title: Quantitative Characterization of Domain Motions in Molecular Machines.
abstract: The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York 10027, United States.
authors.forename: Suvrajit
authors.initials: S
authors.lastname: Maji
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.|Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.|Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.
authors.forename: Rezvan
authors.initials: R
authors.lastname: Shahoei
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.|Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.|Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York 10027, United States.|Howard Hughes Medical Institute, Columbia University , New York, New York 10027, United States.|Department of Biological Sciences, Columbia University , New York, New York 10027, United States.
authors.forename: Joachim
authors.identifier: 0000-0001-5449-6943
authors.initials: J
authors.lastname: Frank
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D000072417:Protein Domains; D012270:Ribosomes / Q000737:chemistry*