title: Protein folding is a convergent problem!
abstract: Protein folding, tagged as a grand challenge/NP hard problem, has been an open area of research in diverse fields. Exploring folding from the configurational volume perspective in terms of phi (ϕ), psi(ψ) backbone dihedral angles, we asked ourselves a fundamental question as to when do the neighborhood effects on the allowed ϕ, ψ values of each residue take over to assure convergence of proteins to their observed unique tertiary structures. A mapping of the higher order steric correlations beyond Ramachandran plots from ∼43612 protein structures comprising ∼26.5 million amino acid residues reveals that conformational restrictions on allowed ϕ, ψ values of each amino acid residue due to the N and C terminal neighbors - essentially a consideration of the sterically allowed regions of a tripeptide - ensure convergence of the configurational volume.
authors.affiliation: Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India.
authors.forename: Debarati
authors.initials: D
authors.lastname: Das Gupta
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Kaushik
authors.affiliation: Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India. Electronic address: bjayaram@chemistry.iitd.ac.in.
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
keywords: Allowed regions; Configurational volume; Higher order Ramachandran maps; Protein folding; Tripeptide unit