title: Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors.
abstract: The Ramachandran plot distributions of nonglycine residues from experimentally determined structures are routinely described as grouping into one of six major basins: β, PII , α, αL , ξ and γ'. Recent work describing the most common conformations adopted by pairs of residues in folded proteins [i.e., (φ,ψ)2 -motifs] showed that commonly described major basins are not true single thermodynamic basins, but are composed of distinct subregions that are associated with various conformations of either the preceding or following neighbor residue. Here, as documentation of the extent to which the conformational preferences of a central residue are influenced by the conformations of its two neighbors, we present a set of φ,ψ-plots that are delimited simultaneously by the φ,ψ-angles of its neighboring residues on both sides. The level of influence seen here is typically greater than the influence associated with considering the identities of neighboring residues, implying that the use of this heretofore untapped information can improve the accuracy of structure prediction algorithms and low resolution protein structure refinement.
authors.affiliation: Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Hollingsworth
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, 97331.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Lewis
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, 97331.
authors.forename: P Andrew
authors.initials: PA
authors.lastname: Karplus
mesh_terms: D020816:Amino Acid Motifs; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: helix; protein conformation; protein standard conformations; secondary structure; turn