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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‚ÄČns 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.


Related in: MedlinePlus

tRNA Conformations.  Both kinked structures for tRNAPhe (PDB code: 1EHZ) and the hybrid state for cryo-EM densities of tRNA are shown.  The different orientations of tRNA depict the unique differences caused from kinking or twisting (A/T and P/E states, resp.).  The arrows depict the transition from A/T state to A-site (A/A state) to P-site and P/E hybrid state. (a) Secondary structure for Phe-tRNAPhe (1EHZ) [33].  (b) Structure of kinked A/T-tRNA, as it enters the ribosome (pre-accommodation) [13]. (c) A-site tRNA after accommodation occurs (post accommodation). (d) Hybrid P/E-tRNA following peptidyl transfer. (e) Comparison of A-site tRNA and kinked A/T-tRNA from modeling with cryo-EM density. (f) Position of tRNA in A-site indicated in cryo-EM density.  (g) Conformation sampled from MD demonstrating an experimentally unidentified twisted conformation for tRNAPhe.
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fig1: tRNA Conformations. Both kinked structures for tRNAPhe (PDB code: 1EHZ) and the hybrid state for cryo-EM densities of tRNA are shown. The different orientations of tRNA depict the unique differences caused from kinking or twisting (A/T and P/E states, resp.). The arrows depict the transition from A/T state to A-site (A/A state) to P-site and P/E hybrid state. (a) Secondary structure for Phe-tRNAPhe (1EHZ) [33]. (b) Structure of kinked A/T-tRNA, as it enters the ribosome (pre-accommodation) [13]. (c) A-site tRNA after accommodation occurs (post accommodation). (d) Hybrid P/E-tRNA following peptidyl transfer. (e) Comparison of A-site tRNA and kinked A/T-tRNA from modeling with cryo-EM density. (f) Position of tRNA in A-site indicated in cryo-EM density. (g) Conformation sampled from MD demonstrating an experimentally unidentified twisted conformation for tRNAPhe.

Mentions: With the first high-resolution crystal structure for tRNA [1, 2], it was suggested that the molecule may possess a flexible hinge between the D-stem and the anticodon stem (Figure 1). Figure S6 (see Figure in Supplementary Material available online at doi: 10.1155/2011/219515) shows a diagrammed version of tRNA for illustration. The interarm consists of the hinge formed between the acceptor stem and the anticodon stem (Supplementary Figure S6). Figure 1(a) schematic shows a two-dimensional layout for the RNA nucleotides that account for the acceptor stem, anticodon stem, D-stem, and T-stem. Early light scattering experiments were interpreted in terms of bending motions between the two arms of the L-shaped tRNA that were thought to facilitate functional flexibility [3]. tRNA binds to aminoacyl tRNA synthetases, elongation factors, as well as different sites on the ribosome.


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)

tRNA Conformations.  Both kinked structures for tRNAPhe (PDB code: 1EHZ) and the hybrid state for cryo-EM densities of tRNA are shown.  The different orientations of tRNA depict the unique differences caused from kinking or twisting (A/T and P/E states, resp.).  The arrows depict the transition from A/T state to A-site (A/A state) to P-site and P/E hybrid state. (a) Secondary structure for Phe-tRNAPhe (1EHZ) [33].  (b) Structure of kinked A/T-tRNA, as it enters the ribosome (pre-accommodation) [13]. (c) A-site tRNA after accommodation occurs (post accommodation). (d) Hybrid P/E-tRNA following peptidyl transfer. (e) Comparison of A-site tRNA and kinked A/T-tRNA from modeling with cryo-EM density. (f) Position of tRNA in A-site indicated in cryo-EM density.  (g) Conformation sampled from MD demonstrating an experimentally unidentified twisted conformation for tRNAPhe.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3116532&req=5

fig1: tRNA Conformations. Both kinked structures for tRNAPhe (PDB code: 1EHZ) and the hybrid state for cryo-EM densities of tRNA are shown. The different orientations of tRNA depict the unique differences caused from kinking or twisting (A/T and P/E states, resp.). The arrows depict the transition from A/T state to A-site (A/A state) to P-site and P/E hybrid state. (a) Secondary structure for Phe-tRNAPhe (1EHZ) [33]. (b) Structure of kinked A/T-tRNA, as it enters the ribosome (pre-accommodation) [13]. (c) A-site tRNA after accommodation occurs (post accommodation). (d) Hybrid P/E-tRNA following peptidyl transfer. (e) Comparison of A-site tRNA and kinked A/T-tRNA from modeling with cryo-EM density. (f) Position of tRNA in A-site indicated in cryo-EM density. (g) Conformation sampled from MD demonstrating an experimentally unidentified twisted conformation for tRNAPhe.
Mentions: With the first high-resolution crystal structure for tRNA [1, 2], it was suggested that the molecule may possess a flexible hinge between the D-stem and the anticodon stem (Figure 1). Figure S6 (see Figure in Supplementary Material available online at doi: 10.1155/2011/219515) shows a diagrammed version of tRNA for illustration. The interarm consists of the hinge formed between the acceptor stem and the anticodon stem (Supplementary Figure S6). Figure 1(a) schematic shows a two-dimensional layout for the RNA nucleotides that account for the acceptor stem, anticodon stem, D-stem, and T-stem. Early light scattering experiments were interpreted in terms of bending motions between the two arms of the L-shaped tRNA that were thought to facilitate functional flexibility [3]. tRNA binds to aminoacyl tRNA synthetases, elongation factors, as well as different sites on the ribosome.

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‚ÄČns 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.


Related in: MedlinePlus