Molecular Dynamics Simulations of a Protein-Protein Dimer: Particle-Mesh Ewald Electrostatic Model Yields Far Superior Results to Standard Cutoff Model

Abstract

In this article we present two 1000 ps molecular dynamics simulations on the ratμ-glutathione S-transferase dimeric enzyme in complex with the product 1-(S-glutathionyl)-2,4-dinitrobenzene, in a periodic box with explicit solvent molecules, and investigate the effect of long-range electrostatics models on the structure and dynamics of the dimer and its components. One simulation used the standard cutoff method (10Å), whilst the other used the particle-mesh Ewald (PME) method. We monitored the root mean-square atomic deviation (RMSD) from the initial crystal structure to examine the convergence of both simulations, as well as several other structural parameters such as the distance between active sites, rigid body rotation between domains in subunits, radius of gyration, B-factors, number of hydrogen bonds and salt bridges and solvent-accessible surface area. For example, with the PME method, the dimer structure remains much closer to the initial crystallographic structure with an average RMSD of 1.3Å ± 0.1Å and 1.0Å ± 0.1Å for all heavy and backbone atoms, respectively, in the last 200 ps; the respective values for the cutoff simulation are 4.7Å ± 0.3Å and 4.2Å ± 0.3Å. The large deviations observed in the cutoff simulation severely affected the stability of the enzyme dimer and its complex with the bound product. This finding is contrary to that found in a similar study of the monomelic protein ubiquitin [Fox, T. & Kollman, P. A. Proteins Struct. Fune. Genet. 25, 315–334 (1996)]. Unlike the earlier published work, the present study provides evidence that the standard cutoff method is not generally valid for the study of protein complexes, or their subunits.