TY  - JOUR
AU  - Janjić, Goran
AU  - Petrović, Predrag V.
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/797
AB  - Stacking interactions of phenanthroline square-planar complexes in crystal structures were studied by analyzing data from the Cambridge Structural Database. In most of the crystal structures, two phenanthroline complexes were oriented "head to tail." Phenanthroline complexes show a wide range of overlap geometries in stacking interactions, while short metal-metal distances were not observed. Stacking chains with alternating overlaps were the predominant type of packing in the crystal structures.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes
VL  - 17
IS  - 8
SP  - 2083
EP  - 2092
DO  - 10.1007/s00894-010-0905-3
ER  - 

@article{
author = "Janjić, Goran and Petrović, Predrag V. and Ninković, Dragan B. and Zarić, Snežana D.",
year = "2011",
abstract = "Stacking interactions of phenanthroline square-planar complexes in crystal structures were studied by analyzing data from the Cambridge Structural Database. In most of the crystal structures, two phenanthroline complexes were oriented "head to tail." Phenanthroline complexes show a wide range of overlap geometries in stacking interactions, while short metal-metal distances were not observed. Stacking chains with alternating overlaps were the predominant type of packing in the crystal structures.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes",
volume = "17",
number = "8",
pages = "2083-2092",
doi = "10.1007/s00894-010-0905-3"
}

Janjić, G., Petrović, P. V., Ninković, D. B.,& Zarić, S. D.. (2011). Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes. in Journal of Molecular Modeling
Springer, New York., 17(8), 2083-2092.
https://doi.org/10.1007/s00894-010-0905-3

Janjić G, Petrović PV, Ninković DB, Zarić SD. Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes. in Journal of Molecular Modeling. 2011;17(8):2083-2092.
doi:10.1007/s00894-010-0905-3 .

Janjić, Goran, Petrović, Predrag V., Ninković, Dragan B., Zarić, Snežana D., "Geometries of stacking interactions between phenanthroline ligands in crystal structures of square-planar metal complexes" in Journal of Molecular Modeling, 17, no. 8 (2011):2083-2092,
https://doi.org/10.1007/s00894-010-0905-3 . .

TY  - JOUR
AU  - Ninković, Dragan B.
AU  - Janjić, Goran
AU  - Veljković, Dušan
AU  - Sredojević, Dušan
AU  - Zarić, Snežana D.
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/878
PB  - Wiley-Blackwell, Malden
T2  - Chemphyschem
T1  - What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements
VL  - 12
IS  - 18
SP  - 3511
EP  - 3514
DO  - 10.1002/cphc.201100777
ER  - 

@article{
author = "Ninković, Dragan B. and Janjić, Goran and Veljković, Dušan and Sredojević, Dušan and Zarić, Snežana D.",
year = "2011",
publisher = "Wiley-Blackwell, Malden",
journal = "Chemphyschem",
title = "What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements",
volume = "12",
number = "18",
pages = "3511-3514",
doi = "10.1002/cphc.201100777"
}

Ninković, D. B., Janjić, G., Veljković, D., Sredojević, D.,& Zarić, S. D.. (2011). What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements. in Chemphyschem
Wiley-Blackwell, Malden., 12(18), 3511-3514.
https://doi.org/10.1002/cphc.201100777

Ninković DB, Janjić G, Veljković D, Sredojević D, Zarić SD. What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements. in Chemphyschem. 2011;12(18):3511-3514.
doi:10.1002/cphc.201100777 .

Ninković, Dragan B., Janjić, Goran, Veljković, Dušan, Sredojević, Dušan, Zarić, Snežana D., "What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements" in Chemphyschem, 12, no. 18 (2011):3511-3514,
https://doi.org/10.1002/cphc.201100777 . .

TY  - JOUR
AU  - Zarić, Božidarka
AU  - Jovanović, Vesna B.
AU  - Stojanović, Srđan
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/924
AB  - The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures.
PB  - Academic Press Ltd- Elsevier Science Ltd, London
T2  - Journal of Theoretical Biology
T1  - Non-covalent interactions across subunit interfaces in Sm proteins
VL  - 271
IS  - 1
SP  - 18
EP  - 26
DO  - 10.1016/j.jtbi.2010.11.025
ER  - 

@article{
author = "Zarić, Božidarka and Jovanović, Vesna B. and Stojanović, Srđan",
year = "2011",
abstract = "The distinguishing property of Sm protein associations is their high stability. In order to understand this property, we analyzed the interface non-covalent interactions and compared the properties of the Sm protein interfaces with those of a test set, Binding Interface Database (BID). The comparison revealed that the main differences between interfaces of Sm proteins and those of the BID set are the content of charged residues, hydrogen bonds, salt bridges, and conservation scores of interface residues. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surface, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Both interfaces of Sm proteins and of test set have a similar number of hydrophobic interactions per 100 angstrom(2). The interfaces of Sm proteins have substantially more hydrogen bonds than the interfaces in test set. The results show clearly that the interfaces of Sm proteins form more salt bridges compared with test set. On average, there are about 16 salt bridges per interface. The high conservation score of amino acids that are involved in non-covalent interactions in protein interfaces is an additional strong argument for their importance. The overriding conclusion from this study is that the non-covalent interactions in Sm protein interfaces considerably contribute to stability of higher order structures.",
publisher = "Academic Press Ltd- Elsevier Science Ltd, London",
journal = "Journal of Theoretical Biology",
title = "Non-covalent interactions across subunit interfaces in Sm proteins",
volume = "271",
number = "1",
pages = "18-26",
doi = "10.1016/j.jtbi.2010.11.025"
}

Zarić, B., Jovanović, V. B.,& Stojanović, S.. (2011). Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology
Academic Press Ltd- Elsevier Science Ltd, London., 271(1), 18-26.
https://doi.org/10.1016/j.jtbi.2010.11.025

Zarić B, Jovanović VB, Stojanović S. Non-covalent interactions across subunit interfaces in Sm proteins. in Journal of Theoretical Biology. 2011;271(1):18-26.
doi:10.1016/j.jtbi.2010.11.025 .

Zarić, Božidarka, Jovanović, Vesna B., Stojanović, Srđan, "Non-covalent interactions across subunit interfaces in Sm proteins" in Journal of Theoretical Biology, 271, no. 1 (2011):18-26,
https://doi.org/10.1016/j.jtbi.2010.11.025 . .

TY  - JOUR
AU  - Janjić, Goran
AU  - Veljković, Dušan
AU  - Zarić, Snežana D.
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/787
AB  - Analysis of crystal structures from the Cambridge Structural Database (CSD) and high level ab initio calculations reveals that the water/aromatic parallel alignment interactions; where the water molecule or one of its 0 H bonds is parallel to the aromatic ring plane, can be significantly strong at large horizontal displacements. We found out that the strongest energies of the interactions are calculated for the water position with the large horizontal displacements, out of the aromatic ring and out of the C-H bond region. For calculated systems, normal distances were decreasing with increasing the horizontal displacement, in accord with the data found in crystal structures. The calculated energies of the interactions are significant, up to Delta E-CCSD(T)(limit) = -10.25 kJ/mol (at a horizontal displacement of 2.6 angstrom), and comparable with the energy of the slipped-parallel benzene/benzene dimer. Both dispersion and electrostatic components of the interaction energy are important. The calculated interaction energies reveal that also at long horizontal displacements of 3.5 angstrom, interaction is substantially strong, up to Delta E-CCSD(T(limit) = -623 kJ/mol. The data show the existence of the water/aromatic parallel alignment interactions in crystal structures and indicate their importance for various systems.
PB  - American Chemical Society (ACS)
T2  - Crystal Growth & Design
T1  - Water/Aromatic Parallel Alignment Interactions. Significant Interactions at Large Horizontal Displacements
VL  - 11
IS  - 7
SP  - 2680
EP  - 2683
DO  - 10.1021/cg101208q
ER  - 

@article{
author = "Janjić, Goran and Veljković, Dušan and Zarić, Snežana D.",
year = "2011",
abstract = "Analysis of crystal structures from the Cambridge Structural Database (CSD) and high level ab initio calculations reveals that the water/aromatic parallel alignment interactions; where the water molecule or one of its 0 H bonds is parallel to the aromatic ring plane, can be significantly strong at large horizontal displacements. We found out that the strongest energies of the interactions are calculated for the water position with the large horizontal displacements, out of the aromatic ring and out of the C-H bond region. For calculated systems, normal distances were decreasing with increasing the horizontal displacement, in accord with the data found in crystal structures. The calculated energies of the interactions are significant, up to Delta E-CCSD(T)(limit) = -10.25 kJ/mol (at a horizontal displacement of 2.6 angstrom), and comparable with the energy of the slipped-parallel benzene/benzene dimer. Both dispersion and electrostatic components of the interaction energy are important. The calculated interaction energies reveal that also at long horizontal displacements of 3.5 angstrom, interaction is substantially strong, up to Delta E-CCSD(T(limit) = -623 kJ/mol. The data show the existence of the water/aromatic parallel alignment interactions in crystal structures and indicate their importance for various systems.",
publisher = "American Chemical Society (ACS)",
journal = "Crystal Growth & Design",
title = "Water/Aromatic Parallel Alignment Interactions. Significant Interactions at Large Horizontal Displacements",
volume = "11",
number = "7",
pages = "2680-2683",
doi = "10.1021/cg101208q"
}

Janjić, G., Veljković, D.,& Zarić, S. D.. (2011). Water/Aromatic Parallel Alignment Interactions. Significant Interactions at Large Horizontal Displacements. in Crystal Growth & Design
American Chemical Society (ACS)., 11(7), 2680-2683.
https://doi.org/10.1021/cg101208q

Janjić G, Veljković D, Zarić SD. Water/Aromatic Parallel Alignment Interactions. Significant Interactions at Large Horizontal Displacements. in Crystal Growth & Design. 2011;11(7):2680-2683.
doi:10.1021/cg101208q .

Janjić, Goran, Veljković, Dušan, Zarić, Snežana D., "Water/Aromatic Parallel Alignment Interactions. Significant Interactions at Large Horizontal Displacements" in Crystal Growth & Design, 11, no. 7 (2011):2680-2683,
https://doi.org/10.1021/cg101208q . .

TY  - JOUR
AU  - Janjić, Goran
AU  - Andrić, Jelena M.
AU  - Kapor, Agnes
AU  - Bugarcic, Zivadin D.
AU  - Zarić, Snežana D.
PY  - 2010
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/672
AB  - Stacking interactions of terpyridyl square-planar complexes in crystal structures were studied analyzing data from the Cambridge Structural Database. In most of the crystal structures, two terpyridyl complexes were oriented "head-to-tail" or "head-to-head", with "head-to-tail orientation" being most prevalent. The number of structures with other orientations was very small. Based on the analysis of interacting geometries, we classified overlaps of terpyridyl complexes into six types. The types were defined by values of several geometrical parameters and all interactions of the same type had very similar overlap patterns.
PB  - Royal Soc Chemistry, Cambridge
T2  - Crystengcomm
T1  - Classification of stacking interaction geometries of terpyridyl square-planar complexes in crystal structures
VL  - 12
IS  - 11
SP  - 3773
EP  - 3779
DO  - 10.1039/b917268h
ER  - 

@article{
author = "Janjić, Goran and Andrić, Jelena M. and Kapor, Agnes and Bugarcic, Zivadin D. and Zarić, Snežana D.",
year = "2010",
abstract = "Stacking interactions of terpyridyl square-planar complexes in crystal structures were studied analyzing data from the Cambridge Structural Database. In most of the crystal structures, two terpyridyl complexes were oriented "head-to-tail" or "head-to-head", with "head-to-tail orientation" being most prevalent. The number of structures with other orientations was very small. Based on the analysis of interacting geometries, we classified overlaps of terpyridyl complexes into six types. The types were defined by values of several geometrical parameters and all interactions of the same type had very similar overlap patterns.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Crystengcomm",
title = "Classification of stacking interaction geometries of terpyridyl square-planar complexes in crystal structures",
volume = "12",
number = "11",
pages = "3773-3779",
doi = "10.1039/b917268h"
}

Janjić, G., Andrić, J. M., Kapor, A., Bugarcic, Z. D.,& Zarić, S. D.. (2010). Classification of stacking interaction geometries of terpyridyl square-planar complexes in crystal structures. in Crystengcomm
Royal Soc Chemistry, Cambridge., 12(11), 3773-3779.
https://doi.org/10.1039/b917268h

Janjić G, Andrić JM, Kapor A, Bugarcic ZD, Zarić SD. Classification of stacking interaction geometries of terpyridyl square-planar complexes in crystal structures. in Crystengcomm. 2010;12(11):3773-3779.
doi:10.1039/b917268h .

Janjić, Goran, Andrić, Jelena M., Kapor, Agnes, Bugarcic, Zivadin D., Zarić, Snežana D., "Classification of stacking interaction geometries of terpyridyl square-planar complexes in crystal structures" in Crystengcomm, 12, no. 11 (2010):3773-3779,
https://doi.org/10.1039/b917268h . .

TY  - JOUR
AU  - Janjić, Goran
AU  - Petrović, Predrag
AU  - Ninković, Dragan
AU  - Veljković, Dušan
AU  - Kapor, Agnes
AU  - Zarić, Snežana D.
PY  - 2010
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/691
AB  - In the crystal structures of terpyridyl complexes from the Cambridge Structural Database (CSD) stacking interaction between the pyridine fragments were studied. Square-planar complexes where the distance between the centers of two pyridine fragments was below 4.6 angstrom were retrieved from CSD. With this search 68 crystal structures with 167 interactions were found. In the interactions one, two or three pyridine fragments of one complex can be involved in overlapping with pyridine fragments of the other complex.
PB  - Univ Babes-Bolyai, Cluj-Napoca
T2  - Studia Universitatis Babes-Bolyai Chemia
T1  - STACKING INTERACTIONS BETWEEN PYRIDINE FRAGMENTS IN CRYSTAL STRUCTURES OF TERPYRIDYL COMPLEXES
VL  - 55
IS  - 3
SP  - 165
EP  - 176
UR  - https://hdl.handle.net/21.15107/rcub_cherry_1159
ER  - 

@article{
author = "Janjić, Goran and Petrović, Predrag and Ninković, Dragan and Veljković, Dušan and Kapor, Agnes and Zarić, Snežana D.",
year = "2010",
abstract = "In the crystal structures of terpyridyl complexes from the Cambridge Structural Database (CSD) stacking interaction between the pyridine fragments were studied. Square-planar complexes where the distance between the centers of two pyridine fragments was below 4.6 angstrom were retrieved from CSD. With this search 68 crystal structures with 167 interactions were found. In the interactions one, two or three pyridine fragments of one complex can be involved in overlapping with pyridine fragments of the other complex.",
publisher = "Univ Babes-Bolyai, Cluj-Napoca",
journal = "Studia Universitatis Babes-Bolyai Chemia",
title = "STACKING INTERACTIONS BETWEEN PYRIDINE FRAGMENTS IN CRYSTAL STRUCTURES OF TERPYRIDYL COMPLEXES",
volume = "55",
number = "3",
pages = "165-176",
url = "https://hdl.handle.net/21.15107/rcub_cherry_1159"
}

Janjić, G., Petrović, P., Ninković, D., Veljković, D., Kapor, A.,& Zarić, S. D.. (2010). STACKING INTERACTIONS BETWEEN PYRIDINE FRAGMENTS IN CRYSTAL STRUCTURES OF TERPYRIDYL COMPLEXES. in Studia Universitatis Babes-Bolyai Chemia
Univ Babes-Bolyai, Cluj-Napoca., 55(3), 165-176.
https://hdl.handle.net/21.15107/rcub_cherry_1159

Janjić G, Petrović P, Ninković D, Veljković D, Kapor A, Zarić SD. STACKING INTERACTIONS BETWEEN PYRIDINE FRAGMENTS IN CRYSTAL STRUCTURES OF TERPYRIDYL COMPLEXES. in Studia Universitatis Babes-Bolyai Chemia. 2010;55(3):165-176.
https://hdl.handle.net/21.15107/rcub_cherry_1159 .

Janjić, Goran, Petrović, Predrag, Ninković, Dragan, Veljković, Dušan, Kapor, Agnes, Zarić, Snežana D., "STACKING INTERACTIONS BETWEEN PYRIDINE FRAGMENTS IN CRYSTAL STRUCTURES OF TERPYRIDYL COMPLEXES" in Studia Universitatis Babes-Bolyai Chemia, 55, no. 3 (2010):165-176,
https://hdl.handle.net/21.15107/rcub_cherry_1159 .

TY  - JOUR
AU  - Pastor, Ferenc T.
AU  - Drakulić, Branko
PY  - 2010
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5854
AB  - Half-wave reduction potentials of a set of twelve (E)-4-aryl-4-oxo-2-butenoic acids obtained by direct current polarography in methanol are reported. E1/2 is correlated with Hammett sigma values as well as with values of frontier molecular orbitals calculated at a semiempirical molecular orbital level. Constant potential electrolysis of a representative compound shows that the first polarographic wave corresponds to one-electron reduction. The isolation of the product proves reduction of the activated double bond.
PB  - Elsevier
T2  - Tetrahedron Letters
T1  - Linear free energy relationships of half-wave reduction potentials of (E)-4-aryl-4-oxo-2-butenoic acids
VL  - 51
IS  - 4
SP  - 734
EP  - 738
DO  - 10.1016/j.tetlet.2009.11.129
ER  - 

@article{
author = "Pastor, Ferenc T. and Drakulić, Branko",
year = "2010",
abstract = "Half-wave reduction potentials of a set of twelve (E)-4-aryl-4-oxo-2-butenoic acids obtained by direct current polarography in methanol are reported. E1/2 is correlated with Hammett sigma values as well as with values of frontier molecular orbitals calculated at a semiempirical molecular orbital level. Constant potential electrolysis of a representative compound shows that the first polarographic wave corresponds to one-electron reduction. The isolation of the product proves reduction of the activated double bond.",
publisher = "Elsevier",
journal = "Tetrahedron Letters",
title = "Linear free energy relationships of half-wave reduction potentials of (E)-4-aryl-4-oxo-2-butenoic acids",
volume = "51",
number = "4",
pages = "734-738",
doi = "10.1016/j.tetlet.2009.11.129"
}

Pastor, F. T.,& Drakulić, B.. (2010). Linear free energy relationships of half-wave reduction potentials of (E)-4-aryl-4-oxo-2-butenoic acids. in Tetrahedron Letters
Elsevier., 51(4), 734-738.
https://doi.org/10.1016/j.tetlet.2009.11.129

Pastor FT, Drakulić B. Linear free energy relationships of half-wave reduction potentials of (E)-4-aryl-4-oxo-2-butenoic acids. in Tetrahedron Letters. 2010;51(4):734-738.
doi:10.1016/j.tetlet.2009.11.129 .

Pastor, Ferenc T., Drakulić, Branko, "Linear free energy relationships of half-wave reduction potentials of (E)-4-aryl-4-oxo-2-butenoic acids" in Tetrahedron Letters, 51, no. 4 (2010):734-738,
https://doi.org/10.1016/j.tetlet.2009.11.129 . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Zarić, Božidarka
AU  - Zarić, Snežana D.
PY  - 2010
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/680
AB  - The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between the interfaces of Sm proteins and those of the BID set are the content of charged residues, the coordination numbers of the residues, knowledge-based pair potentials, and the conservation scores of hot spots. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surfaces, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Hot spots are residues that make up a small fraction of the interfaces, but they contribute most of the binding energy. These residues are critical to protein-protein interactions. Analyses of knowledge-based pair potentials of hot spot and non-hot spot residues in Sm proteins show that they are significantly different; their mean values are 31.5 and 11.3, respectively. In the BID set, this difference is smaller; in this case, the mean values for hot spot and non-hot spot residues are 20.7 and 12.4, respectively. Hence, the pair potentials of hot spots differ significantly for the Sm and BID data sets. In the interfaces of Sm proteins, the amino acids are tightly packed, and the coordination numbers are larger in Sm proteins than in the BID set for both hot spots and non-hot spots. At the same time, the coordination numbers are higher for hot spots; the average coordination number of the hot spot residues in Sm proteins is 7.7, while it is 6.1 for the non-hot spot residues. The difference in the calculated average conservation score for hot spots and non-hot spots in Sm proteins is significantly larger than it is in the BID set. In Sm proteins, the average conservation score for the hot spots is 7.4. Hot spots are surrounded by residues that are moderately conserved (5.9). The average conservation score for the other interface residues is 5.6. The conservation scores in the BID set do not show a significant distinction between hot and non-hot spots: the mean values for hot and non-hot spot residues are 5.5 and 5.2, respectively. These data show that structurally conserved residues and hot spots are significantly correlated in Sm proteins.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins
VL  - 16
IS  - 11
SP  - 1743
EP  - 1751
DO  - 10.1007/s00894-010-0787-4
ER  - 

@article{
author = "Stojanović, Srđan and Zarić, Božidarka and Zarić, Snežana D.",
year = "2010",
abstract = "The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between the interfaces of Sm proteins and those of the BID set are the content of charged residues, the coordination numbers of the residues, knowledge-based pair potentials, and the conservation scores of hot spots. In Sm proteins, the interfaces have more hydrophobic and fewer charged residues than the surfaces, which is also the case for the BID test set and other proteins. However, in the interfaces, the content of charged residues in Sm proteins (26%) is substantially larger than that in the BID set (22%). Hot spots are residues that make up a small fraction of the interfaces, but they contribute most of the binding energy. These residues are critical to protein-protein interactions. Analyses of knowledge-based pair potentials of hot spot and non-hot spot residues in Sm proteins show that they are significantly different; their mean values are 31.5 and 11.3, respectively. In the BID set, this difference is smaller; in this case, the mean values for hot spot and non-hot spot residues are 20.7 and 12.4, respectively. Hence, the pair potentials of hot spots differ significantly for the Sm and BID data sets. In the interfaces of Sm proteins, the amino acids are tightly packed, and the coordination numbers are larger in Sm proteins than in the BID set for both hot spots and non-hot spots. At the same time, the coordination numbers are higher for hot spots; the average coordination number of the hot spot residues in Sm proteins is 7.7, while it is 6.1 for the non-hot spot residues. The difference in the calculated average conservation score for hot spots and non-hot spots in Sm proteins is significantly larger than it is in the BID set. In Sm proteins, the average conservation score for the hot spots is 7.4. Hot spots are surrounded by residues that are moderately conserved (5.9). The average conservation score for the other interface residues is 5.6. The conservation scores in the BID set do not show a significant distinction between hot and non-hot spots: the mean values for hot and non-hot spot residues are 5.5 and 5.2, respectively. These data show that structurally conserved residues and hot spots are significantly correlated in Sm proteins.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins",
volume = "16",
number = "11",
pages = "1743-1751",
doi = "10.1007/s00894-010-0787-4"
}

Stojanović, S., Zarić, B.,& Zarić, S. D.. (2010). Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins. in Journal of Molecular Modeling
Springer, New York., 16(11), 1743-1751.
https://doi.org/10.1007/s00894-010-0787-4

Stojanović S, Zarić B, Zarić SD. Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins. in Journal of Molecular Modeling. 2010;16(11):1743-1751.
doi:10.1007/s00894-010-0787-4 .

Stojanović, Srđan, Zarić, Božidarka, Zarić, Snežana D., "Protein subunit interfaces: a statistical analysis of hot spots in Sm proteins" in Journal of Molecular Modeling, 16, no. 11 (2010):1743-1751,
https://doi.org/10.1007/s00894-010-0787-4 . .

TY  - JOUR
AU  - Đorđević, Dragana
AU  - Tosic, Ivana
AU  - Unkasevic, Miroslava
AU  - Duraskovic, Pavle
PY  - 2010
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/717
AB  - Precipitation samples collected from 1995 to 2000 at meteorological station in the eastern outskirts of Herceg Novi (Montenegro) were analysed on Na(+), K(+), Mg(2+), Ca(2+), Cl(-), SO(4) (2-), NO(3) (-) and NH(4) (+). Four-day backward trajectory simulations were conducted during the precipitation period to investigate the regional transport of main ions and their deposition in the region of the southeastern Adriatic Sea. The air mass trajectories were classified into six trajectory categories by the origin and direction of their approach to Herceg Novi. A bottle and funnel with a small net between them was used for sampling at a height of 1.5 m above the ground. The concentrations of Cl(-), NO(3) (-), NH(4) (+) and SO(4) (2-) were determined spectrophotometrically, the concentrations of Na(+) and K(+) were determined by the FAES method and the concentrations of Mg(2+) and Ca(2+) by the FAAS method. The factor analysis technique (PCA analysis) based on the calculation of the factors was employed to differentiate the contribution of emission sources to the content of the main ions in the precipitation. The obtained data sets were processed using the SPSS 11.5 statistical program. The Hybrid Single-Particle Lagrangian Integrated Trajectory model was used to study the air origin for the city of Herceg Novi (42A degrees 27'N, 18A degrees 33'E), Montenegro. The following origins of the air masses were considered: northern Europe (NE), eastern Europe-northeastern Europe (EE-NE); eastern Mediterranean-southeastern Europe (EM-SE); Africa-Central Mediterranean (A-CM); western Mediterranean (WM); western Europe-Central Europe (WE-CE) and undefined. The heights and frequencies of precipitation coming by air masses from northern Europe and eastern-northeastern Europe are the lowest. On the contrary, the heights and frequencies of precipitation coming by air masses from the western Mediterranean (36.6%) and Africa and the Central Mediterranean (30.6%) are the highest. The sea salt components (Na(+), Cl(-), Mg(2+)) are significantly correlated, except for air masses originating from the northern and eastern European regions. Significant correlations between SO(4) (2-) and NO(3) (-) are found in air masses coming from the western Europe and North Africa, over the Mediterranean. The highest volume-weighted mean (VWM) of: SO(4) (2-) , NH(4) (+) and Mg(2+) are for precipitation from EE-NE while the highest values of VWM of Cl (-) are from WM and of K(+) are from WE-CE. Long-range transport of Sahara dust is confirmed. For better estimation of origins of water-soluble ions in precipitation expanding list of analysis on anions of organic acids, such as HCOO(-), CH(3)COO(-), and C(2)H(2)COO(-), could be indicative of volatile organic compounds emitted by vegetation but also traffic. The chemical composition of precipitation together with a study of air backward trajectories is the proper tool for tracking the long-range transport of water-soluble ions and estimating transboundary pollution.
PB  - Springer Heidelberg, Heidelberg
T2  - Environmental Science and Pollution Research
T1  - Water-soluble main ions in precipitation over the southeastern Adriatic region: chemical composition and long-range transport
VL  - 17
IS  - 9
SP  - 1591
EP  - 1598
DO  - 10.1007/s11356-010-0346-7
ER  - 

@article{
author = "Đorđević, Dragana and Tosic, Ivana and Unkasevic, Miroslava and Duraskovic, Pavle",
year = "2010",
abstract = "Precipitation samples collected from 1995 to 2000 at meteorological station in the eastern outskirts of Herceg Novi (Montenegro) were analysed on Na(+), K(+), Mg(2+), Ca(2+), Cl(-), SO(4) (2-), NO(3) (-) and NH(4) (+). Four-day backward trajectory simulations were conducted during the precipitation period to investigate the regional transport of main ions and their deposition in the region of the southeastern Adriatic Sea. The air mass trajectories were classified into six trajectory categories by the origin and direction of their approach to Herceg Novi. A bottle and funnel with a small net between them was used for sampling at a height of 1.5 m above the ground. The concentrations of Cl(-), NO(3) (-), NH(4) (+) and SO(4) (2-) were determined spectrophotometrically, the concentrations of Na(+) and K(+) were determined by the FAES method and the concentrations of Mg(2+) and Ca(2+) by the FAAS method. The factor analysis technique (PCA analysis) based on the calculation of the factors was employed to differentiate the contribution of emission sources to the content of the main ions in the precipitation. The obtained data sets were processed using the SPSS 11.5 statistical program. The Hybrid Single-Particle Lagrangian Integrated Trajectory model was used to study the air origin for the city of Herceg Novi (42A degrees 27'N, 18A degrees 33'E), Montenegro. The following origins of the air masses were considered: northern Europe (NE), eastern Europe-northeastern Europe (EE-NE); eastern Mediterranean-southeastern Europe (EM-SE); Africa-Central Mediterranean (A-CM); western Mediterranean (WM); western Europe-Central Europe (WE-CE) and undefined. The heights and frequencies of precipitation coming by air masses from northern Europe and eastern-northeastern Europe are the lowest. On the contrary, the heights and frequencies of precipitation coming by air masses from the western Mediterranean (36.6%) and Africa and the Central Mediterranean (30.6%) are the highest. The sea salt components (Na(+), Cl(-), Mg(2+)) are significantly correlated, except for air masses originating from the northern and eastern European regions. Significant correlations between SO(4) (2-) and NO(3) (-) are found in air masses coming from the western Europe and North Africa, over the Mediterranean. The highest volume-weighted mean (VWM) of: SO(4) (2-) , NH(4) (+) and Mg(2+) are for precipitation from EE-NE while the highest values of VWM of Cl (-) are from WM and of K(+) are from WE-CE. Long-range transport of Sahara dust is confirmed. For better estimation of origins of water-soluble ions in precipitation expanding list of analysis on anions of organic acids, such as HCOO(-), CH(3)COO(-), and C(2)H(2)COO(-), could be indicative of volatile organic compounds emitted by vegetation but also traffic. The chemical composition of precipitation together with a study of air backward trajectories is the proper tool for tracking the long-range transport of water-soluble ions and estimating transboundary pollution.",
publisher = "Springer Heidelberg, Heidelberg",
journal = "Environmental Science and Pollution Research",
title = "Water-soluble main ions in precipitation over the southeastern Adriatic region: chemical composition and long-range transport",
volume = "17",
number = "9",
pages = "1591-1598",
doi = "10.1007/s11356-010-0346-7"
}

Đorđević, D., Tosic, I., Unkasevic, M.,& Duraskovic, P.. (2010). Water-soluble main ions in precipitation over the southeastern Adriatic region: chemical composition and long-range transport. in Environmental Science and Pollution Research
Springer Heidelberg, Heidelberg., 17(9), 1591-1598.
https://doi.org/10.1007/s11356-010-0346-7

Đorđević D, Tosic I, Unkasevic M, Duraskovic P. Water-soluble main ions in precipitation over the southeastern Adriatic region: chemical composition and long-range transport. in Environmental Science and Pollution Research. 2010;17(9):1591-1598.
doi:10.1007/s11356-010-0346-7 .

Đorđević, Dragana, Tosic, Ivana, Unkasevic, Miroslava, Duraskovic, Pavle, "Water-soluble main ions in precipitation over the southeastern Adriatic region: chemical composition and long-range transport" in Environmental Science and Pollution Research, 17, no. 9 (2010):1591-1598,
https://doi.org/10.1007/s11356-010-0346-7 . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Božidarka
AU  - Zarić, Snežana
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6531
AB  - This study aims to characterize the interface hot spot
residues of subunits in Sm proteins. We performed an analysis of the X ray structure of 15 Sm
motif containing proteins from the Protein Data Bank (PDB) and summarize physicochemical
properties in an effort to understand the origin of their stabilizing contributions to protein–
protein associations.Our results show that low relCompASA is critical for a residue to be a hot spot. Though
many of the hot spot residues have similar relCompASA values with nonhot spot residues,
they have different mean values (hot spots: 5.1%, non-hot spots: 29.1%). The P-value for
relCompASA is less than 0.05, which indicate that hot spots located near the center of the
interface are a general property of the interfaces, and largely protected from bulk solvent
(corresponding to low relCompASA). RelDASA indicates the change in the solvent
accessibility of a residue, and correlate significantly with relCompASA. Additionally,
knowledge-based pair potentials of residues is statistically significant to discriminate hot
spots and non-hot spots (P-value = 5.7×10−6). These results indicate that hot spots are mostly
buried, tightly packed and form a network of favorable interactions with other residues.
Structurally conserved residues and hot spots correlate significantly, and demonstrate
that hot spots play an important role in the stability of oligomers.
PB  - Belgrade, Serbia : Faculty of Chemistry, University of Belgrade
PB  - Germany : Alexander von Humboldt Foundation
C3  - Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia
T1  - Identification of Hot spots in Sm protein interfaces
SP  - 75
EP  - 75
UR  - https://hdl.handle.net/21.15107/rcub_cer_6531
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Božidarka and Zarić, Snežana",
year = "2009",
abstract = "This study aims to characterize the interface hot spot
residues of subunits in Sm proteins. We performed an analysis of the X ray structure of 15 Sm
motif containing proteins from the Protein Data Bank (PDB) and summarize physicochemical
properties in an effort to understand the origin of their stabilizing contributions to protein–
protein associations.Our results show that low relCompASA is critical for a residue to be a hot spot. Though
many of the hot spot residues have similar relCompASA values with nonhot spot residues,
they have different mean values (hot spots: 5.1%, non-hot spots: 29.1%). The P-value for
relCompASA is less than 0.05, which indicate that hot spots located near the center of the
interface are a general property of the interfaces, and largely protected from bulk solvent
(corresponding to low relCompASA). RelDASA indicates the change in the solvent
accessibility of a residue, and correlate significantly with relCompASA. Additionally,
knowledge-based pair potentials of residues is statistically significant to discriminate hot
spots and non-hot spots (P-value = 5.7×10−6). These results indicate that hot spots are mostly
buried, tightly packed and form a network of favorable interactions with other residues.
Structurally conserved residues and hot spots correlate significantly, and demonstrate
that hot spots play an important role in the stability of oligomers.",
publisher = "Belgrade, Serbia : Faculty of Chemistry, University of Belgrade, Germany : Alexander von Humboldt Foundation",
journal = "Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia",
title = "Identification of Hot spots in Sm protein interfaces",
pages = "75-75",
url = "https://hdl.handle.net/21.15107/rcub_cer_6531"
}

Stojanović, S., Zarić, B.,& Zarić, S.. (2009). Identification of Hot spots in Sm protein interfaces. in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia
Belgrade, Serbia : Faculty of Chemistry, University of Belgrade., 75-75.
https://hdl.handle.net/21.15107/rcub_cer_6531

Stojanović S, Zarić B, Zarić S. Identification of Hot spots in Sm protein interfaces. in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia. 2009;:75-75.
https://hdl.handle.net/21.15107/rcub_cer_6531 .

Stojanović, Srđan, Zarić, Božidarka, Zarić, Snežana, "Identification of Hot spots in Sm protein interfaces" in Book of abstracts - Second Humboldt conference on noncovalent interactions, October 22-25, 2009, Vršac, Serbia (2009):75-75,
https://hdl.handle.net/21.15107/rcub_cer_6531 .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6511
AB  - Structures of porphyrin-containing proteins from the Protein Data Bank (PDB) Select January 2007, were
searched in order to find and systematically characterize hydrogen bonds and hydrophobic interactions of porphyrins in
proteins. The results revealed that every porphyrin is involved in at least one hydrogen bond, most of the porphyrins form
several, while some of them form up to thirteen hydrogen bonds. In most of the hydrogen bonds propionate groups of
porphyrins interact with side-chains of residues. The most frequently observed donor is side chain of arginine. Histidine,
lysine, threonine, serine and tyrozine form substantial number of hydrogen bonds too. The study has revealed that
hydrophobic interactions are common between porphyrin and protein. Side-chains hydrophobic interactions are more
frequent than those with backbone. The average conservation score for the amino acids making hydrogen bonds (7.2) and
hydrophobic interactions (7.3) is statistically significantly higher than for the amino acids that are not involved in
noncovalent interactions (5.7) with the porphyrin, indicating importance of hydrogen bonds and hydrophobic interactions
with the porphyrin.
PB  - Bentham Open
T2  - The Open Structural Biology Journal
T1  - Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins
VL  - 3
SP  - 34
EP  - 41
DO  - 10.2174/1874199100903010034
ER  - 

@article{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2009",
abstract = "Structures of porphyrin-containing proteins from the Protein Data Bank (PDB) Select January 2007, were
searched in order to find and systematically characterize hydrogen bonds and hydrophobic interactions of porphyrins in
proteins. The results revealed that every porphyrin is involved in at least one hydrogen bond, most of the porphyrins form
several, while some of them form up to thirteen hydrogen bonds. In most of the hydrogen bonds propionate groups of
porphyrins interact with side-chains of residues. The most frequently observed donor is side chain of arginine. Histidine,
lysine, threonine, serine and tyrozine form substantial number of hydrogen bonds too. The study has revealed that
hydrophobic interactions are common between porphyrin and protein. Side-chains hydrophobic interactions are more
frequent than those with backbone. The average conservation score for the amino acids making hydrogen bonds (7.2) and
hydrophobic interactions (7.3) is statistically significantly higher than for the amino acids that are not involved in
noncovalent interactions (5.7) with the porphyrin, indicating importance of hydrogen bonds and hydrophobic interactions
with the porphyrin.",
publisher = "Bentham Open",
journal = "The Open Structural Biology Journal",
title = "Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins",
volume = "3",
pages = "34-41",
doi = "10.2174/1874199100903010034"
}

Stojanović, S.,& Zarić, S.. (2009). Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins. in The Open Structural Biology Journal
Bentham Open., 3, 34-41.
https://doi.org/10.2174/1874199100903010034

Stojanović S, Zarić S. Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins. in The Open Structural Biology Journal. 2009;3:34-41.
doi:10.2174/1874199100903010034 .

Stojanović, Srđan, Zarić, Snežana, "Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins" in The Open Structural Biology Journal, 3 (2009):34-41,
https://doi.org/10.2174/1874199100903010034 . .

TY  - JOUR
AU  - Malkov, Saga N.
AU  - Zivkovic, Miodrag V.
AU  - Beljanski, Milos V.
AU  - Stojanović, Srđan
AU  - Zarić, Snežana D.
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/550
AB  - Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.
PB  - Springer, New York
T2  - Protein Journal
T1  - A Reexamination of Correlations of Amino Acids with Particular Secondary Structures
VL  - 28
IS  - 2
SP  - 74
EP  - 86
DO  - 10.1007/s10930-009-9166-3
ER  - 

@article{
author = "Malkov, Saga N. and Zivkovic, Miodrag V. and Beljanski, Milos V. and Stojanović, Srđan and Zarić, Snežana D.",
year = "2009",
abstract = "Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between -9 and 10. The results show that the substituents on C beta or C gamma atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on alpha-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements.",
publisher = "Springer, New York",
journal = "Protein Journal",
title = "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures",
volume = "28",
number = "2",
pages = "74-86",
doi = "10.1007/s10930-009-9166-3"
}

Malkov, S. N., Zivkovic, M. V., Beljanski, M. V., Stojanović, S.,& Zarić, S. D.. (2009). A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal
Springer, New York., 28(2), 74-86.
https://doi.org/10.1007/s10930-009-9166-3

Malkov SN, Zivkovic MV, Beljanski MV, Stojanović S, Zarić SD. A Reexamination of Correlations of Amino Acids with Particular Secondary Structures. in Protein Journal. 2009;28(2):74-86.
doi:10.1007/s10930-009-9166-3 .

Malkov, Saga N., Zivkovic, Miodrag V., Beljanski, Milos V., Stojanović, Srđan, Zarić, Snežana D., "A Reexamination of Correlations of Amino Acids with Particular Secondary Structures" in Protein Journal, 28, no. 2 (2009):74-86,
https://doi.org/10.1007/s10930-009-9166-3 . .

TY  - JOUR
AU  - Janjić, Goran
AU  - Milčić, Miloš
AU  - Zarić, Snežana D.
PY  - 2009
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/590
AB  - Intramolecular metal-ligand OH/π (MLOH/π) and metal-ligand NH/π (MLNH/π) interactions in transition metal complexes between aqua or ammine ligand and ligand containing a C6-aromatic ring were investigated in crystal structures deposited in the Cambridge Structural Database (CSD). These intramolecular interactions appear in 38 structures with aqua ligand as the hydrogen atom donor and in 10 structures with ammine ligand as the hydrogen atom donor. Among all these complexes only one is negatively charged, 14 are positively charged and 33 are neutral indicating that the overall charge of the molecule has an influence on the XH/π (X = O or N) interactions. Energy estimated by DFT calculations is approximately 19 kJ mol-1 for the MLOH/π interactions and approximately 15 kJ mol-1 for the MLNH/π interactions.
PB  - Versita, Warsaw
T2  - Chemical Papers
T1  - Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes
VL  - 63
IS  - 3
SP  - 298
EP  - 305
DO  - 10.2478/s11696-009-0020-z
ER  - 

@article{
author = "Janjić, Goran and Milčić, Miloš and Zarić, Snežana D.",
year = "2009",
abstract = "Intramolecular metal-ligand OH/π (MLOH/π) and metal-ligand NH/π (MLNH/π) interactions in transition metal complexes between aqua or ammine ligand and ligand containing a C6-aromatic ring were investigated in crystal structures deposited in the Cambridge Structural Database (CSD). These intramolecular interactions appear in 38 structures with aqua ligand as the hydrogen atom donor and in 10 structures with ammine ligand as the hydrogen atom donor. Among all these complexes only one is negatively charged, 14 are positively charged and 33 are neutral indicating that the overall charge of the molecule has an influence on the XH/π (X = O or N) interactions. Energy estimated by DFT calculations is approximately 19 kJ mol-1 for the MLOH/π interactions and approximately 15 kJ mol-1 for the MLNH/π interactions.",
publisher = "Versita, Warsaw",
journal = "Chemical Papers",
title = "Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes",
volume = "63",
number = "3",
pages = "298-305",
doi = "10.2478/s11696-009-0020-z"
}

Janjić, G., Milčić, M.,& Zarić, S. D.. (2009). Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes. in Chemical Papers
Versita, Warsaw., 63(3), 298-305.
https://doi.org/10.2478/s11696-009-0020-z

Janjić G, Milčić M, Zarić SD. Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes. in Chemical Papers. 2009;63(3):298-305.
doi:10.2478/s11696-009-0020-z .

Janjić, Goran, Milčić, Miloš, Zarić, Snežana D., "Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes" in Chemical Papers, 63, no. 3 (2009):298-305,
https://doi.org/10.2478/s11696-009-0020-z . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6575
AB  - This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin
containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB)
Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in
order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen
bonds are commonly found in porphyrin containing proteins and are widely present in different
regions of the protein chain, such as the backbone, or side chain, and in different secondary
structural regions such as helices, strands and turns. The results revealed that the significant
number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most
frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains
hydrogen bonds are more frequent than those with peptide donors; they involve water
molecules sometimes that are classified as bridged hydrogen bonds. The average conservation
score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly
higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen
bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples.
AB  - Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima 
koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka 
(PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su 
vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, 
kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima 
(heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i 
propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja 
porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza 
peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene 
vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je 
statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj 
vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na 
nekoliko primera.
PB  - Belgrade : Serbian Chemical Society
C3  - Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia
T1  - Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin
T1  - Hydrogen bonds of porphyrins in porphyrin containing proteins
SP  - 88
EP  - 88
UR  - https://hdl.handle.net/21.15107/rcub_cer_6575
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin
containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB)
Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in
order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen
bonds are commonly found in porphyrin containing proteins and are widely present in different
regions of the protein chain, such as the backbone, or side chain, and in different secondary
structural regions such as helices, strands and turns. The results revealed that the significant
number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most
frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains
hydrogen bonds are more frequent than those with peptide donors; they involve water
molecules sometimes that are classified as bridged hydrogen bonds. The average conservation
score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly
higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen
bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples., Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima 
koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka 
(PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su 
vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, 
kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima 
(heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i 
propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja 
porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza 
peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene 
vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je 
statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj 
vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na 
nekoliko primera.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia",
title = "Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin, Hydrogen bonds of porphyrins in porphyrin containing proteins",
pages = "88-88",
url = "https://hdl.handle.net/21.15107/rcub_cer_6575"
}

Stojanović, S.,& Zarić, S.. (2008). Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin. in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia
Belgrade : Serbian Chemical Society., 88-88.
https://hdl.handle.net/21.15107/rcub_cer_6575

Stojanović S, Zarić S. Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin. in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia. 2008;:88-88.
https://hdl.handle.net/21.15107/rcub_cer_6575 .

Stojanović, Srđan, Zarić, Snežana, "Vodonične veze porfirinskog prstena u proteinima koji sadrže porfirin" in Program i kratki izvodi radova - XLVI savetovanje Srpskog hemijskog društva, 21. februar 2008, Beograd / Programme and Book of Abstracts - 46th Meeting of the Serbian Chemical Society, February 21, 2008, Belgrade, Serbia (2008):88-88,
https://hdl.handle.net/21.15107/rcub_cer_6575 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6569
AB  - This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side­ chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrophobic interactions with the porphyrin is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions with porphyrin.
PB  - Srpsko kristalografsko društvo
C3  - Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac
T1  - Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin
T1  - Hydrophobic interactions of porphyrins in porphyrin containing proteins
SP  - 44
EP  - 44
UR  - https://hdl.handle.net/21.15107/rcub_cer_6569
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic interactions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain. Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side­ chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrophobic interactions with the porphyrin is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions with porphyrin.",
publisher = "Srpsko kristalografsko društvo",
journal = "Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac",
title = "Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin, Hydrophobic interactions of porphyrins in porphyrin containing proteins",
pages = "44-44",
url = "https://hdl.handle.net/21.15107/rcub_cer_6569"
}

Stojanović, S.,& Zarić, S.. (2008). Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin. in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac
Srpsko kristalografsko društvo., 44-44.
https://hdl.handle.net/21.15107/rcub_cer_6569

Stojanović S, Zarić S. Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin. in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac. 2008;:44-44.
https://hdl.handle.net/21.15107/rcub_cer_6569 .

Stojanović, Srđan, Zarić, Snežana, "Hidrofobne interakcije porfirinskog prstena u proteinima koji sadrže porfirin" in Izvodi radova - XV konferencija Srpskog kristalografskog društva, Donji Milanovac / Abstracts - XV Conference of Serbian Crystallographic Society, Donji Milanovac (2008):44-44,
https://hdl.handle.net/21.15107/rcub_cer_6569 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6529
AB  - This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic in­teractions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain.
Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic inte­ractions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.
PB  - Society of Physical Chemists of Serbia
C3  - Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia
T1  - Hydrophobic interactions in the stability of porphyrin-containing proteins
VL  - II
SP  - 707
EP  - 709
UR  - https://hdl.handle.net/21.15107/rcub_cer_6529
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2008",
abstract = "This study aims to systematically characterize hydrophobic interactions of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrophobic interactions of porphyrins in proteins. The study has revealed that hydrophobic in­teractions are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone or side chain.
Examination of the highly cross-linked hydrophobic network points to a core of several residues with multiple contacts. These contacts cross-link the porphyrin ring in the proteins, essentially tying them together. Side-chains hydrophobic inte­ractions are more frequent than those with backbone. Besides, amino acids involving in these interactions shows significant conservation score.",
publisher = "Society of Physical Chemists of Serbia",
journal = "Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia",
title = "Hydrophobic interactions in the stability of porphyrin-containing proteins",
volume = "II",
pages = "707-709",
url = "https://hdl.handle.net/21.15107/rcub_cer_6529"
}

Stojanović, S.,& Zarić, S.. (2008). Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia
Society of Physical Chemists of Serbia., II, 707-709.
https://hdl.handle.net/21.15107/rcub_cer_6529

Stojanović S, Zarić S. Hydrophobic interactions in the stability of porphyrin-containing proteins. in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia. 2008;II:707-709.
https://hdl.handle.net/21.15107/rcub_cer_6529 .

Stojanović, Srđan, Zarić, Snežana, "Hydrophobic interactions in the stability of porphyrin-containing proteins" in Proceedings - 9th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2008, September 24-26, Belgrade, Serbia, II (2008):707-709,
https://hdl.handle.net/21.15107/rcub_cer_6529 .

TY  - JOUR
AU  - Ostojić, Bojana
AU  - Janjić, Goran
AU  - Zarić, Snežana D.
PY  - 2008
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/413
AB  - Analysis of crystal structures from the Cambridge Structural Database (CSD) that involve close contact between water and aryl rings revealed the existance of conformations where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane at distances typical for stacking interactions; attractive interaction energies obtained from ab initio calculations performed on model systems are significant (e. g. Delta(ECCSD(T)) = -1.60 kcal mol(-1)) and consistent with the observed structures.
PB  - Royal Soc Chemistry, Cambridge
T2  - Chemical Communications
T1  - Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction
IS  - 48
SP  - 6546
EP  - 6548
DO  - 10.1039/b812925h
ER  - 

@article{
author = "Ostojić, Bojana and Janjić, Goran and Zarić, Snežana D.",
year = "2008",
abstract = "Analysis of crystal structures from the Cambridge Structural Database (CSD) that involve close contact between water and aryl rings revealed the existance of conformations where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane at distances typical for stacking interactions; attractive interaction energies obtained from ab initio calculations performed on model systems are significant (e. g. Delta(ECCSD(T)) = -1.60 kcal mol(-1)) and consistent with the observed structures.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Chemical Communications",
title = "Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction",
number = "48",
pages = "6546-6548",
doi = "10.1039/b812925h"
}

Ostojić, B., Janjić, G.,& Zarić, S. D.. (2008). Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction. in Chemical Communications
Royal Soc Chemistry, Cambridge.(48), 6546-6548.
https://doi.org/10.1039/b812925h

Ostojić B, Janjić G, Zarić SD. Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction. in Chemical Communications. 2008;(48):6546-6548.
doi:10.1039/b812925h .

Ostojić, Bojana, Janjić, Goran, Zarić, Snežana D., "Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction" in Chemical Communications, no. 48 (2008):6546-6548,
https://doi.org/10.1039/b812925h . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Beljanski, Miloš
AU  - Zarić, Snežana
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6507
AB  - Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.
PB  - Springer
T2  - Journal of Biological Inorganic Chemistry
T1  - XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins
VL  - 12
SP  - 1063
EP  - 1071
DO  - 10.1007/s00775-007-0276-0
ER  - 

@article{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Beljanski, Miloš and Zarić, Snežana",
year = "2007",
abstract = "Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.",
publisher = "Springer",
journal = "Journal of Biological Inorganic Chemistry",
title = "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins",
volume = "12",
pages = "1063-1071",
doi = "10.1007/s00775-007-0276-0"
}

Stojanović, S., Medaković, V., Predović, G., Beljanski, M.,& Zarić, S.. (2007). XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry
Springer., 12, 1063-1071.
https://doi.org/10.1007/s00775-007-0276-0

Stojanović S, Medaković V, Predović G, Beljanski M, Zarić S. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry. 2007;12:1063-1071.
doi:10.1007/s00775-007-0276-0 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Beljanski, Miloš, Zarić, Snežana, "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins" in Journal of Biological Inorganic Chemistry, 12 (2007):1063-1071,
https://doi.org/10.1007/s00775-007-0276-0 . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Zarić, Snežana
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6530
AB  - Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds and XH/pi interactions of porphyrins in proteins.Side-chains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. Besides, pi-system of every porphyrin ring is involved in XH/pi interactions, most of the porphyrins are making several interactions. The average conservation score for the amino acids making noncovalent interactions with the porphyrin is statistically significantly higher than for the amino acids that do not make interactions.
PB  - Belgrade, Serbia : Faculty of Chemistry, University of Belgrade
PB  - Germany : Alexander von Humboldt Foundation
C3  - Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia
T1  - Hydrogen bonds and XH/pi interactions of porphyrins in proteins
SP  - 39
EP  - 39
UR  - https://hdl.handle.net/21.15107/rcub_cer_6530
ER  - 

@conference{
author = "Stojanović, Srđan and Zarić, Snežana",
year = "2007",
abstract = "Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds and XH/pi interactions of porphyrins in proteins.Side-chains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. Besides, pi-system of every porphyrin ring is involved in XH/pi interactions, most of the porphyrins are making several interactions. The average conservation score for the amino acids making noncovalent interactions with the porphyrin is statistically significantly higher than for the amino acids that do not make interactions.",
publisher = "Belgrade, Serbia : Faculty of Chemistry, University of Belgrade, Germany : Alexander von Humboldt Foundation",
journal = "Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia",
title = "Hydrogen bonds and XH/pi interactions of porphyrins in proteins",
pages = "39-39",
url = "https://hdl.handle.net/21.15107/rcub_cer_6530"
}

Stojanović, S.,& Zarić, S.. (2007). Hydrogen bonds and XH/pi interactions of porphyrins in proteins. in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia
Belgrade, Serbia : Faculty of Chemistry, University of Belgrade., 39-39.
https://hdl.handle.net/21.15107/rcub_cer_6530

Stojanović S, Zarić S. Hydrogen bonds and XH/pi interactions of porphyrins in proteins. in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia. 2007;:39-39.
https://hdl.handle.net/21.15107/rcub_cer_6530 .

Stojanović, Srđan, Zarić, Snežana, "Hydrogen bonds and XH/pi interactions of porphyrins in proteins" in Book of abstracts - Humboldt conference on noncovalent interactions, November 15-18. 2007, Vršac, Serbia (2007):39-39,
https://hdl.handle.net/21.15107/rcub_cer_6530 .

TY  - JOUR
AU  - Milčić, Miloš
AU  - Ostojić, Bojana
AU  - Zarić, Snežana D.
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4081
AB  - The aromaticity of the chelate rings of acetylacetonato (acac) and o-benzoquinonediimine (bqdi) ligands was
investigated theoretically by calculating nucleus-independent chemical shifts (NICS). The calculations were done
for the complexes with various metals and various other ligands. The results show that acac chelate rings in none
of the complexes satisfy this magnetic criterion for aromaticity. According to the results for bqdi chelate rings, there
is only the Ru2+-bqdi chelate ring with large negative NICS values, indicating possible aromaticity by magnetic
criterion.
PB  - American Chemical Society (ACS)
T2  - Inorganic Chemistry
T1  - Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings
VL  - 46
IS  - 17
SP  - 7109
EP  - 7114
DO  - 10.1021/ic062292w
ER  - 

@article{
author = "Milčić, Miloš and Ostojić, Bojana and Zarić, Snežana D.",
year = "2007",
abstract = "The aromaticity of the chelate rings of acetylacetonato (acac) and o-benzoquinonediimine (bqdi) ligands was
investigated theoretically by calculating nucleus-independent chemical shifts (NICS). The calculations were done
for the complexes with various metals and various other ligands. The results show that acac chelate rings in none
of the complexes satisfy this magnetic criterion for aromaticity. According to the results for bqdi chelate rings, there
is only the Ru2+-bqdi chelate ring with large negative NICS values, indicating possible aromaticity by magnetic
criterion.",
publisher = "American Chemical Society (ACS)",
journal = "Inorganic Chemistry",
title = "Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings",
volume = "46",
number = "17",
pages = "7109-7114",
doi = "10.1021/ic062292w"
}

Milčić, M., Ostojić, B.,& Zarić, S. D.. (2007). Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings. in Inorganic Chemistry
American Chemical Society (ACS)., 46(17), 7109-7114.
https://doi.org/10.1021/ic062292w

Milčić M, Ostojić B, Zarić SD. Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings. in Inorganic Chemistry. 2007;46(17):7109-7114.
doi:10.1021/ic062292w .

Milčić, Miloš, Ostojić, Bojana, Zarić, Snežana D., "Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings" in Inorganic Chemistry, 46, no. 17 (2007):7109-7114,
https://doi.org/10.1021/ic062292w . .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6528
AB  - The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.
PB  - Society of Physical Chemists of Serbia
C3  - Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
T1  - Non-conventional interactions in proteins containing porphyrine
VL  - I
SP  - 368
EP  - 370
UR  - https://hdl.handle.net/21.15107/rcub_cer_6528
ER  - 

@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran",
year = "2006",
abstract = "The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.",
publisher = "Society of Physical Chemists of Serbia",
journal = "Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia",
title = "Non-conventional interactions in proteins containing porphyrine",
volume = "I",
pages = "368-370",
url = "https://hdl.handle.net/21.15107/rcub_cer_6528"
}

Stojanović, S., Medaković, V.,& Predović, G.. (2006). Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
Society of Physical Chemists of Serbia., I, 368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528

Stojanović S, Medaković V, Predović G. Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia. 2006;I:368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, "Non-conventional interactions in proteins containing porphyrine" in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia, I (2006):368-370,
https://hdl.handle.net/21.15107/rcub_cer_6528 .

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Zarić, Snežana
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6577
AB  - For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability.
AB  - Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.
PB  - Belgrade : Serbian Crystallographic Society
C3  - XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
T1  - Nekonvencionalne interakcije u proteinima koji sadrže hem
T1  - Non-conventional interactions in proteins with the heme group
SP  - 38
EP  - 39
UR  - https://hdl.handle.net/21.15107/rcub_cer_6577
ER  - 

@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Zarić, Snežana",
year = "2006",
abstract = "For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability., Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.",
publisher = "Belgrade : Serbian Crystallographic Society",
journal = "XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia",
title = "Nekonvencionalne interakcije u proteinima koji sadrže hem, Non-conventional interactions in proteins with the heme group",
pages = "38-39",
url = "https://hdl.handle.net/21.15107/rcub_cer_6577"
}

Stojanović, S., Medaković, V., Predović, G.,& Zarić, S.. (2006). Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
Belgrade : Serbian Crystallographic Society., 38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577

Stojanović S, Medaković V, Predović G, Zarić S. Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia. 2006;:38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577 .

Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Zarić, Snežana, "Nekonvencionalne interakcije u proteinima koji sadrže hem" in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia (2006):38-39,
https://hdl.handle.net/21.15107/rcub_cer_6577 .