Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations

Craigc C. Jolley, Stephena Wells, Petra Fromme, Michael Thorpe

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with the biomolecule. We develop a new technique that maintains the local geometry and chemistry at each stage of the fitting procedure. A geometric simulation is used to drive the structure from some appropriate starting point (a nearby experimental structure or a modeled structure) toward the experimental density, via a set of small incremental motions. Structural motifs such as α-helices can be held rigid during the fitting procedure as the starting structure is brought into alignment with the experimental density. After validating this procedure on simulated data for adenylate kinase and lactoferrin, we show how cryo-EM data for two different GroEL structures can be fit using a starting x-ray crystal structure. We show that by incorporating the correct local stereochemistry in the modeling, structures can be obtained with effective resolution that is significantly higher than might be expected from the nominal cryo-EM resolution.

Original languageEnglish (US)
Pages (from-to)1613-1621
Number of pages9
JournalBiophysical Journal
Volume94
Issue number5
DOIs
StatePublished - Mar 1 2008

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Cryoelectron Microscopy
Adenylate Kinase
Proteins
Lactoferrin
Structural Models
X-Rays

ASJC Scopus subject areas

  • Biophysics

Cite this

Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. / Jolley, Craigc C.; Wells, Stephena; Fromme, Petra; Thorpe, Michael.

In: Biophysical Journal, Vol. 94, No. 5, 01.03.2008, p. 1613-1621.

Research output: Contribution to journalArticle

Jolley, Craigc C. ; Wells, Stephena ; Fromme, Petra ; Thorpe, Michael. / Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. In: Biophysical Journal. 2008 ; Vol. 94, No. 5. pp. 1613-1621.
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