Protein structure fitting and refinement guided by cryo-EM density.
For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (<15 A). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures.
Topf
Maya
M
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom. m.topf@cryst.bbk.ac.uk
Lasker
Keren
K
Webb
Ben
B
Wolfson
Haim
H
Chiu
Wah
W
Sali
Andrej
A
D018834:Chaperonin 60 / Q000737:chemistry; D020285:Cryoelectron Microscopy; D008958:Models, Molecular; D009010:Monte Carlo Method; D010444:Peptide Elongation Factor Tu / Q000737:chemistry; D017434:Protein Structure, Tertiary
D018834:Chaperonin 60; D010444:Peptide Elongation Factor Tu