Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data
Joint Authors
Rollins, Geoffrey C.
Devkota, Batsal
Caulfield, Thomas R.
Source
Issue
Vol. 2011, Issue 2011 (31 Dec. 2011), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2011-03-28
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Caulfield, Thomas R.& Devkota, Batsal& Rollins, Geoffrey C.. 2011. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data. Journal of Biophysics،Vol. 2011, no. 2011, pp.1-11.
https://search.emarefa.net/detail/BIM-455613
Modern Language Association (MLA)
Caulfield, Thomas R.…[et al.]. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data. Journal of Biophysics No. 2011 (2011), pp.1-11.
https://search.emarefa.net/detail/BIM-455613
American Medical Association (AMA)
Caulfield, Thomas R.& Devkota, Batsal& Rollins, Geoffrey C.. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data. Journal of Biophysics. 2011. Vol. 2011, no. 2011, pp.1-11.
https://search.emarefa.net/detail/BIM-455613
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-455613