For instance, it is essential for deciphering protein folding code, for assessing the factors that modulate protein activity, for understanding the effect of mutations on protein structures and, thus, for designing suitable mutants for biotechnological applications. A full understanding of the factors that determine protein structures would be crucial for many research fields. From the chemical-physical point of view, a large variety of different interactions modulate protein structures, such as salt bridges, hydrogen bonds, NH-π interactions, van der Waals interactions, and so on. relative to the interaction with the solvent, ligands and/or other macromolecular partners). inherent to the polypeptide chain) and environmental (i.e. The structure adopted by a protein is the result of a complex and subtle balance of a number of different stabilization interactions, both intrinsic (i.e. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. The authors thank CINECA Supercomputing for computational support (project number 953). This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This work has been funded by Minstero Istruzione Universita Ricerca (MIUR) (PRIN2008 and FIRB RBFR08DUX6). Received: JAccepted: AugPublished: September 16, 2011Ĭopyright: © 2011 Improta et al. PLoS ONE 6(9):Įditor: Annalisa Pastore, National Institute for Medical Research, Medical Research Council, United Kingdom The implications of the present findings for protein structure determination, validation and prediction are also discussed.Ĭitation: Improta R, Vitagliano L, Esposito L (2011) Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Orbital analysis shows that orbital interactions between the σ system of C α substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures.
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