Molecular Simulation with Elastic Network Model Potential in Gromacs

V. Spiwok^1,2, I. Tvaroška², B. Králová¹

¹Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 3, Prague 6, 166 28, Czech Republic

²Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, 845 38, Slovakia

spiwokv@vscht.cz

Elastic network model and its follow-ups (Gaussian and anisotropic network models), despite their simplicity, have been successfully applied in prediction of flexibility and coupled motions in proteins. Here we present an application of molecular dynamics simulation in Gromacs package with potential energy calculated by the elastic network model. It allows for microsecond simulations per day on a single commodity personal computer. The method was applied on the structure of ubiquitin and the resulting trajectory was analyzed in terms of residue flexibility and coupled molecular motions. The results were compared with atomistic molecular dynamics simulation in explicit solvent and with published experimental data. We show that simulation of elastic network models of proteins is useful in modelling of biomolecular systems where mechanical properties become more important than atomistic details.

This work was supported by the Czech Ministry of Education, Youth and Sports (MSM6046137305), Scientific Grant Agency of the Ministry of Education of Slovak Republic and the Slovak Academy of Sciences (VEGA 2/0176/09) and Slovak Research and Development Agency (APVV-51-011706).