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Molecular dynamics of ribosomal elongation factors G and Tu.

Kulczycka K, Długosz M, Trylska J - Eur. Biophys. J. (2010)

Bottom Line: We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex.EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions.The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.

ABSTRACT
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.

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Graphical representation of extreme projections along first three eigenvectors illustrating collective motion of EF-G (top) and EF-Tu:tRNA (bottom). Arrows show the directions of the first three eigenvectors derived from PCA
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Fig6: Graphical representation of extreme projections along first three eigenvectors illustrating collective motion of EF-G (top) and EF-Tu:tRNA (bottom). Arrows show the directions of the first three eigenvectors derived from PCA

Mentions: To investigate collective motion of EF-G and EF-Tu:tRNA, we performed PCA. As described in the “Methods” section, the covariance matrices corresponding to the and P coordinates were calculated and the eigenproblem was solved. We present the PCA results with the MD trajectory fitted to the first frame using atoms of the I and II domains. These domains are homologous in both systems. The first five eigenvectors span over 90% of the total motion of EF-G and 75% of the total motion of EF-Tu:tRNA. The amplitudes of movements are comparable for both systems except for the motion along the first eigenvector. The first three vectors are presented in Fig. 6. The largest contributions are provided by the collective motions of EF-G domains III, IV, and V and tRNA of the EF-Tu:tRNA complex. For domain positions see Fig. 1.Fig. 6


Molecular dynamics of ribosomal elongation factors G and Tu.

Kulczycka K, Długosz M, Trylska J - Eur. Biophys. J. (2010)

Graphical representation of extreme projections along first three eigenvectors illustrating collective motion of EF-G (top) and EF-Tu:tRNA (bottom). Arrows show the directions of the first three eigenvectors derived from PCA
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045518&req=5

Fig6: Graphical representation of extreme projections along first three eigenvectors illustrating collective motion of EF-G (top) and EF-Tu:tRNA (bottom). Arrows show the directions of the first three eigenvectors derived from PCA
Mentions: To investigate collective motion of EF-G and EF-Tu:tRNA, we performed PCA. As described in the “Methods” section, the covariance matrices corresponding to the and P coordinates were calculated and the eigenproblem was solved. We present the PCA results with the MD trajectory fitted to the first frame using atoms of the I and II domains. These domains are homologous in both systems. The first five eigenvectors span over 90% of the total motion of EF-G and 75% of the total motion of EF-Tu:tRNA. The amplitudes of movements are comparable for both systems except for the motion along the first eigenvector. The first three vectors are presented in Fig. 6. The largest contributions are provided by the collective motions of EF-G domains III, IV, and V and tRNA of the EF-Tu:tRNA complex. For domain positions see Fig. 1.Fig. 6

Bottom Line: We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex.EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions.The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.

ABSTRACT
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.

Show MeSH