Protein Structure Fitting and Refinement Guided by cryo-EM Density

Structure. 2008 Feb;16(2):295-307. doi: 10.1016/j.str.2007.11.016.

Abstract

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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chaperonin 60 / chemistry
  • Cryoelectron Microscopy*
  • Models, Molecular*
  • Monte Carlo Method
  • Peptide Elongation Factor Tu / chemistry
  • Protein Structure, Tertiary*

Substances

  • Chaperonin 60
  • Peptide Elongation Factor Tu