Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

ABSTRACT: We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformatio

SUBMITTER: Caulfield TR 

PROVIDER: S-EPMC3116532 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature