Prediction of Folding Equilibria of Differently Substituted Peptides Using One-Step Perturbation

摘要

Today, the folding equilibrium of short polypeptides can be sampled using molecular dynamics (MD) computer simulation over hundreds of nanoseconds. For example, the folding equilibrium of a hepta-β-peptide with different side-chain substitutions was investigated by such long-time MD simulations, which showed that a slight change of the side-chain substitution did affect the folding equilibrium dramatically. However, a systematic investigation of the influence of the side-chain composition and position at the backbone is computationally as well as experimentally too expensive because of the exponentially growing number of possible side-chain compositions and combinations along the peptide chain.