An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units

Author:

Rosenberg Aviv A.1ORCID,Yehishalom Nitsan2,Marx Ailie1ORCID,Bronstein Alex M.1

Affiliation:

1. Department of Computer Science, Technion–Israel Institute of Technology, Haifa 32000, Israel

2. Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel

Abstract

Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method.

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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