title: Automated real-space refinement of protein structures using a realistic backbone move set.
abstract: Crystals of many important biological macromolecules diffract to limited resolution, rendering accurate model building and refinement difficult and time-consuming. We present a torsional optimization protocol that is applicable to many such situations and combines Protein Data Bank-based torsional optimization with real-space refinement against the electron density derived from crystallography or cryo-electron microscopy. Our method converts moderate- to low-resolution structures at initial (e.g., backbone trace only) or late stages of refinement to structures with increased numbers of hydrogen bonds, improved crystallographic R-factors, and superior backbone geometry. This automated method is applicable to DNA-binding and membrane proteins of any size and will aid studies of structural biology by improving model quality and saving considerable effort. The method can be extended to improve NMR and other structures. Our backbone score and its sequence profile provide an additional standard tool for evaluating structural quality.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors.forename: Esmael J
authors.initials: EJ
authors.lastname: Haddadian
authors.forename: Haipeng
authors.initials: H
authors.lastname: Gong
authors.forename: Abhishek K
authors.initials: AK
authors.lastname: Jha
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Yang
authors.forename: Joe
authors.initials: J
authors.lastname: Debartolo
authors.forename: James R
authors.initials: JR
authors.lastname: Hinshaw
authors.forename: Phoebe A
authors.initials: PA
authors.lastname: Rice
authors.forename: Tobin R
authors.initials: TR
authors.lastname: Sosnick
authors.forename: Karl F
authors.initials: KF
authors.lastname: Freed
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001331:Automation; D020285:Cryoelectron Microscopy; D008565:Membrane Proteins / Q000737:chemistry / Q000648:ultrastructure; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D054159:Torsion, Mechanical
chemical_list: D008565:Membrane Proteins; D011506:Proteins