Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability.
A non-redundant database of 4536 structural domains, comprising more than 790,000 residues, has been used for the calculation of their solvent accessibility in the native protein environment and then in the isolated domain environment. Nearly 140,000 (18%) residues showed a change in accessible surface area in the above two conditions. General features of this change under these two circumstances have been pointed out. Propensities of these interfacing amino acid residues have been calculated and their variation for different secondary structure types has been analyzed. Actual amount of surface area lost by different secondary structures is higher in the case of helix and strands compared to coil and other conformations. Overall change in surface area in hydrophobic and uncharged residues is higher than that in charged residues. An attempt has been made to know the predictability of interface residues from sequence environments. This analysis and prediction results have significant implications towards determining interacting residues in proteins and for the prediction of protein-protein, protein-ligand, protein-DNA and similar interactions.
Raih
Mohd Firdaus
MF
National Institute for Genomics and Molecular Biology (Interim Laboratory), and School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
Ahmad
Shandar
S
Zheng
Rong
R
Mohamed
Rahmah
R
D000596:Amino Acids / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D011237:Predictive Value of Tests; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties
D000596:Amino Acids; D008024:Ligands; D011506:Proteins; D012997:Solvents; D004247:DNA