TY - JOUR
T1 - Low-resolution structure refinement in electron microscopy
AU - Chen, James Z.
AU - Fürst, Johannes
AU - Chapman, Michael S.
AU - Grigorieff, Nikolaus
N1 - Funding Information:
The authors greatly appreciate the insightful discussions with our colleagues during the development of this project. Particularly, we thank Dennis Thomas, Fadel Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba, and David DeRosier for their help with the flagella hook helical structure and Jamie McKnight, Gretta Ouyang, and David DeRosier for their input in the actin–DHP complex docking simulation. We also thank David DeRosier for proofreading this manuscript. This work was in part supported by NIH Grant P01 GM-62580, and by a Max Kade Fellowship to Dr. Johannes Fürst.
PY - 2003/10
Y1 - 2003/10
N2 - A real-space structure refinement method, originally developed for macromolecular X-ray crystallography, has been applied to protein structure analysis by electron microscopy (EM). This method simultaneously optimizes the fit of an atomic model to a density map and the stereo-chemical properties of the model by minimizing an energy function. The performance of this method is characterized at different resolution and signal-to-noise ratio conditions typical for EM electron density maps. A multi-resolution scheme is devised to improve the convergence of the refinement on the global energy minimum. Applications of the method to various model systems are demonstrated here. The first case is the arrangement of FlgE molecules in the helical filament of flagellar hook, in which refinement with segmented rigid bodies improves the density correlation and reduces severe van der Waals contacts among the symmetry-related subunits. The second case is a conformational analysis of the NSF AAA ATPase in which a multi-conformer model is used in the refinement to investigate the arrangement of the two ATPase domains in the molecule. The third case is a docking simulation in which the crystal structure of actin and the NOE data from NMR experiments on the dematin headpiece are combined with a low-resolution EM density map to generate an atomic model of the F-actin-dematin headpiece structure.
AB - A real-space structure refinement method, originally developed for macromolecular X-ray crystallography, has been applied to protein structure analysis by electron microscopy (EM). This method simultaneously optimizes the fit of an atomic model to a density map and the stereo-chemical properties of the model by minimizing an energy function. The performance of this method is characterized at different resolution and signal-to-noise ratio conditions typical for EM electron density maps. A multi-resolution scheme is devised to improve the convergence of the refinement on the global energy minimum. Applications of the method to various model systems are demonstrated here. The first case is the arrangement of FlgE molecules in the helical filament of flagellar hook, in which refinement with segmented rigid bodies improves the density correlation and reduces severe van der Waals contacts among the symmetry-related subunits. The second case is a conformational analysis of the NSF AAA ATPase in which a multi-conformer model is used in the refinement to investigate the arrangement of the two ATPase domains in the molecule. The third case is a docking simulation in which the crystal structure of actin and the NOE data from NMR experiments on the dematin headpiece are combined with a low-resolution EM density map to generate an atomic model of the F-actin-dematin headpiece structure.
KW - Electron density map
KW - Electron microscopy
KW - Empirical force field
KW - Macromolecular structure
KW - Real-space structure refinement
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U2 - 10.1016/j.jsb.2003.09.008
DO - 10.1016/j.jsb.2003.09.008
M3 - Article
C2 - 14643217
AN - SCOPUS:0344120716
SN - 1047-8477
VL - 144
SP - 144
EP - 151
JO - Journal of Structural Biology
JF - Journal of Structural Biology
IS - 1-2
ER -