title: Prediction and analysis of surface hydrophobic residues in tertiary structure of proteins.
abstract: The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. In general, hydrophobic residues such as Val, Leu, Ile, Phe, and Met tend to be buried in the interior and polar side chains exposed to solvent. The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions.
authors.affiliation: Department of Biotechnology, The Oxford College of Engineering, Bangalore 560068, India.
authors.forename: Shambhu
authors.initials: S
authors.lastname: Malleshappa Gowder
authors.affiliation: Department of Biotechnology, PES Institute of Technology, Bangalore 560085, India.
authors.forename: Jhinuk
authors.identifier: 0000-0003-1193-5488
authors.initials: J
authors.lastname: Chatterjee
authors.affiliation: Department of Biotechnology, The Oxford College of Engineering, Bangalore 560068, India.
authors.forename: Tanusree
authors.initials: T
authors.lastname: Chaudhuri
authors.affiliation: Department of Biotechnology, The Oxford College of Engineering, Bangalore 560068, India.
authors.forename: Kusum
authors.initials: K
authors.lastname: Paul
mesh_terms: D019951:DNA Polymerase beta / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D048229:Sulfolobus solfataricus / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents; D019951:DNA Polymerase beta