Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.

Michael M H Graf,Manuela Maurer,Chris Oostenbrink

doi:10.1002/jcc.24488

Abstract

Previous free‐energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2/ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one‐step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Highlights

This study roots in previous investigations on the oligopeptide binding Protein A (OppA), one of the most abundant periplasmic proteins in gram-negative bacteria such as Escherichia coli and Salmonella typhimurium.[1]
As described in the introduction, residue mutations of the tripeptide KXK ! KGK were already investigated in previous studies employing either thermodynamic integration (TI) or a combination of k-dynamics and local-elevation umbrella-sampling (k-LEUS).[11,12]
The sampling problem was tackled with the k-LEUS approach,[12] in which the coupling parameter k is treated as a dynamic variable, which is subsequently biased to cycle repeatedly between states A and B, with a prolonged residence time at the end-states

Summary

Introduction

This study roots in previous investigations on the oligopeptide binding Protein A (OppA), one of the most abundant periplasmic proteins in gram-negative bacteria such as Escherichia coli and Salmonella typhimurium.[1] OppA binds nutrients (i.e., peptide fragments) in the periplasm and shuttles them to a transmembrane transporter, thereby playing a key role in nutrient transport.[2] The accepted peptide fragments can have two to five residues with no preference for their composition, which confers OppA a broad substrate promiscuity.[3,4,5] because of the negative charge at its binding site, OppA has a preference toward positively charged substrates, lysine containing tripeptides.[6] Experimental studies revealed that the substrate promiscuity is especially pronounced for the central amino acid of KXK tripeptides, where X may represent 20 natural and 8 non-natural amino acids.[7,8,9] The 28 tripeptides bind with a wide range of binding affinities, which could, not straightforwardly be correlated to the nature (polar, apolar, aromatic, or charged) of the central residue.[10]

Methods

Results

Conclusion