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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 distances between the centres of masses of the CCA-end phenylalanine and histidine 67 rings observed in the crystal structure (blue) and in MD simulation (orange) of EF-Tu:tRNA
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Fig9: The distances between the centres of masses of the CCA-end phenylalanine and histidine 67 rings observed in the crystal structure (blue) and in MD simulation (orange) of EF-Tu:tRNA

Mentions: For EF-Tu:tRNA we observe that the CCA-end phenylalanine ring changes its position from that observed in the crystal structure. It moves from a position between the CCA-terminus and one of the strands of the β-sheet of domain II to the inside of the protein (Fig. 9). The distances between the centres of masses of the six-membered ring of phenylalanine and the five-membered ring of His 67 in the crystal structure and in the last MD trajectory frame were 5.1 and 11.6 Å, respectively. The movement of the amino acid and the CCA-terminal tRNA single strand has been noticed before (Frank et al. 2005). The CCA-attached amino acid brought by tRNA must be flexible to be appropriately positioned in the peptidyl transferase centre for peptide bond synthesis (Frank et al. 2005). Also, we found that the tip of the EF-Tu switch I moves toward the tRNA acceptor stem.Fig. 9


Molecular dynamics of ribosomal elongation factors G and Tu.

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

The distances between the centres of masses of the CCA-end phenylalanine and histidine 67 rings observed in the crystal structure (blue) and in MD simulation (orange) of EF-Tu:tRNA
© Copyright Policy
Related In: Results  -  Collection

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

Fig9: The distances between the centres of masses of the CCA-end phenylalanine and histidine 67 rings observed in the crystal structure (blue) and in MD simulation (orange) of EF-Tu:tRNA
Mentions: For EF-Tu:tRNA we observe that the CCA-end phenylalanine ring changes its position from that observed in the crystal structure. It moves from a position between the CCA-terminus and one of the strands of the β-sheet of domain II to the inside of the protein (Fig. 9). The distances between the centres of masses of the six-membered ring of phenylalanine and the five-membered ring of His 67 in the crystal structure and in the last MD trajectory frame were 5.1 and 11.6 Å, respectively. The movement of the amino acid and the CCA-terminal tRNA single strand has been noticed before (Frank et al. 2005). The CCA-attached amino acid brought by tRNA must be flexible to be appropriately positioned in the peptidyl transferase centre for peptide bond synthesis (Frank et al. 2005). Also, we found that the tip of the EF-Tu switch I moves toward the tRNA acceptor stem.Fig. 9

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