Project RNAP - Ribonucleic acid polymerases
RNA polymerases (RNAPs) are complex molecular machines that contain a highly conserved catalytic site surrounded by flexible domains. The enzyme is responsible for translating the information written down in DNA into an RNA bluecopy. This represents one of the key and tightly regulated steps in gene expression. The core structural elements as well as the overall pincer-like shape are the same in all RNA polymerases.
The aim of the presented research was to model RNAP structure using standard molecular dynamics (MD) methods.
A complex workflow in the NGS P-GRADE portal was created, as it is illustrated on the figure below.
The mdrun simulation engine was applied from the GROMACS suit with a forcefield generated by Amber 10.0. The Amber forcefields seem to be more thoroughly tested especially with respect to DNA and small molecules. Gromacs on the other hand is much faster and easy to implement on parallel platforms. Simulations were carried out over 100 ns in explicit solvent using 8-16 CPU cores for each run. The NGS P-GRADE portal was utilised as user interface to submit jobs to various NGS sites.
Preliminary results show some surprising behaviour of the bridge helix with respect to the secondary structure leading to a new understanding of the interaction between strictly conserved residues on that structure.
The catalytic center of RNAP (PDB #2O5I). The bridge-helix (cartoon structure in teal) is located near the catalytic site. The template DNA strand (light blue) and nascent transcript (red) are shown as space-filling structures. In this diagram the template DNA strand enters the catalytic site from the right hand side and the DNA-RNA hybrid exits towards the left.
File:Rnapresults2.gif Sequential snapshots of a fully atomistic molecular dynamics simulation of a BH-HC kinking event.
Left Panel: structure near the beginning of the simulation. The side chains of the residues shown in space-filling mode extend horizontally from the essentially straight a-helical axis. Central Panel: structure after ~90 picoseconds simulation. The side chains induce a minor bend in the a-helical axis. Right Panel: Formation of extensive cation-p interactions involving after 130 picoseconds of simulation.
Heindl, H., Greenwell, P., Weingarten, N., Kiss, T., Terstyanszky, G., and Weinzierl, R.O.J. (2011). Cation-p interactions induce kinking of a molecular hinge in the RNA polymerase bridge helix domain. Biochem. Soc. Trans.; in press.