ArticleProceedings of the National Academy of Sciences of the United States of America2023
An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Advancing the Identification of Bioactive Molecules and the Construction of a Synergistic Drug Delivery System in Combating Lung Injury.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers.Journal of cheminformatics · 2025Article
- Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping.Nature communications · 2024Article
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4 authors.
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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.
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