Analysis of accessible surface of residues in proteins

Analysis of accessible surface of residues in proteins

Understanding the folding of proteins remains one of the major scientific challenges. One way to explore this complex problem is to get information from the protein structures themselves. We recently developed an analytical tool, named Pex files, in which numerical data on various structural parameters of proteins are described, such as secondary structures, side chain interactions, H-bonds, and more (Thomas et al. 2001, 2002a,b). Here we introduce a new Pex file that, in addition to the major structural parameters of proteins, lists a series of parameters describing the solvent accessibility. The folding process of soluble proteins decreases the surface in contact with the solvent. This is related to the secondary structures of proteins. Accurate knowledge of residue accessibility would thus aid the prediction of secondary structures. Different methods of prediction are based on the use of protein structure databases and on multiple sequence alignments. They have various efficiencies, notably depending on the number of relative accessibility states (i.e., exposed, buried, and in-between; Rost and Sander 1994; Rost 1996; Li and Pan 2001; Naderi-Manesh et al. 2001; Yuan et al. 2002). Further, because active sites of proteins are often located at the surface of the protein, greater insight into residue accessibility would be important in understanding and predicting structure/function relationships