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

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 experime

SUBMITTER: Rosenberg AA 

PROVIDER: S-EPMC10623034 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature