Low-resolution structure refinement in electron microscopy.
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.
Chen
James Z
JZ
Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
Fürst
Johannes
J
Chapman
Michael S
MS
Grigorieff
Nikolaus
N
D000199:Actins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D055592:Biophysical Phenomena; D001703:Biophysics; D001798:Blood Proteins / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods*; D004583:Electrons; D008024:Ligands; D008854:Microscopy, Electron / Q000379:methods*; D008958:Models, Molecular; D052066:N-Ethylmaleimide-Sensitive Proteins; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D033921:Vesicular Transport Proteins
D000199:Actins; D001426:Bacterial Proteins; D001798:Blood Proteins; D002352:Carrier Proteins; C097681:FlgE protein, Bacteria; D008024:Ligands; D033921:Vesicular Transport Proteins; D052066:N-Ethylmaleimide-Sensitive Proteins