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The fully-extended conformation in peptides and proteins

Crisma, Marco and Formaggio, Fernando and Aleman, Carlos and Torras, Joan and Ramakrishnan, Chandrasekharan and Kalmankar, Neha and Balaram, Padmanabhan and Toniolo, Claudio (2018) The fully-extended conformation in peptides and proteins. In: PEPTIDE SCIENCE, 110 (5, SI).

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Official URL: http://dx.doi.org/10.1002/bip.23100

Abstract

The intramolecularly H-bonded, fully-extended conformation (C-5) of an alpha-amino acid residue (and the resulting 2.0(5)-helix obtained via its propagation) is one of the least extensively investigated types of peptide and protein backbone secondary structure. This situation does still currently occur despite its unique ability to enjoy by far the largest separation per residue among peptide conformations. In this article, we offer a detailed update of our present knowledge on this intriguing 3D-structure of peptides in the crystal state as obtained from recently published investigations, complemented by a statistical analysis for its occurrence in the crystal structures of alpha-amino acid derivatives and peptides available in the Cambridge Structural Database. We have expanded this useful information to the results of a bioinformatics analysis performed on this (so far largely unappreciated) conformation authenticated in all proteins solved by X-ray diffraction to a resolution of <= 1.5 angstrom. In the last section, we describe the results of our DFT calculations on the conformational preferences of a set of homopeptides (from monomer to octamer) based on as many as six proteins and two noncoded, carefully selected, alpha-amino acids. From this literature survey integrated by new energy calculations, we have definitely provided strong support to the thesis that this polypeptide 3D-structure does indeed exist, it should be not neglected in future studies by structural biochemists, and it represents a very attractive, novel backbone for applications for organic, medicinal, and biomaterials chemists.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to WILEY
Keywords: 2.0(5)-helix; conformational energy calculations; crystal-state conformation; fully-extended peptide conformation; X-ray diffraction
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 23 Dec 2018 06:50
Last Modified: 23 Dec 2018 06:50
URI: http://eprints.iisc.ac.in/id/eprint/61256

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