila
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1157
AB  - The aim of this report was to study the biochemical parameters in sheep blood under conditions of various intensities of parasitic infection with Strongyloides papillosus, as well as after therapy with albendazole (ABZ). Investigations were performed on sheep of the Würtemberg race (n = 30) in which were detected mild, moderate and high intensities of parasitic infection with S. papillosus. The control group (n = 10) was composed of sheep negative to parasitic infections. The degree and type of changes were monitored by determining the concentrations of glucose, total proteins, albumin, A/G ratio, AST, urea, total bilirubin, calcium, phosphorus, total LDH activity and isoenzymatic LDH1-5 distributions. On the basis of the obtained results, we determined, through isoenzymatic LDH distribution, that during parasitic infection with S. papillosus, there is ongoing damage to the liver, heart muscle and lung, while after therapy with ABZ, the liver suffers the most damage. The concentration of glucose, total proteins and albumin fell linearly with the rise in the intensity of parasitic infection (p LT 0.05), while after therapy with ABZ, the fall of these parameters was at a statistically significantly higher level (p LT 0.01). The activity of AST, concentration of urea and total bilirubin also rose linearly with the intensity of parasitic infection (p LT 0.05). After therapy with ABZ, the activity of AST and the concentration of total bilirubin were at a statistically significantly higher level (p LT 0.001), while the concentration of urea retained the same levels as in the case of parasitic infection. Values of calcium concentrations (p>0.05) and phosphorus (p LT 0.05) also fall linearly with the rise of the intesity of the parasitic infection. The trend in the concentration fall of these macroelements, continues also after treatment with albendazole (p LT 0.001). Having in mind our previous studies in the field of oxidative stress and phenomena lying behind these changes, we strongly recommend that in antiparasitic treatment protocols, beside antihelminthics, compounds with antioxidative properties should also be used.
AB  - Cilj ovog rada je bio da se ispitaju biohemijski parametri u krvi ovaca u uslovima različitog intenziteta parazitske infekcije sa Strongyloides papillosus, kao i nakon terapije sa albendazolom (ABZ). Istraživanje je izvedeno na ovcama Wurtemberg rase (n = 30) kod kojih je utvrđen blagi, srednji i visoki intenzitet parazitske infekcije sa S. papillosus. Kontrolnu grupu (n = 10) činile su ovce negativne na prisustvo parazitske infekcije. Stepen i vrsta promene praćeni su određivanjem koncentracije glukoze, ukupnih proteina, albumina, A/G ratio, AST, urea, ukupnog bilirubina, kalcijuma, fosfora, ukupne aktivnosti LDH i izoenzimske distribucije LDH1-5. Na osnovu dobijenih rezultata utvrdili smo, preko izoenzimske distribucije LDH, da u toku parazitske infekcije sa S. papillosus dolazi do oštećenja jetre, srčanog mišića i pluća, dok nakon terapije sa ABZ jetra je organ koji je najviše oštećen. Koncentracija glukoze, ukupnih proteina i albumina linearno je opadala sa rastom intenziteta parazitske infekcije (p LT 0.05), a nakon terapije sa ABZ pad koncentracije ovih parametara bio je na statistički značajnom većem nivou (p LT 0.01). Aktivnost AST, koncentracija uree i ukupnog bilirubina takođe su linearno rasle sa intenzitetom parazitske infekcije (p LT 0.05). Nakon terapije sa ABZ aktivnost AST i koncentracija ukupnog bilirubina bile su na statistički značajno većem nivou (p LT 0.001), dok je koncentracija uree zadržala iste nivoe kao u slučaju parazitske infekcije. Vrednosti koncentracija kalcijuma (p > 0.05) i fosfora (p LT 0.05) takođe linearno opadaju sa rastom intenziteta parazitske infekcije. Trend pada koncentracije ovih makroelemenata, nastavlja se i nakon terapije sa albendazolom (p LT 0.001). Imajući u vidu naša prethodna istraživanja na polju oksidativnog stresa, fenomena koji se nalazi u osnovi ovih promena, strogo preporučujemo da se u antiparazitske protokole, pored antihelmintika koriste i preparati sa antioksidativnim osobinama.
PB  - Veterinary Faculty, Univ Beogradu, Belgrade
T2  - Acta veterinaria
T1  - The effect of the intensity of parasitic infection with Strongyloides papillosus and albendazole therapy on biochemical parameters in sheep blood
T1  - Uticaj intenziteta parazitske infekcije sa Strongyloides papillosus i terapije albendazolom na biohemijske parametre u krvi ovaca
VL  - 63
IS  - 5-6
SP  - 581
EP  - 600
DO  - 10.2298/AVB1306581D
ER  - 

@article{
author = "Dimitrijević, Blagoje P. and Borozan, Sunčica and Jović, Slavoljub and Bacić, Dragan and Katić-Radivojević, Sofija and Stojanović, Srđan and Savić, Mila",
year = "2013",
abstract = "The aim of this report was to study the biochemical parameters in sheep blood under conditions of various intensities of parasitic infection with Strongyloides papillosus, as well as after therapy with albendazole (ABZ). Investigations were performed on sheep of the Würtemberg race (n = 30) in which were detected mild, moderate and high intensities of parasitic infection with S. papillosus. The control group (n = 10) was composed of sheep negative to parasitic infections. The degree and type of changes were monitored by determining the concentrations of glucose, total proteins, albumin, A/G ratio, AST, urea, total bilirubin, calcium, phosphorus, total LDH activity and isoenzymatic LDH1-5 distributions. On the basis of the obtained results, we determined, through isoenzymatic LDH distribution, that during parasitic infection with S. papillosus, there is ongoing damage to the liver, heart muscle and lung, while after therapy with ABZ, the liver suffers the most damage. The concentration of glucose, total proteins and albumin fell linearly with the rise in the intensity of parasitic infection (p LT 0.05), while after therapy with ABZ, the fall of these parameters was at a statistically significantly higher level (p LT 0.01). The activity of AST, concentration of urea and total bilirubin also rose linearly with the intensity of parasitic infection (p LT 0.05). After therapy with ABZ, the activity of AST and the concentration of total bilirubin were at a statistically significantly higher level (p LT 0.001), while the concentration of urea retained the same levels as in the case of parasitic infection. Values of calcium concentrations (p>0.05) and phosphorus (p LT 0.05) also fall linearly with the rise of the intesity of the parasitic infection. The trend in the concentration fall of these macroelements, continues also after treatment with albendazole (p LT 0.001). Having in mind our previous studies in the field of oxidative stress and phenomena lying behind these changes, we strongly recommend that in antiparasitic treatment protocols, beside antihelminthics, compounds with antioxidative properties should also be used., Cilj ovog rada je bio da se ispitaju biohemijski parametri u krvi ovaca u uslovima različitog intenziteta parazitske infekcije sa Strongyloides papillosus, kao i nakon terapije sa albendazolom (ABZ). Istraživanje je izvedeno na ovcama Wurtemberg rase (n = 30) kod kojih je utvrđen blagi, srednji i visoki intenzitet parazitske infekcije sa S. papillosus. Kontrolnu grupu (n = 10) činile su ovce negativne na prisustvo parazitske infekcije. Stepen i vrsta promene praćeni su određivanjem koncentracije glukoze, ukupnih proteina, albumina, A/G ratio, AST, urea, ukupnog bilirubina, kalcijuma, fosfora, ukupne aktivnosti LDH i izoenzimske distribucije LDH1-5. Na osnovu dobijenih rezultata utvrdili smo, preko izoenzimske distribucije LDH, da u toku parazitske infekcije sa S. papillosus dolazi do oštećenja jetre, srčanog mišića i pluća, dok nakon terapije sa ABZ jetra je organ koji je najviše oštećen. Koncentracija glukoze, ukupnih proteina i albumina linearno je opadala sa rastom intenziteta parazitske infekcije (p LT 0.05), a nakon terapije sa ABZ pad koncentracije ovih parametara bio je na statistički značajnom većem nivou (p LT 0.01). Aktivnost AST, koncentracija uree i ukupnog bilirubina takođe su linearno rasle sa intenzitetom parazitske infekcije (p LT 0.05). Nakon terapije sa ABZ aktivnost AST i koncentracija ukupnog bilirubina bile su na statistički značajno većem nivou (p LT 0.001), dok je koncentracija uree zadržala iste nivoe kao u slučaju parazitske infekcije. Vrednosti koncentracija kalcijuma (p > 0.05) i fosfora (p LT 0.05) takođe linearno opadaju sa rastom intenziteta parazitske infekcije. Trend pada koncentracije ovih makroelemenata, nastavlja se i nakon terapije sa albendazolom (p LT 0.001). Imajući u vidu naša prethodna istraživanja na polju oksidativnog stresa, fenomena koji se nalazi u osnovi ovih promena, strogo preporučujemo da se u antiparazitske protokole, pored antihelmintika koriste i preparati sa antioksidativnim osobinama.",
publisher = "Veterinary Faculty, Univ Beogradu, Belgrade",
journal = "Acta veterinaria",
title = "The effect of the intensity of parasitic infection with Strongyloides papillosus and albendazole therapy on biochemical parameters in sheep blood, Uticaj intenziteta parazitske infekcije sa Strongyloides papillosus i terapije albendazolom na biohemijske parametre u krvi ovaca",
volume = "63",
number = "5-6",
pages = "581-600",
doi = "10.2298/AVB1306581D"
}

Dimitrijević, B. P., Borozan, S., Jović, S., Bacić, D., Katić-Radivojević, S., Stojanović, S.,& Savić, M.. (2013). The effect of the intensity of parasitic infection with Strongyloides papillosus and albendazole therapy on biochemical parameters in sheep blood. in Acta veterinaria
Veterinary Faculty, Univ Beogradu, Belgrade., 63(5-6), 581-600.
https://doi.org/10.2298/AVB1306581D

Dimitrijević BP, Borozan S, Jović S, Bacić D, Katić-Radivojević S, Stojanović S, Savić M. The effect of the intensity of parasitic infection with Strongyloides papillosus and albendazole therapy on biochemical parameters in sheep blood. in Acta veterinaria. 2013;63(5-6):581-600.
doi:10.2298/AVB1306581D .

Dimitrijević, Blagoje P., Borozan, Sunčica, Jović, Slavoljub, Bacić, Dragan, Katić-Radivojević, Sofija, Stojanović, Srđan, Savić, Mila, "The effect of the intensity of parasitic infection with Strongyloides papillosus and albendazole therapy on biochemical parameters in sheep blood" in Acta veterinaria, 63, no. 5-6 (2013):581-600,
https://doi.org/10.2298/AVB1306581D . .

TY  - JOUR
AU  - Zarić, Božidarka
AU  - Bukorović, Milica
AU  - Stojanović, Srđan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1210
AB  - The Sm and Sm-like (LSm) proteins are a widespread protein family with members in all kingdoms of life. Sm proteins form complexes engaging in various RNA-processing events. Sm proteins do form and act as oligomeric assemblies whose characteristic is their exceptional stability. This study compares strong and weak hydrogen bonds in the interior of monomers and at interfaces of Sm/LSm proteins in order to better understand the stability of oligomers. According to our results, the stability of oligomeric assemblies is achieved by CH center dot center dot center dot O, NH center dot center dot center dot O and CH center dot center dot center dot N interactions including, NH center dot center dot center dot N, OH center dot center dot center dot O, XH center dot center dot center dot pi interactions present in small percentages. Intrachain hydrogen bonds behave in respect to geometry, distances and angles, like interchain hydrogen bonds. It is also shown that amino acids Arg and Lys participate significantly as donors or acceptors in some of the strong or weak interactions at interfaces to a higher extent than in the monomers. There is a trend for most polar amino acids to cross into more solvent exposed position in interfaces, which is not the case for nonpolar or charged amino acids. There is no exclusive preference for particular secondary structure both for intrachains and for interfaces.
PB  - Inst Materials Physics, Bucharest
T2  - Digest Journal of Nanomaterials and Biostructures
T1  - Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction
VL  - 8
IS  - 2
SP  - 639
EP  - 654
UR  - https://hdl.handle.net/21.15107/rcub_cer_1210
ER  - 

@article{
author = "Zarić, Božidarka and Bukorović, Milica and Stojanović, Srđan",
year = "2013",
abstract = "The Sm and Sm-like (LSm) proteins are a widespread protein family with members in all kingdoms of life. Sm proteins form complexes engaging in various RNA-processing events. Sm proteins do form and act as oligomeric assemblies whose characteristic is their exceptional stability. This study compares strong and weak hydrogen bonds in the interior of monomers and at interfaces of Sm/LSm proteins in order to better understand the stability of oligomers. According to our results, the stability of oligomeric assemblies is achieved by CH center dot center dot center dot O, NH center dot center dot center dot O and CH center dot center dot center dot N interactions including, NH center dot center dot center dot N, OH center dot center dot center dot O, XH center dot center dot center dot pi interactions present in small percentages. Intrachain hydrogen bonds behave in respect to geometry, distances and angles, like interchain hydrogen bonds. It is also shown that amino acids Arg and Lys participate significantly as donors or acceptors in some of the strong or weak interactions at interfaces to a higher extent than in the monomers. There is a trend for most polar amino acids to cross into more solvent exposed position in interfaces, which is not the case for nonpolar or charged amino acids. There is no exclusive preference for particular secondary structure both for intrachains and for interfaces.",
publisher = "Inst Materials Physics, Bucharest",
journal = "Digest Journal of Nanomaterials and Biostructures",
title = "Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction",
volume = "8",
number = "2",
pages = "639-654",
url = "https://hdl.handle.net/21.15107/rcub_cer_1210"
}

Zarić, B., Bukorović, M.,& Stojanović, S.. (2013). Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction. in Digest Journal of Nanomaterials and Biostructures
Inst Materials Physics, Bucharest., 8(2), 639-654.
https://hdl.handle.net/21.15107/rcub_cer_1210

Zarić B, Bukorović M, Stojanović S. Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction. in Digest Journal of Nanomaterials and Biostructures. 2013;8(2):639-654.
https://hdl.handle.net/21.15107/rcub_cer_1210 .

Zarić, Božidarka, Bukorović, Milica, Stojanović, Srđan, "Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction" in Digest Journal of Nanomaterials and Biostructures, 8, no. 2 (2013):639-654,
https://hdl.handle.net/21.15107/rcub_cer_1210 .

TY  - JOUR
AU  - Borozan, Sunčica
AU  - Stojanović, Srđan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1235
AB  - In this work, we have analyzed the influence of halogen bonding to the stability of 44 complexes of proteins and non-natural amino acids. Fluorine- and chlorine-containing non-natural amino acids are more prevalent in the dataset, and an even larger number of contacts made by iodine-containing ligands are found. Only few halogen bonds with the hydroxyl oxygens and carboxylate side chains are found in the dataset. Halogen bonds with the nitrogen-containing side chains have higher occurrence than other acceptors. Backbone carbonyl oxygens and nitrogens are to a substantial extent involved in our dataset We have observed a small percentage of interactions involving water as hydrogen bond donors. Additionally, most of the interacting residues comprising the interfaces also show a great degree of conservation. There is a clear interaction hot spot at distances of 3.5-3.7 angstrom and Theta(1) angles of 100-120 degrees. There is also a cluster of contacts featuring short distances (2.6-2.9 angstrom) but only nearly optimal Theta(1) angles (140-160 degrees). 51.3% of stabilizing residues are involved in building halogen bonds with the non-natural amino acids. We discovered three types of structural motifs significantly over-represented: beta-turn-ir, beta-turn-il and niche-4r. The halogen-bonding statistics of the dataset do not show any preference for alpha-helices (36%), beta-sheets (36%), or turns/coils (28%) structures. Most of the amino acid residues that were involved in halogen bonds prefer to be in the solvent excluded environment (buried). Furthermore, we have shown that in amino acid-protein complexes halogen atoms can sometimes be involved in hydrogen bonding interactions with hydrogen bonding-donors. The results from this study might be used for the rational design of halogenated ligands as inhibitors and drugs, and in biomolecular engineering.
PB  - Elsevier Sci Ltd, Oxford
T2  - Computational Biology and Chemistry
T1  - Halogen bonding in complexes of proteins and non-natural amino acids
VL  - 47
SP  - 231
EP  - 239
DO  - 10.1016/j.compbiolchem.2013.10.002
ER  - 

@article{
author = "Borozan, Sunčica and Stojanović, Srđan",
year = "2013",
abstract = "In this work, we have analyzed the influence of halogen bonding to the stability of 44 complexes of proteins and non-natural amino acids. Fluorine- and chlorine-containing non-natural amino acids are more prevalent in the dataset, and an even larger number of contacts made by iodine-containing ligands are found. Only few halogen bonds with the hydroxyl oxygens and carboxylate side chains are found in the dataset. Halogen bonds with the nitrogen-containing side chains have higher occurrence than other acceptors. Backbone carbonyl oxygens and nitrogens are to a substantial extent involved in our dataset We have observed a small percentage of interactions involving water as hydrogen bond donors. Additionally, most of the interacting residues comprising the interfaces also show a great degree of conservation. There is a clear interaction hot spot at distances of 3.5-3.7 angstrom and Theta(1) angles of 100-120 degrees. There is also a cluster of contacts featuring short distances (2.6-2.9 angstrom) but only nearly optimal Theta(1) angles (140-160 degrees). 51.3% of stabilizing residues are involved in building halogen bonds with the non-natural amino acids. We discovered three types of structural motifs significantly over-represented: beta-turn-ir, beta-turn-il and niche-4r. The halogen-bonding statistics of the dataset do not show any preference for alpha-helices (36%), beta-sheets (36%), or turns/coils (28%) structures. Most of the amino acid residues that were involved in halogen bonds prefer to be in the solvent excluded environment (buried). Furthermore, we have shown that in amino acid-protein complexes halogen atoms can sometimes be involved in hydrogen bonding interactions with hydrogen bonding-donors. The results from this study might be used for the rational design of halogenated ligands as inhibitors and drugs, and in biomolecular engineering.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Computational Biology and Chemistry",
title = "Halogen bonding in complexes of proteins and non-natural amino acids",
volume = "47",
pages = "231-239",
doi = "10.1016/j.compbiolchem.2013.10.002"
}

Borozan, S.,& Stojanović, S.. (2013). Halogen bonding in complexes of proteins and non-natural amino acids. in Computational Biology and Chemistry
Elsevier Sci Ltd, Oxford., 47, 231-239.
https://doi.org/10.1016/j.compbiolchem.2013.10.002

Borozan S, Stojanović S. Halogen bonding in complexes of proteins and non-natural amino acids. in Computational Biology and Chemistry. 2013;47:231-239.
doi:10.1016/j.compbiolchem.2013.10.002 .

Borozan, Sunčica, Stojanović, Srđan, "Halogen bonding in complexes of proteins and non-natural amino acids" in Computational Biology and Chemistry, 47 (2013):231-239,
https://doi.org/10.1016/j.compbiolchem.2013.10.002 . .

TY  - JOUR
AU  - Borozan, Sunčica
AU  - Dimitrijević, Blagoje P.
AU  - Stojanović, Srđan
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1247
AB  - In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.
PB  - Elsevier Sci Ltd, Oxford
T2  - Computational Biology and Chemistry
T1  - Cation-pi interactions in high resolution protein-RNA complex crystal structures
VL  - 47
SP  - 105
EP  - 112
DO  - 10.1016/j.compbiolchem.2013.08.005
ER  - 

@article{
author = "Borozan, Sunčica and Dimitrijević, Blagoje P. and Stojanović, Srđan",
year = "2013",
abstract = "In this work, we have analyzed the influence of cation-pi interactions to the stability of 59 high resolution protein-RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation-pi interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation-pi interactions. The multiple cation-pi interactions have been conserved more than the single interactions. The analysis of the geometry of the cation-pi interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 angstrom) and single (5.50 angstrom) cation-pi interactions. The G-Arg pair has the strongest interaction energy of -3.68 kcal mol(-1) among all the possible pairs of amino acids and bases. Further, we found that the cation-pi interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation-pi interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein-RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein-RNA interfaces. Amino acids deployed in the protein-RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation-pi interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure-based prediction and as scaffolds for future protein-RNA complex design.",
publisher = "Elsevier Sci Ltd, Oxford",
journal = "Computational Biology and Chemistry",
title = "Cation-pi interactions in high resolution protein-RNA complex crystal structures",
volume = "47",
pages = "105-112",
doi = "10.1016/j.compbiolchem.2013.08.005"
}

Borozan, S., Dimitrijević, B. P.,& Stojanović, S.. (2013). Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry
Elsevier Sci Ltd, Oxford., 47, 105-112.
https://doi.org/10.1016/j.compbiolchem.2013.08.005

Borozan S, Dimitrijević BP, Stojanović S. Cation-pi interactions in high resolution protein-RNA complex crystal structures. in Computational Biology and Chemistry. 2013;47:105-112.
doi:10.1016/j.compbiolchem.2013.08.005 .

Borozan, Sunčica, Dimitrijević, Blagoje P., Stojanović, Srđan, "Cation-pi interactions in high resolution protein-RNA complex crystal structures" in Computational Biology and Chemistry, 47 (2013):105-112,
https://doi.org/10.1016/j.compbiolchem.2013.08.005 . .