title: Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
abstract: Molecular modeling and information processing techniques were combined to refine the structure of translocase (EF-G) in the ribosome-bound form against data from cryoelectron microscopy (cryo-EM). We devised a novel multi-scale refinement method based on vector quantization and force-field methods that gives excellent agreement between the flexibly docked structure of GDP. EF-G and the cryo-EM density map at 17 A resolution. The refinement reveals a dramatic "induced fit" conformational change on the 70S ribosome, mainly involving EF-G's domains III, IV, and V. The rearrangement of EF-G's structurally preserved regions, mediated and guided by flexible linkers, defines the site of interaction with the GTPase-associated center of the ribosome.
authors.affiliation: Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, USA. wriggers@scripps.edu
authors.forename: W
authors.initials: W
authors.lastname: Wriggers
authors.forename: R K
authors.initials: RK
authors.lastname: Agrawal
authors.forename: D L
authors.initials: DL
authors.lastname: Drew
authors.forename: A
authors.initials: A
authors.lastname: McCammon
authors.forename: J
authors.initials: J
authors.lastname: Frank
mesh_terms: D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D020558:GTP Phosphohydrolases / Q000378:metabolism; D006153:Guanosine Diphosphate / Q000378:metabolism; D008958:Models, Molecular; D020653:Peptide Elongation Factor G / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012270:Ribosomes / Q000378:metabolism* / Q000648:ultrastructure*; D012984:Software
chemical_list: D020653:Peptide Elongation Factor G; D006153:Guanosine Diphosphate; D020558:GTP Phosphohydrolases