title: Influence of long-range contacts and surrounding residues on the transition state structures of proteins.
abstract: Understanding the parameters influencing the formation of transition state structures in proteins is an important problem in protein folding and kinetics. In this work, we have analyzed the structure-based parameters, surrounding hydrophobicity, secondary structure, solvent accessibility, number of medium- and long-range contacts, and surrounding residues for understanding the transition state structures of 15 proteins. The analysis of Φ-values shows that 29% of the studied 378 mutants have a Φ-value of more than 0.5. The combination of different structure-based parameters could discriminate the residues that have a Φ-value cutoff of more than 0.5 with a 5-fold cross-validation accuracy of 68%, which indicates that the surrounding residues and contacts play important roles in the formation of transition state structures. Systematic analysis on different proteins reveals that the proteins azurin, cold shock protein, and C-terminal domain of ribosomal protein L9 are influenced by the number of medium- and long-range proteins, whereas barnase, FK506 binding protein, and IM9 are influenced by surrounding residues. The discrimination accuracy lies in the ranges of 81-95% and 74-85% for these respective classes of protein. Furthermore, the combination of surrounding residues and contacts improved the accuracy up to 24% in other considered proteins. We suggest that the structure-based parameters along with noncovalent interactions and conservation of residues may aid in identifying the potential residues in the formation of transition state structures in proteins.
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo, Japan. michael-gromiha@aist.go.jp
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
mesh_terms: D001400:Azurin / Q000737:chemistry; D001426:Bacterial Proteins; D057773:Cold Shock Proteins and Peptides / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012260:Ribonucleases / Q000737:chemistry; D012269:Ribosomal Proteins / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D022021:Tacrolimus Binding Proteins / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D057773:Cold Shock Proteins and Peptides; D011506:Proteins; D012269:Ribosomal Proteins; D012997:Solvents; C049650:ribosomal protein L9; D001400:Azurin; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D022021:Tacrolimus Binding Proteins