High-resolution structure of viruses from random diffraction snapshots
Abstract
The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the threedimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution.We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.
- Authors:
-
- Univ. of Wisconsin, Milwaukee, WI (United States)
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Milwaukee, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
- OSTI Identifier:
- 1598192
- Grant/Contract Number:
- FG02-09ER16114; SC0002164
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
- Additional Journal Information:
- Journal Volume: 369; Journal Issue: 1647; Journal ID: ISSN 0962-8436
- Publisher:
- The Royal Society Publishing
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; dimensionality reduction; symmetry; X-ray lasers; macromolecular assemblies; manifold embedding
Citation Formats
Hosseinizadeh, A., Schwander, P., Dashti, A., Fung, R., D'Souza, R. M., and Ourmazd, A. High-resolution structure of viruses from random diffraction snapshots. United States: N. p., 2014.
Web. doi:10.1098/rstb.2013.0326.
Hosseinizadeh, A., Schwander, P., Dashti, A., Fung, R., D'Souza, R. M., & Ourmazd, A. High-resolution structure of viruses from random diffraction snapshots. United States. https://doi.org/10.1098/rstb.2013.0326
Hosseinizadeh, A., Schwander, P., Dashti, A., Fung, R., D'Souza, R. M., and Ourmazd, A. Thu .
"High-resolution structure of viruses from random diffraction snapshots". United States. https://doi.org/10.1098/rstb.2013.0326. https://www.osti.gov/servlets/purl/1598192.
@article{osti_1598192,
title = {High-resolution structure of viruses from random diffraction snapshots},
author = {Hosseinizadeh, A. and Schwander, P. and Dashti, A. and Fung, R. and D'Souza, R. M. and Ourmazd, A.},
abstractNote = {The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the threedimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution.We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.},
doi = {10.1098/rstb.2013.0326},
journal = {Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences},
number = 1647,
volume = 369,
place = {United States},
year = {Thu Jul 17 00:00:00 EDT 2014},
month = {Thu Jul 17 00:00:00 EDT 2014}
}
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Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
journal, May 2005
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Manifold parametrizations by eigenfunctions of the Laplacian and heat kernels
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Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid
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