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Protein structure fitting and refinement guided by cryo-EM density.

Maya Topf1, Keren Lasker, Ben Webb

  • 1School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom. m.topf@cryst.bbk.ac.uk

Structure (London, England : 1993)
|February 16, 2008
PubMed
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This study introduces an automated method for fitting atomic structures into intermediate-resolution cryo-electron microscopy maps. The technique refines protein models, improving accuracy for macromolecular assembly analysis.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Cryo-electron microscopy (cryo-EM) provides low-resolution maps of macromolecular assemblies.
  • Atomic structures of individual proteins are often available.
  • Integrating these data requires robust fitting and refinement methods.

Purpose of the Study:

  • To develop and validate an automated method for fitting and refining atomic structures within intermediate-resolution cryo-EM maps (<15 Å).
  • To enhance the accuracy of atomic models in the context of their native macromolecular environment.

Main Methods:

  • A novel scoring function incorporating cross-correlation, stereochemical, and nonbonded interaction terms.
  • A heuristic optimization strategy combining Monte Carlo search, conjugate-gradients minimization, and simulated annealing molecular dynamics.

Related Experiment Videos

  • Progressive rigid-body refinement using progressively smaller structural subdivisions.

    • Main Results:

    • The method was tested on 15 proteins using simulated and experimental cryo-EM maps.
    • At ~10 Å resolution, the Cα root-mean-square deviation (RMSD) was reduced by an average of 53%.
    • The automated process successfully refined both experimental and predicted atomic structures.

    Conclusions:

    • The developed method provides an efficient and automated approach for atomic model building in intermediate-resolution cryo-EM maps.
    • This technique facilitates the interpretation of macromolecular structures and aids in understanding their function.
    • The refinement strategy significantly improves the accuracy of atomic positions within the map context.