title: MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.
abstract: Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.
authors.affiliation: Cell and Molecular Biology Department, Uppsala University, Box 596, Uppsala 751 24, Sweden.
authors.forename: Alex
authors.initials: A
authors.lastname: Tek
authors.affiliation: RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA.
authors.forename: Andrei A
authors.initials: AA
authors.lastname: Korostelev
authors.affiliation: Cell and Molecular Biology Department, Uppsala University, Box 596, Uppsala 751 24, Sweden sam@xray.bmc.uu.se.
authors.forename: Samuel Coulbourn
authors.initials: SC
authors.lastname: Flores
mesh_terms: D008958:Models, Molecular; D008968:Molecular Conformation; D020653:Peptide Elongation Factor G / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics*; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D020653:Peptide Elongation Factor G; D012343:RNA, Transfer