title: Molecular dynamics of ribosomal elongation factors G and Tu.
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.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Kulczycka
authors.forename: Maciej
authors.initials: M
authors.lastname: Długosz
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D001665:Binding Sites; D006153:Guanosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009038:Motion; D020653:Peptide Elongation Factor G / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism; D010444:Peptide Elongation Factor Tu / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D014176:Protein Biosynthesis / Q000502:physiology; D011487:Protein Conformation; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism; D013824:Thermus / Q000201:enzymology / Q000378:metabolism
chemical_list: D020653:Peptide Elongation Factor G; D012346:RNA, Transfer, Amino Acyl; D006153:Guanosine Diphosphate; D006160:Guanosine Triphosphate; D010444:Peptide Elongation Factor Tu