A MOLECULAR-DYNAMICS SIMULATION OF THE C-TERMINAL FRAGMENT OF THE L7/L12 RIBOSOMAL-PROTEIN IN SOLUTION

Herein we present the results of a molecular dynamics simulation of the C-terminal fragment of the L7/L12 ribosomal protein (CTF) in solution for 200 ps. The overall features of the crystal structure were well-reproduced during the simulation, although there were some differences. Namely, the hydrogen bonding pattern changes slightly during the simulation, with surface residues that were previously involved in intra-protein hydrogen bonds opting for interactions with the solvent. The alpha-carbon deviation from the crystal structure was 1.05 angstrom and the all atom deviation was 1.63 angstrom. Although, the conformations generated were near the crystal structure by these measures, at least five different conformational regions were sampled. These conformations do not cluster around the crystal structure, but they remain close to the crystal structure overall and mostly represent local conformational changes. Therefore, it will be interesting to see if these conformations truly reflect the solution structure of CTF, when it becomes available, as opposed to merely revealing artifactual drifts from the crystal structure.