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Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ)

  • Loïc Salmon
  • Logan S. Ahlstrom
  • James C. A. Bardwell
  • Scott Horowitz
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

Abstract

Heterogeneous and dynamic biomolecular complexes play a central role in many cellular processes but are poorly understood due to experimental challenges in characterizing their structural ensembles. To address these difficulties, we developed a hybrid methodology that combines X-ray crystallography with ensemble selections typically used in NMR studies to determine structural ensembles of heterogeneous biomolecular complexes. The method, termed READ, for residual electron and anomalous density, enables the visualization of heterogeneous conformational ensembles of complexes within crystals. Here we present a detailed protocol for performing the ensemble selections to construct READ ensembles. From a diverse pool of binding poses, a selection scheme is used to determine a subset of conformations that maximizes agreement with the X-ray data. Overall, READ is a general approach for obtaining a high-resolution view of dynamic protein-protein complexes.

Key words

Crystallography Ensemble Conformational dynamics Protein structure Structural biology 

Notes

Acknowledgment

This work was supported by the National Institutes of Health (R01-GM102829 to J.C.A.B. and K99/R00-GM120388 to S.H.). J.C.A.B. is a Howard Hughes Medical Investigator. The authors would like to thank S. Rocchio for comments on the manuscript and M. Mourao for useful discussions. The authors would also like to thank C. Stockbridge and the LSA-IT development team for the assistance in coding.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280CNRS, ENS Lyon, UCB Lyon 1, Université de LyonVilleurbanneFrance
  2. 2.Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical InstituteUniversity of MichiganAnn ArborUSA
  3. 3.Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUSA
  4. 4.Department of Chemistry and Biochemistry, Knoebel Institute for Healthy AgingUniversity of DenverDenverUSA

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