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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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Radius of gyration (top) and RMSD (bottom) calculated for the Cα atoms of EF-G (black line) and for the Cα and P atoms of the EF-Tu:tRNA complex (grey line) plotted as a function of the simulation time
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Fig2: Radius of gyration (top) and RMSD (bottom) calculated for the Cα atoms of EF-G (black line) and for the Cα and P atoms of the EF-Tu:tRNA complex (grey line) plotted as a function of the simulation time

Mentions: In MD simulations both EF-G and EF-Tu:tRNA have significant internal mobility. The radius of gyration, which is a measure of the size and the compactness of an object, changes in the explored time scale (Fig. 2, top). The initial radii of gyration corresponding to crystallographic structures are 30.8 and 29.4 Å for EF-G and EF-Tu:tRNA, respectively. For EF-G the radius of gyration decreases during MD simulations and its fluctuations are related to the movements of the domain IV. For EF-Tu:tRNA the radius of gyration increases in comparison with the one calculated for the crystal structure and its changes result from the movement of tRNA.Fig. 2


Molecular dynamics of ribosomal elongation factors G and Tu.

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

Radius of gyration (top) and RMSD (bottom) calculated for the Cα atoms of EF-G (black line) and for the Cα and P atoms of the EF-Tu:tRNA complex (grey line) plotted as a function of the simulation time
© Copyright Policy
Related In: Results  -  Collection

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

Fig2: Radius of gyration (top) and RMSD (bottom) calculated for the Cα atoms of EF-G (black line) and for the Cα and P atoms of the EF-Tu:tRNA complex (grey line) plotted as a function of the simulation time
Mentions: In MD simulations both EF-G and EF-Tu:tRNA have significant internal mobility. The radius of gyration, which is a measure of the size and the compactness of an object, changes in the explored time scale (Fig. 2, top). The initial radii of gyration corresponding to crystallographic structures are 30.8 and 29.4 Å for EF-G and EF-Tu:tRNA, respectively. For EF-G the radius of gyration decreases during MD simulations and its fluctuations are related to the movements of the domain IV. For EF-Tu:tRNA the radius of gyration increases in comparison with the one calculated for the crystal structure and its changes result from the movement of tRNA.Fig. 2

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