Non-canonical interactions of porphyrins in porphyrin-containing proteins.
In this study we have described the noncanonical 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····O and CH····N interactions, with a small percentage of CH···π and noncanonical 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 noncanonical 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) noncanonical 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.
Department of Chemistry, ICTM, University of Belgrade, Njegoševa 12, Belgrade 11000, Serbia. srdjanst@chem.bg.ac.rs
Srđan Ð
SÐ
Stojanović
Esma R
ER
Isenović
Božidarka L
BL
Zarić
D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D001419:Bacteria; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D010944:Plants; D011166:Porphyrins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
D000596:Amino Acids; D008024:Ligands; D011166:Porphyrins; D011506:Proteins; D012997:Solvents; D014867:Water