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

Caulfield TR, Devkota B, Rollins GC - J Biophys (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Avenue, Atlanta, GA 30332-0230, USA.

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.

No MeSH data available.


RMSD graph for three types of tRNA simulations presented in this study.  This graph represents the root mean square deviation between the simulation of tRNAPhe with that of the crystal structure for tRNAPhe (1EHZ) [33].  As time progresses the initial tRNAPhe  relaxes under the force field and the biased and unbiased states of tRNA progress toward the crystal form.  (a) “Line a” represents the constrained anticodon MD simulation of the A/T state kinked model, which converges to the A-site ensemble after 4 ns.  (b) “Line b” represents the free MD simulation of the A/T state kinked model that converges much quicker to the A-site ensemble of structures (2 ns). (c) “Line c” represents the free molecular dynamics simulation for the A-site crystal structure model, which moves from the starting structure to an average ensemble around 4 Å RMSD from the original as it relaxes under MD.
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fig6: RMSD graph for three types of tRNA simulations presented in this study. This graph represents the root mean square deviation between the simulation of tRNAPhe with that of the crystal structure for tRNAPhe (1EHZ) [33]. As time progresses the initial tRNAPhe relaxes under the force field and the biased and unbiased states of tRNA progress toward the crystal form. (a) “Line a” represents the constrained anticodon MD simulation of the A/T state kinked model, which converges to the A-site ensemble after 4 ns. (b) “Line b” represents the free MD simulation of the A/T state kinked model that converges much quicker to the A-site ensemble of structures (2 ns). (c) “Line c” represents the free molecular dynamics simulation for the A-site crystal structure model, which moves from the starting structure to an average ensemble around 4 Å RMSD from the original as it relaxes under MD.

Mentions: Our results suggest that tRNA deforms quite readily at the anticodon stem from an initial free tRNA state. We found that (1) the kinked A/T structure's trajectory converged toward the crystal structure of tRNAPhe (Figure 6, Supplementary Figure S2), and (2) tRNAPhe (1EHZ) relaxed under unbiased MD to an equilibrated state [13, 33]. This relaxed structure for tRNAPhe sampled regions of conformational space that were similar to those sampled by the kinked A/T structure. The trajectory of the kinked A/T and the trajectory of the native tRNAPhe structure overlapped in conformational space around 1.4 ns, 2.7 ns, and after 5 ns (Supplementary Figure S2). The RMSD matrix plot identifies several well-populated regions of conformational space between the A/T and A/A states (Figure S2). Also, we were able to rapidly drive the crystal structure of tRNAPhe (1EHZ) to form the kinked A/T structure with MdMD (~8 ns) (Supplementary Movie S3, Figure S2). Both force fields were successful in achieving unkinking, but the helical parameters of base pairing were better modeled with the amber force field [36, 37, 39].


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

Caulfield TR, Devkota B, Rollins GC - J Biophys (2011)

RMSD graph for three types of tRNA simulations presented in this study.  This graph represents the root mean square deviation between the simulation of tRNAPhe with that of the crystal structure for tRNAPhe (1EHZ) [33].  As time progresses the initial tRNAPhe  relaxes under the force field and the biased and unbiased states of tRNA progress toward the crystal form.  (a) “Line a” represents the constrained anticodon MD simulation of the A/T state kinked model, which converges to the A-site ensemble after 4 ns.  (b) “Line b” represents the free MD simulation of the A/T state kinked model that converges much quicker to the A-site ensemble of structures (2 ns). (c) “Line c” represents the free molecular dynamics simulation for the A-site crystal structure model, which moves from the starting structure to an average ensemble around 4 Å RMSD from the original as it relaxes under MD.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3116532&req=5

fig6: RMSD graph for three types of tRNA simulations presented in this study. This graph represents the root mean square deviation between the simulation of tRNAPhe with that of the crystal structure for tRNAPhe (1EHZ) [33]. As time progresses the initial tRNAPhe relaxes under the force field and the biased and unbiased states of tRNA progress toward the crystal form. (a) “Line a” represents the constrained anticodon MD simulation of the A/T state kinked model, which converges to the A-site ensemble after 4 ns. (b) “Line b” represents the free MD simulation of the A/T state kinked model that converges much quicker to the A-site ensemble of structures (2 ns). (c) “Line c” represents the free molecular dynamics simulation for the A-site crystal structure model, which moves from the starting structure to an average ensemble around 4 Å RMSD from the original as it relaxes under MD.
Mentions: Our results suggest that tRNA deforms quite readily at the anticodon stem from an initial free tRNA state. We found that (1) the kinked A/T structure's trajectory converged toward the crystal structure of tRNAPhe (Figure 6, Supplementary Figure S2), and (2) tRNAPhe (1EHZ) relaxed under unbiased MD to an equilibrated state [13, 33]. This relaxed structure for tRNAPhe sampled regions of conformational space that were similar to those sampled by the kinked A/T structure. The trajectory of the kinked A/T and the trajectory of the native tRNAPhe structure overlapped in conformational space around 1.4 ns, 2.7 ns, and after 5 ns (Supplementary Figure S2). The RMSD matrix plot identifies several well-populated regions of conformational space between the A/T and A/A states (Figure S2). Also, we were able to rapidly drive the crystal structure of tRNAPhe (1EHZ) to form the kinked A/T structure with MdMD (~8 ns) (Supplementary Movie S3, Figure S2). Both force fields were successful in achieving unkinking, but the helical parameters of base pairing were better modeled with the amber force field [36, 37, 39].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Avenue, Atlanta, GA 30332-0230, USA.

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.

No MeSH data available.