Molecular dynamics derived side chain order parameters for Asp, Glu, Asn, and Gln residues in ribonucleases H, and molecular dynamics trajectories for E. coli ribonuclease H

This dataset contains tab-delimited text files reporting the complete calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues (Asp, Glu, Asn, Gln) in all RNase H homologs studied, as well as complete simulation trajectory data for the E. coli apo, site A, and site B simulations described in the text. We hope that easy access to the complete trajectory data for the experimentally best-characterized homolog will facilitate future comparison between simulation and experiments.

order_parameters_magnesium.dat contains the calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues in each of the three E. coli trajectories supplied in this dataset. These data are sufficient to reproduce Figure 6.

2RN2.apo.pdb, 2RN2.MG.siteA.pdb, and 2RN2.MG.siteB.pdb define the equilibrated structure from which the E. coli apo, site A, and site B trajectories were initiated. All protein atoms, including hydrogens, are included, as well as Mg ions. Explicit waters and chloride counterions have been removed.

2RN2.apo.dcd, 2RN2.MG.siteA.dcd, and 2RN2.MG.siteB.dcd contain 100ns trajectories initiated from the starting structures in the corresponding pdb files. Frames were written every 4.5ps. Trajectories have been aligned to the initial structure of the apo trajectory to facilitate visualization.

The remaining *.S2.CO.dat files contain the calculated S2 side chain order parameters for all apo RNases H simulated in this study. Each file is named for the PDB ID of its corresponding structure (see Table 1). These data are sufficient to reproduce Figure 8 (which reports on only the conserved active-site residues).