Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations
| Autor: | Michael Thorpe, Petra Fromme, Craig Jolley, Stephen A. Wells |
|---|---|
| Rok vydání: | 2008 |
| Předmět: |
chemistry.chemical_classification
0303 health sciences Protein Conformation Chemistry Cryo-electron microscopy Biomolecule Low resolution Cryoelectron Microscopy 030302 biochemistry & molecular biology Geometric simulation Resolution (electron density) Biophysics Structure (category theory) Chaperonin 60 Biophysical Theory and Modeling Crystallography X-Ray Set (abstract data type) 03 medical and health sciences Crystallography Computer Simulation Point (geometry) Biological system Algorithms Protein Binding 030304 developmental biology |
| Zdroj: | Biophysical Journal. 94:1613-1621 |
| ISSN: | 0006-3495 |
| DOI: | 10.1529/biophysj.107.115949 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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