title: Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.
abstract: Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Singharoy
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.|Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.
authors.forename: Ivan
authors.initials: I
authors.lastname: Teo
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors.forename: Ryan
authors.initials: R
authors.lastname: McGreevy
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.affiliation: Department of Biochemistry and Biophysics, University of California San Francisco School of Medicine, San Francisco, United States.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.|Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.
authors.forename: Klaus
authors.identifier: 0000-0001-7192-9632
authors.initials: K
authors.lastname: Schulten
mesh_terms: D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D056004:Molecular Dynamics Simulation; D050916:TRPV Cation Channels / Q000737:chemistry / Q000648:ultrastructure; D001616:beta-Galactosidase / Q000737:chemistry / Q000648:ultrastructure
chemical_list: D050916:TRPV Cation Channels; C493922:Trpv1 protein, rat; D001616:beta-Galactosidase
keywords: B-factors; biophysics; cloud computing; computational biology; cryoelectron microscopy; flexible fitting; high-resolution; hybrid methods; none; structural biology; systems biology