Open AccessExploring structural variability in X‐ray crystallographic models using protein local optimization by torsion‐angle sampling
Author(s) -
Knight Jennifer L.,
Zhou Zhiyong,
Gallicchio Emilio,
Himmel Daniel M.,
Friesner Richard A.,
Arnold Eddy,
Levy Ronald M.
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s090744490800070x
Subject(s) - dihedral angle , docking (animal) , protein structure , energy minimization , torsion (gastropod) , molecular dynamics , umbrella sampling , biological system , computer science , crystallography , statistical physics , algorithm , physics , chemistry , computational chemistry , biology , molecule , nuclear magnetic resonance , nursing , quantum mechanics , medicine , zoology , hydrogen bond
Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time‐intensive nature of manual X‐ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0–2.8 Å, it is demonstrated how torsion‐angle sampling of backbone and side‐chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal‐space X‐ray target function, can generate multiple structurally variable models which fit the X‐ray data well. Torsion‐angle sampling as implemented in the Protein Local Optimization Program ( PLOP ) has been used in this work. Models with the lowest R free values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV‐1 protease, calmodulin and SUMO‐conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble‐refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates.