Residues environment study - Solvent accessibility in globins protein family

Abstract

Attempts to match protein sequences to folds by describing the fold in terms of the environment of each residue in the structure could be a more efficient way to detect structural similarities in divergent proteins. In this report, the environment of each residue is described in terms of solvent accessibility. In an aqueous environment, hydrophobic residues tend to segregate into the core of the protein whereas polar residues remain exposed on the protein surface. In order to quantify hydrophobic residues burial, the residue solvent accessible area (SAA) is introduced. We computed the environment score of a particular residue resides in a buried, partly buried or exposed environment. Our study used the globins protein family, which belongs to the all-alpha class in the SCOP database. The SAA data are retrieved from the DSSP database. We obtained a 20x3 scoring matrix that describes the preference of a particular residue resides in one of the three buried states. This matrix allows us to construct a 3D profile for the globins protein and used as a template for the threading method; that is for each position in the sequence one can determine its environment class and the score of a particular residue in this position.