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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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The root mean square fluctuation of Cα and P atoms of a EF-G:GDP, EF-G, and b EF-Tu:tRNA, EF-Tu:GDP, EF-Tu
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Fig8: The root mean square fluctuation of Cα and P atoms of a EF-G:GDP, EF-G, and b EF-Tu:tRNA, EF-Tu:GDP, EF-Tu

Mentions: Figure 8 shows the RMSF of and P atoms computed for the studied systems. The difference in the RMSF of the free EF-G and in the complex with GDP and (presented in Fig. 8a) is not substantial. This result corroborates experimental data (Liljas 2004; Hansson et al. 2005) which show that upon GDP or GTP analogue binding, EF-G does not significantly alter its configuration.Fig. 8


Molecular dynamics of ribosomal elongation factors G and Tu.

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

The root mean square fluctuation of Cα and P atoms of a EF-G:GDP, EF-G, and b EF-Tu:tRNA, EF-Tu:GDP, EF-Tu
© Copyright Policy
Related In: Results  -  Collection

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

Fig8: The root mean square fluctuation of Cα and P atoms of a EF-G:GDP, EF-G, and b EF-Tu:tRNA, EF-Tu:GDP, EF-Tu
Mentions: Figure 8 shows the RMSF of and P atoms computed for the studied systems. The difference in the RMSF of the free EF-G and in the complex with GDP and (presented in Fig. 8a) is not substantial. This result corroborates experimental data (Liljas 2004; Hansson et al. 2005) which show that upon GDP or GTP analogue binding, EF-G does not significantly alter its configuration.Fig. 8

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
Related in: MedlinePlus