Computational simulation of trimer rotation in hexameric Argine repressor from E.coli

Saurabh Pandey¹, Chris Shuck², Jannette Carey², David Reha¹ and Rudiger Ettrich¹

¹Faculty of Science, University of South Bohemia in České Budějovice and Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Nové Hrady, e-mail: pandey@nh.cas.cz

²Department of Chemistry, Princeton University, Princeton, New Jersey, USA

Argine Repressor ArgR from E.coli is the master feedback regulator of transcription in bacterial L-arginine metabolism. Molecular dynamics simulations reveal that conserved Arg and Asp sidechains in each L-arginine binding pocket promote rotational oscillation of apoArgR trimers by engagement and release of salt bridges.¹ However, this rotation of trimers in earlier simulations using the gmx force field occured on a very short timescale during the equilibration phase of the simulations, which made a proper study of the dynamics of this transition very difficult. In new simulations using the Amber99SB forcefield we succeeded to shift the rotation to the production phase. The whole transition takes now more than 20ns reaching full equilibrium around 50 ns. The degree of rotation corresponds to the 13 degrees described earlier, and all six salt-bridges are formed. This allows to study in detail the molecular changes during the transition, in which Arg110 competes with the solvent for an interaction with Asp128, leading to the consequent rotation. These simulations now help to adress the question how the rotation is propagated throughout the hexameric structure and if all six subunits act in a concerted manner. Additionally, unbinding of L-Arg from ArgR was explored by umbrella sampling and PMF calculations.

Support from the Czech Science Foundation, no 13-21053S, is ackowleged.

1. R. Strawn, M. Melichercik, M. Green, T. Stockner, J. Carey, R. Ettrich, PLOS Computational Biology, 2010, 6: 6. e1000801