On the van der Waals interactions and the stability of polypeptide chains in helical conformations

Abstract

In this work, we aim to investigate the contribution of van der Waals (vdW) interactions to the stability of polypeptides in helical conformations studying infinitely long chains of alanine and glycine with density functional theory. To account for vdW interactions, we have used the interatomic pairwise dispersion approach proposed by Tkatchenko–Scheffler (TS), the TS approach with self-consistent screening (SCS) that self-consistently includes long-range electrostatic effects (TS + SCS), the D2 and D3 methods of Grimme et al., and the Langreth–Lundqvist procedure that treats nonlocally the correlation part of the approximation to the exchange-correlation (xc) functional (called DF). First, we have tested the performance of these strategies studying a set of representative hydrogen bonded dimers. Next, we have studied polyalanine and polyglicine in π-helix, α-helix, -helix, 27, and polyproline-II conformations and in a fully extended structure. We have found that the DF methodology in combination with a modified version for the Becke approximation to the exchange (optB86b), the D2, D3, TS, and TS + SCS strategies in combination with the Perdew–Burke–Ernzerhof approximation to the xc functional, describe fairly well dimer association energies. Furthermore, the DF method and the D2, D3, TS, and TS + SCS strategies predict very similar helical stabilities even though the approximation used in DF for describing the long-range dispersion interactions is different that the one used in D2/D3 and TS/TS + SCS. We found that the stability doubles for π and α helices if vdW interactions are taken into account. © 2015 Wiley Periodicals, Inc.