Charles Cobb
Last active: 1/20/2015

Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex.

Edwards SJ, Moth CW, Kim S, Brandon S, Zhou Z, Cobb CE, Hustedt EJ, Beth AH, Smith JA, Lybrand TP
J Phys Chem B. 2014 118 (18): 4717-26

PMID: 24758720 · PMCID: PMC4018176 · DOI:10.1021/jp4099705

We report here specialized functions incorporated recently in the rigid-body docking software toolkit TagDock to utilize electron paramagnetic resonance derived (EPR-derived) interresidue distance measurements and spin-label accessibility data. The TagDock package extensions include a custom methanethiosulfonate spin label rotamer library to enable explicit, all-atom spin-label side-chain modeling and scripts to evaluate spin-label surface accessibility. These software enhancements enable us to better utilize the biophysical data routinely available from various spin-labeling experiments. To illustrate the power and utility of these tools, we report the refinement of an ankyrin:CDB3 complex model that exhibits much improved agreement with the EPR distance measurements, compared to model structures published previously.

MeSH Terms (9)

Algorithms Anion Exchange Protein 1, Erythrocyte Ankyrins Electron Spin Resonance Spectroscopy Humans Models, Molecular Molecular Docking Simulation Protein Multimerization Software

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