TY  - JOUR
AU  - Stojanović, Srđan
AU  - Isenovic, Esma R.
AU  - Zarić, Božidarka
PY  - 2012
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1099
AB  - In this study we have described the non-canonical interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The analysis reported in this study shows that the predominant type of non-canonical interactions at porphyrins are CH center dot center dot center dot O and CH center dot center dot center dot N interactions, with a small percentage of CH center dot center dot center dot pi and non-canonical interactions involving sulfur atoms. The majority of non-canonical interactions are formed from side-chains of charged and polar amino acids, whereas backbone groups are not frequently involved. The main-chain non-canonical interactions might be slightly more linear than the side-chain interactions, and they have somewhat shorter median distances. The analysis, performed in this study, shows that about 44% of the total interactions in the dataset are involved in the formation of multiple (furcated) non-canonical interactions. The high number of porphyrin-water interactions show importance of the inclusion of solvent in protein-ligand interaction studies. Furthermore, in the present study we have observed that stabilization centers are composed predominantly from nonpolar amino acid residues. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.
PB  - Springer Wien, Wien
T2  - Amino Acids
T1  - Non-canonical interactions of porphyrins in porphyrin-containing proteins
VL  - 43
IS  - 4
SP  - 1535
EP  - 1546
DO  - 10.1007/s00726-012-1228-8
ER  - 

@article{
author = "Stojanović, Srđan and Isenovic, Esma R. and Zarić, Božidarka",
year = "2012",
abstract = "In this study we have described the non-canonical interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The analysis reported in this study shows that the predominant type of non-canonical interactions at porphyrins are CH center dot center dot center dot O and CH center dot center dot center dot N interactions, with a small percentage of CH center dot center dot center dot pi and non-canonical interactions involving sulfur atoms. The majority of non-canonical interactions are formed from side-chains of charged and polar amino acids, whereas backbone groups are not frequently involved. The main-chain non-canonical interactions might be slightly more linear than the side-chain interactions, and they have somewhat shorter median distances. The analysis, performed in this study, shows that about 44% of the total interactions in the dataset are involved in the formation of multiple (furcated) non-canonical interactions. The high number of porphyrin-water interactions show importance of the inclusion of solvent in protein-ligand interaction studies. Furthermore, in the present study we have observed that stabilization centers are composed predominantly from nonpolar amino acid residues. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.",
publisher = "Springer Wien, Wien",
journal = "Amino Acids",
title = "Non-canonical interactions of porphyrins in porphyrin-containing proteins",
volume = "43",
number = "4",
pages = "1535-1546",
doi = "10.1007/s00726-012-1228-8"
}

Stojanović, S., Isenovic, E. R.,& Zarić, B.. (2012). Non-canonical interactions of porphyrins in porphyrin-containing proteins. in Amino Acids
Springer Wien, Wien., 43(4), 1535-1546.
https://doi.org/10.1007/s00726-012-1228-8

Stojanović S, Isenovic ER, Zarić B. Non-canonical interactions of porphyrins in porphyrin-containing proteins. in Amino Acids. 2012;43(4):1535-1546.
doi:10.1007/s00726-012-1228-8 .

Stojanović, Srđan, Isenovic, Esma R., Zarić, Božidarka, "Non-canonical interactions of porphyrins in porphyrin-containing proteins" in Amino Acids, 43, no. 4 (2012):1535-1546,
https://doi.org/10.1007/s00726-012-1228-8 . .

TY  - JOUR
AU  - Soskic, Sanja S.
AU  - Dobutovic, Branislava D.
AU  - Sudar, Emina M.
AU  - Obradovic, Milan M.
AU  - Nikolic, Dragana M.
AU  - Zarić, Božidarka
AU  - Stojanović, Srđan
AU  - Stokic, Edita J.
AU  - Mikhailidis, Dimitri P.
AU  - Isenovic, Esma R.
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/762
AB  - The peroxisome proliferator-activated receptors (PPARs) represent the family of 3 nuclear receptor isoforms-PPAR alpha, -gamma, and -delta/beta, which are encoded by different genes. As lipid sensors, they are primarily involved in regulation of lipid metabolism and subsequently in inflammation and atherosclerosis. Atherosclerosis considers accumulation of the cells and extracellular matrix in the vessel wall leading to the formation of atherosclerotic plaque, atherothrombosis, and other vascular complications. Besides existence of natural ligands for PPARs, their more potent synthetic ligands are fibrates and thiazolidindiones. Future investigations should now focus on the mechanisms of PPARs activation, which might present new approaches involved in the antiatherosclerotic effects revealed in this review. In addition, in this review we are presenting latest data from recent performed clinical studies which have focus on novel approach to PPARs agonists as potential therapeutic agents in the treatment of complex disease such as atherosclerosis.
PB  - Sage Publications Inc, Thousand Oaks
T2  - Angiology
T1  - Peroxisome Proliferator-Activated Receptors and Atherosclerosis
VL  - 62
IS  - 7
SP  - 523
EP  - 534
DO  - 10.1177/0003319711401012
ER  - 

@article{
author = "Soskic, Sanja S. and Dobutovic, Branislava D. and Sudar, Emina M. and Obradovic, Milan M. and Nikolic, Dragana M. and Zarić, Božidarka and Stojanović, Srđan and Stokic, Edita J. and Mikhailidis, Dimitri P. and Isenovic, Esma R.",
year = "2011",
abstract = "The peroxisome proliferator-activated receptors (PPARs) represent the family of 3 nuclear receptor isoforms-PPAR alpha, -gamma, and -delta/beta, which are encoded by different genes. As lipid sensors, they are primarily involved in regulation of lipid metabolism and subsequently in inflammation and atherosclerosis. Atherosclerosis considers accumulation of the cells and extracellular matrix in the vessel wall leading to the formation of atherosclerotic plaque, atherothrombosis, and other vascular complications. Besides existence of natural ligands for PPARs, their more potent synthetic ligands are fibrates and thiazolidindiones. Future investigations should now focus on the mechanisms of PPARs activation, which might present new approaches involved in the antiatherosclerotic effects revealed in this review. In addition, in this review we are presenting latest data from recent performed clinical studies which have focus on novel approach to PPARs agonists as potential therapeutic agents in the treatment of complex disease such as atherosclerosis.",
publisher = "Sage Publications Inc, Thousand Oaks",
journal = "Angiology",
title = "Peroxisome Proliferator-Activated Receptors and Atherosclerosis",
volume = "62",
number = "7",
pages = "523-534",
doi = "10.1177/0003319711401012"
}

Soskic, S. S., Dobutovic, B. D., Sudar, E. M., Obradovic, M. M., Nikolic, D. M., Zarić, B., Stojanović, S., Stokic, E. J., Mikhailidis, D. P.,& Isenovic, E. R.. (2011). Peroxisome Proliferator-Activated Receptors and Atherosclerosis. in Angiology
Sage Publications Inc, Thousand Oaks., 62(7), 523-534.
https://doi.org/10.1177/0003319711401012

Soskic SS, Dobutovic BD, Sudar EM, Obradovic MM, Nikolic DM, Zarić B, Stojanović S, Stokic EJ, Mikhailidis DP, Isenovic ER. Peroxisome Proliferator-Activated Receptors and Atherosclerosis. in Angiology. 2011;62(7):523-534.
doi:10.1177/0003319711401012 .

Soskic, Sanja S., Dobutovic, Branislava D., Sudar, Emina M., Obradovic, Milan M., Nikolic, Dragana M., Zarić, Božidarka, Stojanović, Srđan, Stokic, Edita J., Mikhailidis, Dimitri P., Isenovic, Esma R., "Peroxisome Proliferator-Activated Receptors and Atherosclerosis" in Angiology, 62, no. 7 (2011):523-534,
https://doi.org/10.1177/0003319711401012 . .

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Isenovic, Esma R.
AU  - Zarić, Božidarka
PY  - 2011
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/785
AB  - The distinguishing property of Sm/LSm protein assemblies is their high stability. In order to better understand the nature of Sm/LSm protein oligomers in this study we have analyzed the contribution of non-canonical interactions to the stability of assemblies. The predominant types of non-canonical interactions at Sm/LSm protein interfaces are CH center dot center dot center dot O, and CH center dot center dot center dot N interactions represented at interfaces. Our results show low percentages of XH-pi and non-canonical interactions involving sulfur atoms, while the backbone groups were less frequently involved. The data show a high percentage of non-canonical interactions in interfaces formed by charged residues with Lys and Arg, these being the major charged donors. The main chain non-canonical interactions might be slightly more linear than the side chain interactions, and they have somewhat shorter median distances. Comparing the stabilizing amino acid residues with amino acids which build non-canonical interactions at interfaces shows that certain amino acids like Phe, Pro, His and Tyr are involved with a high percentage. The high conservation score of amino acids that are involved in non-canonical interactions in protein interfaces is an additional strong argument for their importance in the stabilization of Sm/LSm protein assemblies.
PB  - Wiley-V C H Verlag Gmbh, Weinheim
T2  - Molecular Informatics
T1  - Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies
VL  - 30
IS  - 5
SP  - 430
EP  - 442
DO  - 10.1002/minf.201000176
ER  - 

@article{
author = "Stojanović, Srđan and Isenovic, Esma R. and Zarić, Božidarka",
year = "2011",
abstract = "The distinguishing property of Sm/LSm protein assemblies is their high stability. In order to better understand the nature of Sm/LSm protein oligomers in this study we have analyzed the contribution of non-canonical interactions to the stability of assemblies. The predominant types of non-canonical interactions at Sm/LSm protein interfaces are CH center dot center dot center dot O, and CH center dot center dot center dot N interactions represented at interfaces. Our results show low percentages of XH-pi and non-canonical interactions involving sulfur atoms, while the backbone groups were less frequently involved. The data show a high percentage of non-canonical interactions in interfaces formed by charged residues with Lys and Arg, these being the major charged donors. The main chain non-canonical interactions might be slightly more linear than the side chain interactions, and they have somewhat shorter median distances. Comparing the stabilizing amino acid residues with amino acids which build non-canonical interactions at interfaces shows that certain amino acids like Phe, Pro, His and Tyr are involved with a high percentage. The high conservation score of amino acids that are involved in non-canonical interactions in protein interfaces is an additional strong argument for their importance in the stabilization of Sm/LSm protein assemblies.",
publisher = "Wiley-V C H Verlag Gmbh, Weinheim",
journal = "Molecular Informatics",
title = "Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies",
volume = "30",
number = "5",
pages = "430-442",
doi = "10.1002/minf.201000176"
}

Stojanović, S., Isenovic, E. R.,& Zarić, B.. (2011). Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies. in Molecular Informatics
Wiley-V C H Verlag Gmbh, Weinheim., 30(5), 430-442.
https://doi.org/10.1002/minf.201000176

Stojanović S, Isenovic ER, Zarić B. Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies. in Molecular Informatics. 2011;30(5):430-442.
doi:10.1002/minf.201000176 .

Stojanović, Srđan, Isenovic, Esma R., Zarić, Božidarka, "Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies" in Molecular Informatics, 30, no. 5 (2011):430-442,
https://doi.org/10.1002/minf.201000176 . .