Role of side-chain interactions on the formation of α -helices in model peptides

Document Type

Article

Publication Date

3-25-2015

Abstract

The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.

Identifier

84926058203 (Scopus)

Publication Title

Physical Review E Statistical Nonlinear and Soft Matter Physics

External Full Text Location

https://doi.org/10.1103/PhysRevE.91.032710

e-ISSN

15502376

ISSN

15393755

PubMed ID

25871147

Issue

3

Volume

91

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