Molecular dynamics of ribosomal elongation factors G and Tu |
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Authors: | Katarzyna Kulczycka Maciej D?ugosz Joanna Trylska |
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Institution: | (1) Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland;(2) College of Inter-Faculty Individual Studies in Mathematics and Natural Science, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland; |
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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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