BIOPHYSICAL THEORY AND MODELING |
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
Craig C Jolley 1, Stephen A Wells 1, Petra Fromme 1 and Michael F Thorpe 1*
1 Arizona State University
* To whom correspondence should be addressed. E-mail: mft{at}asu.edu.
Submitted on June 22, 2007
Revised on August 4, 2007
Accepted on 29 October 2007
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Abstract |
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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. Here 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) towards the experimental density, via a set of small incremental motions. Structural motifs such as alpha 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 ADK 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.
Key Words:
GroEL, constrained geometric simulations, cryo-electron microscopy, rigidity, structural biology
