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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.


tRNA Catalog.  (a) Six crystal structures of unbound Phe-tRNAPhe.  The ribbon in the middle is from 1EHZ.   (b) Crystal structures (41) of tRNA free and in complexes, including synthetases and ribosomal (Table S1) aligned at the acceptor stems and the anticodon stems.  The ribbon in the middle is from 1EHZ.  (c) Phe-tRNAPhe crystal structures (6) aligned at the acceptor stem (shown in divergent stereo), thus illustrating the range of motion at the anticodon stem loops, and notice the closely aligned acceptor stem regions.
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fig2: tRNA Catalog. (a) Six crystal structures of unbound Phe-tRNAPhe. The ribbon in the middle is from 1EHZ. (b) Crystal structures (41) of tRNA free and in complexes, including synthetases and ribosomal (Table S1) aligned at the acceptor stems and the anticodon stems. The ribbon in the middle is from 1EHZ. (c) Phe-tRNAPhe crystal structures (6) aligned at the acceptor stem (shown in divergent stereo), thus illustrating the range of motion at the anticodon stem loops, and notice the closely aligned acceptor stem regions.

Mentions: We compiled a set of tRNA crystal structures from structural databases to quantify any tRNA flexibility from experimental data. The Nucleic Acid Database and the Protein Data Bank RCSB [50, 51] contain over 80 structures of tRNAs alone or in complexes with other molecules at a resolution of 3.3 Å or better. For the study presented we focused on a subset that were in good alignment with tRNAPhe. Thus, thirty-four of the crystal structures are tRNA-protein complexes. The remaining six are free, unbound tRNA structures. Most of the complexes are aminoacyl-tRNA synthetases (32 structures), but there is also one cocrystal of tRNAGlu with its amidotransferase, and another between tRNAfMet and its formyltransferase (Figure 2(b)). Of the isolated tRNA structures, six are unique and of the highest available resolution, while four are distinct: Asp from E. coli and S. cerevisae, Lys from B. taurus, Phe from S. cerevisae and T. thermophilus, and fMet from E. coli and S. cerevisae (Figure 2(b)) [3]. tRNAs for fMet and 16 other amino acids are represented (Figures 2(a) and 2(b)). Supplementary Table S1 summarizes the crystal structures that we examined. Figure 2 demonstrates the conformational variability among the full set of structures, and Figure 2(c) shows the variability in just phenylalanine-tRNAPhe.


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 Catalog.  (a) Six crystal structures of unbound Phe-tRNAPhe.  The ribbon in the middle is from 1EHZ.   (b) Crystal structures (41) of tRNA free and in complexes, including synthetases and ribosomal (Table S1) aligned at the acceptor stems and the anticodon stems.  The ribbon in the middle is from 1EHZ.  (c) Phe-tRNAPhe crystal structures (6) aligned at the acceptor stem (shown in divergent stereo), thus illustrating the range of motion at the anticodon stem loops, and notice the closely aligned acceptor stem regions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig2: tRNA Catalog. (a) Six crystal structures of unbound Phe-tRNAPhe. The ribbon in the middle is from 1EHZ. (b) Crystal structures (41) of tRNA free and in complexes, including synthetases and ribosomal (Table S1) aligned at the acceptor stems and the anticodon stems. The ribbon in the middle is from 1EHZ. (c) Phe-tRNAPhe crystal structures (6) aligned at the acceptor stem (shown in divergent stereo), thus illustrating the range of motion at the anticodon stem loops, and notice the closely aligned acceptor stem regions.
Mentions: We compiled a set of tRNA crystal structures from structural databases to quantify any tRNA flexibility from experimental data. The Nucleic Acid Database and the Protein Data Bank RCSB [50, 51] contain over 80 structures of tRNAs alone or in complexes with other molecules at a resolution of 3.3 Å or better. For the study presented we focused on a subset that were in good alignment with tRNAPhe. Thus, thirty-four of the crystal structures are tRNA-protein complexes. The remaining six are free, unbound tRNA structures. Most of the complexes are aminoacyl-tRNA synthetases (32 structures), but there is also one cocrystal of tRNAGlu with its amidotransferase, and another between tRNAfMet and its formyltransferase (Figure 2(b)). Of the isolated tRNA structures, six are unique and of the highest available resolution, while four are distinct: Asp from E. coli and S. cerevisae, Lys from B. taurus, Phe from S. cerevisae and T. thermophilus, and fMet from E. coli and S. cerevisae (Figure 2(b)) [3]. tRNAs for fMet and 16 other amino acids are represented (Figures 2(a) and 2(b)). Supplementary Table S1 summarizes the crystal structures that we examined. Figure 2 demonstrates the conformational variability among the full set of structures, and Figure 2(c) shows the variability in just phenylalanine-tRNAPhe.

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.