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Non-canonical interactions of porphyrins in porphyrin-containing proteins

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2012
Authors
Stojanović, Srđan
Isenovic, Esma R.
Zarić, Božidarka
Article (Published version)
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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.

Keywords:
Non-canonical interactions / Proteins / Porphyrins / Stabilization centers
Source:
Amino Acids, 2012, 43, 4, 1535-1546
Publisher:
  • Springer Wien, Wien
Funding / projects:
  • The study of physicochemical and biochemical processes in living environment that have impacts on pollution and the investigation of possibilities for minimizing the consequences (RS-172001)
  • Hormonal regulation of expression and activity of the nitric oxide synthase and sodium-potassium pump in experimental models of insulin resistance, diabetes and cardiovascular disorders (RS-173033)

DOI: 10.1007/s00726-012-1228-8

ISSN: 0939-4451

PubMed: 22302367

WoS: 000309070700012

Scopus: 2-s2.0-84867582759
[ Google Scholar ]
13
13
URI
https://cer.ihtm.bg.ac.rs/handle/123456789/1099
Collections
  • Radovi istraživača / Researchers' publications
Institution/Community
IHTM
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 . .

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