Inclusion of Thermal Motion in Crystallographic Structures by Restrained Molecular Dynamics

A protein crystal structure is usually described by one single structure, which largely omits the dynamical behavior of the molecule. A molecular dynamics method with a time-averaged crystallographic restraint was used to overcome this limitation. This method yields an ensemble of structures in whic...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 1990-09, Vol.249 (4973), p.1149-1152
Main Authors: Gros, Piet, van Gunsteren, Wilfred F., Wim G. J. Hol
Format: Article
Language:English
Subjects:
Animals
Arithmetic mean
Atoms
Biological and medical sciences
Cattle
Crystal structure
Crystalline structure
Crystallography
Crystalloids (Botany)
Crystals
Electron density
Fundamental and applied biological sciences. Psychology
Hot Temperature
Isomorphism (Crystallography)
Models, Molecular
Molecular biophysics
Molecular dynamics
Molecular structure
Molecules
Motion
Phospholipases
Phospholipases A
Phospholipases A2
Protein Conformation
Structure in molecular biology
Thermal properties
Trajectories
Ungulates
X-Ray Diffraction
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Summary:A protein crystal structure is usually described by one single structure, which largely omits the dynamical behavior of the molecule. A molecular dynamics method with a time-averaged crystallographic restraint was used to overcome this limitation. This method yields an ensemble of structures in which all possible thermal motions are allowed, that is, in addition to isotropic distributions, anisotropic and anharmonic positional distributions occur as well. In the case of bovine pancreatic phospholipase A$_2$, this description markedly improves agreement with the observed x-ray diffraction data compared to the results of the classical one-model structure description. Time-averaged crystallographically restrained molecular dynamics reveals large mobilities in the loops involved in lipid bilayer association.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.2396108