Non-canonical interactions of porphyrins in porphyrin-containing proteins
Апстракт
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.
Кључне речи:
Non-canonical interactions / Proteins / Porphyrins / Stabilization centersИзвор:
Amino Acids, 2012, 43, 4, 1535-1546Финансирање / пројекти:
- Проучавање физичкохемијских и биохемијских процеса у животној средини који утичу на загађење и истраживање могућности за минимизирање последица (RS-MESTD-Basic Research (BR or ON)-172001)
- Хормонска регулација експресије и активности азот оксид синтазе и натријум-калијумове пумпе у експерименталним моделима инсулинске резистенције, дијабетеса и кардиоваскуларних поремећаја (RS-MESTD-Basic Research (BR or ON)-173033)
DOI: 10.1007/s00726-012-1228-8
ISSN: 0939-4451
PubMed: 22302367
WoS: 000309070700012
Scopus: 2-s2.0-84867582759
Колекције
Институција/група
VinčaTY - JOUR AU - Stojanovic, Srdan D. AU - Isenović, Esma R. AU - Zarić, Božidarka PY - 2012 UR - https://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", 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" }
Stojanovic, S. D., Isenović, E. R.,& Zarić, B.. (2012). Non-canonical interactions of porphyrins in porphyrin-containing proteins. in Amino Acids, 43(4), 1535-1546. https://doi.org/10.1007/s00726-012-1228-8
Stojanovic SD, Isenović 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 .
Stojanovic, Srdan D., Isenović, 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 . .