Energetics of β-turn formation in a mutant peptide YPGDV from influenza hemagglutinin: an MD simulation study

Abstract

Reverse turns play an important role in protein folding, molecular recognition and in eliciting immune response. While sequence determinants of reverse turns are known, not much is known about their energetics. In this paper we have investigated the thermodynamics of a reverse turn sequence YPGDV, an experimentally well characterized turn sequence, using molecular dynamics simulations performed over a range of temperatures from 280-360 K using GROMACS 4.0.4 software and all atom OPLS-AA/L force field. The change in folding free energy (ΔAfolding) for the β-turn formation in YPGDV peptide shows a linear relationship with temperature. We find that the entropy change (ΔSfolding) for the β-turn formation is close to zero and the internal energy change (ΔUfolding) is a modest -3.8 kJ mol(-1). These thermodynamic quantities are interpreted in terms of intra-molecular (intra-peptide) and inter-molecular (peptide-solvent) hydrogen bonding interactions. Implications for protein folding and peptide immunogenicity are discussed.

Fluorescence and Piezoresistive Cantilever Sensing of Trinitrotoluene by an Upper-Rim Tetrabenzimidazole Conjugate of Calix[4]arene and Delineation of the Features of the Complex by Molecular Dynamics

“…At the time of carrying out the computations, R and the guest species were coupled separately to a V-rescale temperature bath. The V-rescale bath is stable enough to control fluctuations in the kinetic energy of R and the guest species separately. − The electrostatic interactions were calculated by using the particle-mesh Ewald summation method . All of the bond lengths of R and the guest species were constrained using the LINCS algorithm .…”