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• W2018267310 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 conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16." @default.
• W2018267310 created "2016-06-24" @default.
• W2018267310 creator A5063872833 @default.
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• W2018267310 date "2011-03-28" @default.
• W2018267310 modified "2023-09-26" @default.
• W2018267310 title "Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data" @default.
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• W2018267310 doi "https://doi.org/10.1155/2011/219515" @default.
• W2018267310 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3116532" @default.
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