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Stojanovic, Srdan D.

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  • Stojanovic, Srdan D. (3)
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Author's Bibliography

Non-canonical interactions of porphyrins in porphyrin-containing proteins

Stojanovic, Srdan D.; Isenović, Esma R.; Zarić, Božidarka

(2012)

TY  - JOUR
AU  - Stojanovic, Srdan D.
AU  - Isenović, Esma R.
AU  - Zarić, Božidarka
PY  - 2012
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/5045
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.
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 = "Stojanovic, Srdan D. and Isenović, Esma R. and Zarić, Božidarka",
year = "2012",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/5045",
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.",
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"
}
12
12
12

Peroxisome Proliferator-Activated Receptors and Atherosclerosis

Soskić, Sanja S.; Dobutovic, Branislava D.; Sudar, Emina; Obradović, Milan M.; Nikolić, Dragana; Zarić, Božidarka; Stojanovic, Srdan D.; Stokić, Edita; Mikhailidis, Dimitri P.; Isenović, Esma R.

(2011)

TY  - JOUR
AU  - Soskić, Sanja S.
AU  - Dobutovic, Branislava D.
AU  - Sudar, Emina
AU  - Obradović, Milan M.
AU  - Nikolić, Dragana
AU  - Zarić, Božidarka
AU  - Stojanovic, Srdan D.
AU  - Stokić, Edita
AU  - Mikhailidis, Dimitri P.
AU  - Isenović, Esma R.
PY  - 2011
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/4519
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.
T2  - Angiology
T1  - Peroxisome Proliferator-Activated Receptors and Atherosclerosis
VL  - 62
IS  - 7
SP  - 523
EP  - 534
DO  - 10.1177/0003319711401012
ER  - 
@article{
author = "Soskić, Sanja S. and Dobutovic, Branislava D. and Sudar, Emina and Obradović, Milan M. and Nikolić, Dragana and Zarić, Božidarka and Stojanovic, Srdan D. and Stokić, Edita and Mikhailidis, Dimitri P. and Isenović, Esma R.",
year = "2011",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/4519",
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.",
journal = "Angiology",
title = "Peroxisome Proliferator-Activated Receptors and Atherosclerosis",
volume = "62",
number = "7",
pages = "523-534",
doi = "10.1177/0003319711401012"
}
17
22
25

Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies

Stojanovic, Srdan D.; Isenović, Esma R.; Zarić, Božidarka

(2011)

TY  - JOUR
AU  - Stojanovic, Srdan D.
AU  - Isenović, Esma R.
AU  - Zarić, Božidarka
PY  - 2011
UR  - http://vinar.vin.bg.ac.rs/handle/123456789/4381
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.
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 = "Stojanovic, Srdan D. and Isenović, Esma R. and Zarić, Božidarka",
year = "2011",
url = "http://vinar.vin.bg.ac.rs/handle/123456789/4381",
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.",
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"
}
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