title: Highly constrained multiple-copy refinement of protein crystal structures.
abstract: In the course of refining atomic protein structures, one often encounters difficulty with molecules that are unusually flexible or otherwise disordered. We approach the problem by combining two relatively recent developments: simultaneous refinement of multiple protein conformations and highly constrained refinement. A constrained Langevin dynamics refinement is tested on two proteins: neurotrophin-3 and glutamine synthetase. The method produces closer agreement between the calculated and observed scattering amplitudes than standard, single-copy, Gaussian atomic displacement parameter refinement. This is accomplished without significantly increasing the number of fitting parameters in the model. These results suggest that loop motion in proteins within a crystal lattice can be extensive and that it is poorly modeled by isotropic Gaussian distributions for each atom.
authors.affiliation: Molecular Biology Institute, University of California, Los Angeles 90095-1570, USA.
authors.forename: M
authors.initials: M
authors.lastname: Pellegrini
authors.forename: N
authors.initials: N
authors.lastname: Grønbech-Jensen
authors.forename: J A
authors.initials: JA
authors.lastname: Kelly
authors.forename: G M
authors.initials: GM
authors.lastname: Pfluegl
authors.forename: T O
authors.initials: TO
authors.lastname: Yeates
mesh_terms: D000818:Animals; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D005974:Glutamate-Ammonia Ligase / Q000737:chemistry; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D009414:Nerve Growth Factors / Q000737:chemistry; D020933:Neurotrophin 3; D016011:Normal Distribution; D011487:Protein Conformation
chemical_list: D009414:Nerve Growth Factors; D020933:Neurotrophin 3; D005974:Glutamate-Ammonia Ligase