title: Analysis of secondary structural and physicochemical changes in protein-protein complexes.
abstract: Conformation switching in protein-protein complexes is considered important for the molecular recognition process. Overall analysis of 123 protein-protein complexes in a benchmark data-set showed that 6.8% of residues switched over their secondary structure conformation upon complex formation. Amino acid residue-wise preference for conformation change has been analyzed in binding and non-binding site residues separately. In this analysis, residues such as Ser, Leu, Glu, and Lys had higher frequency of secondary structural conformation change. The change of helix to coil and sheet to coil conformation and vice versa has been observed frequently, whereas the conformation change of helix to extended sheet occurred rarely in the studied complexes. Influence of conformation change toward the N and C terminal on either side of the binding site residues has been analyzed. Further, analysis on φ and ψ angle variation, conservation, stability, and solvent accessibility have been performed on binding site residues. Knowledge obtained from the present study could be effectively employed in the protein-protein modeling and docking studies.
authors.affiliation: a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India.|b Department of Plant Molecular Biology and Bioinformatics , Tamil Nadu Agricultural University , Coimbatore , Tamil Nadu 641003 , India.
authors.forename: N
authors.initials: N
authors.lastname: Saranya
authors.affiliation: a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India.|c Center of Excellence in Bioinformatics, School of Biotechnology , Madurai Kamaraj University , Madurai , Tamil Nadu 625 021 , India.
authors.forename: K M
authors.initials: KM
authors.lastname: Saravanan
authors.affiliation: d Department of Biotechnology , Indian Institute of Technology Madras , Chennai , Tamil Nadu 600036 , India.
authors.forename: M
authors.initials: M
authors.lastname: Michael Gromiha
authors.affiliation: a Department of Bioinformatics , School of Life Sciences, Bharathidasan University , Tiruchirappalli 620024 , India.
authors.forename: S
authors.initials: S
authors.lastname: Selvaraj
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D017124:Conserved Sequence; D066264:Datasets as Topic; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012997:Solvents / Q000737:chemistry
chemical_list: D000596:Amino Acids; D046912:Multiprotein Complexes; D011506:Proteins; D012997:Solvents
keywords: binding and non-binding sites; conformation switching; protein stability; protein–protein recognition; residue conservation; secondary structure; solvent accessibility