Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/ Protein Crystal Structures Roberto Improta*, Luigi Vitagliano, Luciana Esposito* Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy Abstract 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. 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. 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 y dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the s system of Ca substituents and the p system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. 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. The implications of the present findings for protein structure determination, validation and prediction are also discussed. Citation: Improta R, Vitagliano L, Esposito L (2011) Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/ Protein Crystal Structures. PLoS ONE 6(9): e24533. doi:10.1371/journal.pone.0024533 Editor: Annalisa Pastore, National Institute for Medical Research, Medical Research Council, United Kingdom Received June 17, 2011; Accepted August 11, 2011; Published September 16, 2011 Copyright: 2011 Improta et al. 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. Funding: This work has been funded by Minstero Istruzione Universita Ricerca (MIUR) (PRIN2008 and FIRB RBFR08DUX6). The authors thank CINECA Supercomputing for computational support (project number 953). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: robimp@unina.it. (RI); luciana.esposito@unina.it. (LE) Introduction 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. inherent to the polypeptide chain) and environmental (i.e. relative to the interaction with the solvent, ligands and/or other macromolecular partners) [1]. From the chemical-physical point of view, a large variety of different interactions modulate protein structures, such as salt bridges, hydrogen bonds, NH-p interactions, van der Waals interactions, and so on. A full understanding of the factors that determine protein structures would be crucial for many research fields. For instance, it is essential for deciphering protein folding code, for assessing the factors that modulate protein activity, for under- standing the effect of mutations on protein structures and, thus, for designing suitable mutants for biotechnological applications [1]. Due to the complexity of the polypeptide chain organization, the structure of protein building blocks is affected by both local and non-local interactions [1–3]. Therefore, a preliminary but fundamental step towards a full understanding of the factors determining the protein structural stability is the discrimination between local and non-local effects. In this context, one of the most important and controversial aspects of protein structures regards the peptide bond deviation from planarity [4–7], which has also relevant implications for the interpretation of experimen- tal results from many different experimental techniques (NMR, FT Raman, IR, CD) [8–12]. The planarity of the peptide bond represents one of the major constraints imposed on the possible configurations of the polypeptide chain [13]. By postulating that the peptide substitu- ents should lie in the same plane, and, in particular, that v angle (Fig. 1) could exhibit only perfect cis (0u) or trans (180u) configurations, Pauling & Corey successfully predicted protein secondary structure elements [13]. The peptide bond planarity was traditionally explained by resorting to the resonance model (Fig. 1A), providing the existence of a partial N-C double bond. This simple but powerful picture is the one commonly reported in all biochemistry textbooks, and it is part of the scientific background of most of the researchers in this field. Actually, already four decades ago, several studies showed that in protein and peptide structures significant distortions of the peptide bond from planarity are allowed [14–16]. In more recent years, investigations, carried out by using computational and experimental techniques, have been focused on the entity of peptide bond distortions and on the role that the local context plays in this phenomenon [16–22]. In principle, there are different deformation modes of the peptide bond depending on which atom(s) moves out of the plane [14]. Rotations around the C-N bond, that leads to departures of the v angle from perfect cis (0u) or trans (180u) states, are the most PLoS ONE | www.plosone.org 1 September 2011 | Volume 6 | Issue 9 | e24533