This Article Full Text Full Text (PDF) Supplement A correction has been published All Versions of this Article: biophysj.107.115949v1 94/5/1613    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Jolley, C. C. Articles by Thorpe, M. F. PubMed PubMed Citation Articles by Jolley, C. C. Articles by Thorpe, M. F.

Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations

Center for Biological Physics, Bateman Physical Sciences, Arizona State University, Tempe, Arizona

Correspondence: Address reprint requests to Michael Thorpe, Arizona State University, Bateman Physical Sciences, Tempe, AZ 85287-1504. Tel.: 480-965 3085; E-mail: mft{at}asu.edu.

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 -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.