5 years ago

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective
Peter I. Maxwell, Paul L. A. Popelier
Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (Oi–1, Ci, Ni, Ni+1) and some sidechain hydrogen atoms (Hγ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the Oi–1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. We use a minimal, rigorous and parameter-free energy partitioning to obtain chemical insight into the origin of φ and ψ torsional barriers in three amino acids. We obtain four primary and unbiased energy contributions called intra-atomic (self) energy, electrostatic energy, exchange(-correlation) energy, and the sum of all three, EIQA, which we analyze at three levels: molecular, functional group, and atomic. The peptide groups are the cause of the barriers at φ = −15° and ψ = −120°, with the barriers at φ = +165° and ψ = +15° resulting from both peptides and sidechain groups becoming destabilized, cooperatively.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24904

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