title: Trajectories of the ribosome as a Brownian nanomachine.
abstract: A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.
authors.affiliation: Department of Physics, University of Wisconsin, Milwaukee, WI 53211;
authors.forename: Ali
authors.initials: A
authors.lastname: Dashti
authors.affiliation: Department of Physics, University of Wisconsin, Milwaukee, WI 53211;
authors.forename: Peter
authors.initials: P
authors.lastname: Schwander
authors.affiliation: Department of Biochemistry and Molecular Biophysics, and.
authors.forename: Robert
authors.initials: R
authors.lastname: Langlois
authors.affiliation: Department of Physics, University of Wisconsin, Milwaukee, WI 53211;
authors.forename: Russell
authors.initials: R
authors.lastname: Fung
authors.affiliation: Department of Biochemistry and Molecular Biophysics, and.
authors.forename: Wen
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Physics, University of Wisconsin, Milwaukee, WI 53211;
authors.forename: Ahmad
authors.initials: A
authors.lastname: Hosseinizadeh
authors.affiliation: Department of Biochemistry and Molecular Biophysics, and.
authors.forename: Hstau Y
authors.initials: HY
authors.lastname: Liao
authors.affiliation: Howard Hughes Medical Institute, Columbia University, New York, NY 10032; and.
authors.forename: Jesper
authors.initials: J
authors.lastname: Pallesen
authors.affiliation: Department of Biochemistry and Molecular Biophysics, and.
authors.forename: Gyanesh
authors.initials: G
authors.lastname: Sharma
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.
authors.forename: Vera A
authors.initials: VA
authors.lastname: Stupina
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Simon
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Dinman
authors.affiliation: Department of Biochemistry and Molecular Biophysics, and Howard Hughes Medical Institute, Columbia University, New York, NY 10032; and jf2192@columbia.edu ourmazd@uwm.edu.
authors.forename: Joachim
authors.initials: J
authors.lastname: Frank
authors.affiliation: Department of Physics, University of Wisconsin, Milwaukee, WI 53211; jf2192@columbia.edu ourmazd@uwm.edu.
authors.forename: Abbas
authors.initials: A
authors.lastname: Ourmazd
mesh_terms: D002021:Buffers; D020285:Cryoelectron Microscopy; D005656:Fungal Proteins / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009038:Motion; D053758:Nanoparticles / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D014176:Protein Biosynthesis; D011487:Protein Conformation; D012270:Ribosomes / Q000737:chemistry / Q000502:physiology*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002021:Buffers; D005656:Fungal Proteins
keywords: cryo-electron microscopy; elongation cycle; manifold embedding; nanomachines; translation