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.
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.
Department of Chemistry, ‡Department of Molecular Physiology & Biophysics, §Department of Biochemistry, ∥Department of Pharmacology, ⊥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States.
Sarah J
SJ
Edwards
Christopher W
CW
Moth
Sunghoon
S
Kim
Suzanne
S
Brandon
Zheng
Z
Zhou
Charles E
CE
Cobb
Eric J
EJ
Hustedt
Albert H
AH
Beth
Jarrod A
JA
Smith
Terry P
TP
Lybrand
D000465:Algorithms; D001457:Anion Exchange Protein 1, Erythrocyte / Q000737:chemistry* / Q000378:metabolism; D017487:Ankyrins / Q000737:chemistry* / Q000378:metabolism; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D006801:Humans; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D055503:Protein Multimerization; D012984:Software
C110202:ANK1 protein, human; D001457:Anion Exchange Protein 1, Erythrocyte; D017487:Ankyrins