Is there a connection between peptide bond geometry and aminoacid residue conformational preferences?
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Databases
- Keywords
- aminoacid residue preferences, secondary structure, protein conformation, Ramachandran plot, propensity scales, local geometry
- Copyright
- © 2016 Balasco et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Is there a connection between peptide bond geometry and aminoacid residue conformational preferences? PeerJ Preprints 4:e2665v1 https://doi.org/10.7287/peerj.preprints.2665v1
Abstract
The definition of the structural basis of the conformational preferences of the genetically encoded aminoacid residues is crucial to decipher the physical code of protein folding and would have a huge impact on our understanding of protein structure and function. Indeed, although a large number of computational and experimental investigations have highlighted that the different protein residues show distinct conformational propensities, none of the current hypotheses is able to satisfactorily explain these preferences. In the last decades, we and others have clearly demonstrated that several geometrical parameters of protein backbone (bond angles, peptide bond distortions from planarity, and pyramidalization of the carbonyl carbon atom) are heavily dependent on the local conformation (φ/ψ dihedral angles) [1-8]. Moreover, a correlation between bond distances such as CO and CN has been detected in ultrahigh resolution protein structures [9]. Concerning bond angles, most of these investigations have been focused on the NCαC (τ) angle, shown to be significantly affected by both φ/ψ dihedral angles. In this framework, we here evaluated the impact of the local geometry on the residues conformational preferences by performing statistical analyses on a dataset of non-redundant protein chains selected from the Protein data Bank (PDB). Our data highlight a clear link between residue conformational preferences and local geometry.
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Author Comment
The abstract is part of the "BBCC2016" collection.