Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?

Abstract

The conformational preference for different ϕ/Ψ backbone torsion angles is a key determinant of peptide and protein secondary structure. Often, dipeptides are used as models for understanding protein backbone dynamics and to derive force field parameters. Here, the question is examined to what extent the conformational preferences in dipeptides reflect the backbone dynamics in polypeptides and proteins and to what extent an alanine dipeptide-based backbone torsion parametrization can lead to accurate reproduction of amino acid dependent ϕ/Ψ preferences in protein structures. Results from a comparison of the analysis of Protein Data Bank (PDB) structures with long simulations of selected proteins and amino acid dipeptides suggest that a common alanine dipeptide-based torsion potential does in fact lead to excellent agreement between protein simulations and PDB structures. At the same time, the ϕ/Ψ preferences in the dipeptides are significantly different, suggesting that dipeptides are not good model systems for studying protein backbone dynamics.