Effective interactions in molecular dynamics simulations of lysozyme solutions

Giuseppe Pellicane, Lev Sarkisov

Research output: Contribution to journalArticlepeer-review

Abstract

In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces.

Original languageEnglish
Article number191
JournalThe European Physical Journal B
Volume87
Issue number9
DOIs
Publication statusPublished - 1 Jan 2014

Keywords

  • Statistical and Nonlinear Physics

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