Folding Very Short Peptides Using Molecular Dynamics

Abstract

Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water) implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides), the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the β hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

Synopsis

To carry out specific biochemical reactions, proteins must adopt precise three-dimensional conformations. During the folding of a protein, the protein picks out the right conformation out of billions of other conformations. It is not yet possible to do this computationally. Picking out the native conformation using physics-based atomically detailed models, sampled by molecular dynamics, is presently beyond the reach of computer methods. How can we speed up computational protein-structure prediction? One idea is that proteins start folding at specific parts of a chain that kink up early in the folding process. If we can identify these kinks, we should be able to speed up protein-structure prediction. Previous studies have identified likely kinks through bioinformatic analysis of existing protein structures. The goal of the authors here is to identify these putative folding initiation sites with a physical model instead. In this study, Ho and Dill show that, by chopping a protein chain into peptide pieces, then simulating the pieces in molecular dynamics, they can identify those peptide fragments that have conformational biases. These peptides identify the kinks in the protein chain.