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Identifying dynamic, partially occupied residues using anomalous scattering

Serena Rocchio, Ramona Duman, Kamel El Omari, Vitaliy Mykhaylyk, Zhen Yan, Armin Wagner, James C. A. Bardwell, Scott Horowitz
doi: https://doi.org/10.1101/642686
Serena Rocchio
aDepartment of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
bDepartment of Biochemical Sciences “A Rossi Fanelli”, Sapienza University of Roma, 00185, Rome, Italy
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Ramona Duman
cDiamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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Kamel El Omari
cDiamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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Vitaliy Mykhaylyk
cDiamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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Zhen Yan
aDepartment of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
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Armin Wagner
cDiamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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  • For correspondence: armin.wagner@diamond.ac.uk jbardwel@umich.edu Scott.Horowitz@du.edu
James C. A. Bardwell
aDepartment of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
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  • For correspondence: armin.wagner@diamond.ac.uk jbardwel@umich.edu Scott.Horowitz@du.edu
Scott Horowitz
dDepartment of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA
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  • For correspondence: armin.wagner@diamond.ac.uk jbardwel@umich.edu Scott.Horowitz@du.edu
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Abstract

X-ray crystallography is generally used to take single snapshots of a protein’s conformation. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes Residual Anomalous and Electron Density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data collection and analysis strategy for partially occupied iodine anomalous signals. Using the long wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with as low as ~12% occupancy is demonstrated. The number and position of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly dynamic sections of crystal structures.

Synopsis Structural studies on partially occupied, dynamic protein systems by crystallography are difficult. We present methods here for detecting these states in crystals.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 20, 2019.
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Identifying dynamic, partially occupied residues using anomalous scattering
Serena Rocchio, Ramona Duman, Kamel El Omari, Vitaliy Mykhaylyk, Zhen Yan, Armin Wagner, James C. A. Bardwell, Scott Horowitz
bioRxiv 642686; doi: https://doi.org/10.1101/642686
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Identifying dynamic, partially occupied residues using anomalous scattering
Serena Rocchio, Ramona Duman, Kamel El Omari, Vitaliy Mykhaylyk, Zhen Yan, Armin Wagner, James C. A. Bardwell, Scott Horowitz
bioRxiv 642686; doi: https://doi.org/10.1101/642686

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