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 | Zendy

Sarah J. Edwards | Zendy; Christopher W. Moth | Zendy; SungHoon Kim | Zendy; Suzanne Brandon | Zendy; Zheng Zhou | Zendy; Charles E. Cobb | Zendy; Eric J. Hustedt | Zendy; Albert H. Beth | Zendy; Jarrod A. Smith | Zendy; Terry P. Lybrand | Zendy

Open Access

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

Author(s) -

Sarah J. Edwards,

Christopher W. Moth,

SungHoon Kim,

Suzanne Brandon,

Zheng Zhou,

Charles E. Cobb,

Eric J. Hustedt,

Albert H. Beth,

Jarrod A. Smith,

Terry P. Lybrand

Publication year - 2014

Publication title -

the journal of physical chemistry b

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.864

H-Index - 392

eISSN - 1520-6106

pISSN - 1520-5207

DOI - 10.1021/jp4099705

Subject(s) - electron paramagnetic resonance , spin label , docking (animal) , site directed spin labeling , software , computer science , cartesian coordinate system , algorithm , chemistry , biological system , crystallography , molecular physics , chemical physics , physics , nuclear magnetic resonance , mathematics , geometry , programming language , medicine , nursing , biology

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.

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