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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 electrostatic potential of EF-G (left) and the EF-Tu:tRNA complex (right) projected on to their van der Waals surfaces (partially transparent). Interior black detail shows the secondary structure of EF-G and EF-Tu:tRNA
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Fig10: The electrostatic potential of EF-G (left) and the EF-Tu:tRNA complex (right) projected on to their van der Waals surfaces (partially transparent). Interior black detail shows the secondary structure of EF-G and EF-Tu:tRNA

Mentions: Here, to compare the electrostatic surfaces of the two elongation factors, we calculated the electrostatic potential of EF-G and EF-Tu:tRNA and projected it on to their surfaces (Fig. 10). Figure 11 magnifies the electrostatic potential of the GTP/GDP binding region in both factors. The qualitative comparison suggests there is no global electrostatic similarity between the systems. The total charge of EF-G is and that of EF-Tu:tRNA is . Hence, the factors differ in the net charge by . Also, EF-G has one more extension (G′), which is not present in EF-Tu:tRNA. However, we note that under physiological conditions tRNA is partially neutralized by divalent and monovalent structural counter-ions that we are not able to explicitly include within the framework of the Poisson–Boltzmann model (Grochowski and Trylska 2008).Fig. 10


Molecular dynamics of ribosomal elongation factors G and Tu.

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

The electrostatic potential of EF-G (left) and the EF-Tu:tRNA complex (right) projected on to their van der Waals surfaces (partially transparent). Interior black detail shows the secondary structure of EF-G and EF-Tu:tRNA
© Copyright Policy
Related In: Results  -  Collection

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

Fig10: The electrostatic potential of EF-G (left) and the EF-Tu:tRNA complex (right) projected on to their van der Waals surfaces (partially transparent). Interior black detail shows the secondary structure of EF-G and EF-Tu:tRNA
Mentions: Here, to compare the electrostatic surfaces of the two elongation factors, we calculated the electrostatic potential of EF-G and EF-Tu:tRNA and projected it on to their surfaces (Fig. 10). Figure 11 magnifies the electrostatic potential of the GTP/GDP binding region in both factors. The qualitative comparison suggests there is no global electrostatic similarity between the systems. The total charge of EF-G is and that of EF-Tu:tRNA is . Hence, the factors differ in the net charge by . Also, EF-G has one more extension (G′), which is not present in EF-Tu:tRNA. However, we note that under physiological conditions tRNA is partially neutralized by divalent and monovalent structural counter-ions that we are not able to explicitly include within the framework of the Poisson–Boltzmann model (Grochowski and Trylska 2008).Fig. 10

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