Limits...
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.

Show MeSH
The electrostatic potential calculated for the isolated EF-Tu projected on to its van der Waals surface. The tRNA molecule (black ribbon) is also shown to present its binding mode
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3045518&req=5

Fig12: The electrostatic potential calculated for the isolated EF-Tu projected on to its van der Waals surface. The tRNA molecule (black ribbon) is also shown to present its binding mode

Mentions: EF-Tu is a negatively charged protein () and binds a negatively charged aa-tRNA. We calculated the electrostatic potential around the EF-Tu and analysed the regions in the vicinity of domains II and III that bind aa-tRNA. The projection of the electrostatic potential on the EF-Tu surface is presented in Fig. 12. Positive potential patches exist in the areas of binding of the T-arm (see also Fig. 1) and the 5′ and 3′ termini of tRNA. However, there is no global and continuous positive potential area from the side of the tRNA binding. Nevertheless, both non-catalytic domains of EF-Tu are important for tRNA binding because it was found that deletion of either domain II or III weakens the interactions of EF-Tu with tRNA (Cetin et al. 1998).Fig. 12


Molecular dynamics of ribosomal elongation factors G and Tu.

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

The electrostatic potential calculated for the isolated EF-Tu projected on to its van der Waals surface. The tRNA molecule (black ribbon) is also shown to present its binding mode
© Copyright Policy
Related In: Results  -  Collection

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

Fig12: The electrostatic potential calculated for the isolated EF-Tu projected on to its van der Waals surface. The tRNA molecule (black ribbon) is also shown to present its binding mode
Mentions: EF-Tu is a negatively charged protein () and binds a negatively charged aa-tRNA. We calculated the electrostatic potential around the EF-Tu and analysed the regions in the vicinity of domains II and III that bind aa-tRNA. The projection of the electrostatic potential on the EF-Tu surface is presented in Fig. 12. Positive potential patches exist in the areas of binding of the T-arm (see also Fig. 1) and the 5′ and 3′ termini of tRNA. However, there is no global and continuous positive potential area from the side of the tRNA binding. Nevertheless, both non-catalytic domains of EF-Tu are important for tRNA binding because it was found that deletion of either domain II or III weakens the interactions of EF-Tu with tRNA (Cetin et al. 1998).Fig. 12

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