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Title: Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

Abstract

Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

Authors:
 [1];  [2];  [2];  [1];  [1];  [2];  [2];  [3];  [2];  [1]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division.
  2. Univ. of California, Los Angeles, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Los Angeles, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1190539
Grant/Contract Number:  
AC02-05CH11231; FC02-02ER63421
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography (Online)
Additional Journal Information:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 2; Journal ID: ISSN 1399-0047
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 59 BASIC BIOLOGICAL SCIENCES; XFEL; Sup35 yeast prion; indexing methods; crystallography

Citation Formats

Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., and Sauter, Nicholas K. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns. United States: N. p., 2015. Web. doi:10.1107/S1399004714026145.
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Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., & Sauter, Nicholas K. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns. United States. https://doi.org/10.1107/S1399004714026145
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Brewster, Aaron S., Sawaya, Michael R., Rodriguez, Jose, Hattne, Johan, Echols, Nathaniel, McFarlane, Heather T., Cascio, Duilio, Adams, Paul D., Eisenberg, David S., and Sauter, Nicholas K. Fri . "Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns". United States. https://doi.org/10.1107/S1399004714026145. https://www.osti.gov/servlets/purl/1190539.
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@article{osti_1190539,
title = {Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns},
author = {Brewster, Aaron S. and Sawaya, Michael R. and Rodriguez, Jose and Hattne, Johan and Echols, Nathaniel and McFarlane, Heather T. and Cascio, Duilio and Adams, Paul D. and Eisenberg, David S. and Sauter, Nicholas K.},
abstractNote = {Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.},
doi = {10.1107/S1399004714026145},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 2,
volume = 71,
place = {United States},
year = {Fri Jan 23 00:00:00 EST 2015},
month = {Fri Jan 23 00:00:00 EST 2015}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1107/S1399004714026145
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Works referenced in this record:

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Advances in powder diffraction pattern indexing: N-TREOR09
journal, September 2009

  • Altomare, Angela; Campi, Gaetano; Cuocci, Corrado
  • Journal of Applied Crystallography, Vol. 42, Issue 5
  • DOI: 10.1107/S0021889809025503

An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated  -sheet structure for amyloid
journal, February 2001

  • Balbirnie, M.; Grothe, R.; Eisenberg, D. S.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 5
  • DOI: 10.1073/pnas.041617698

ReX.Cell : a user-friendly program for powder diffraction indexing
journal, December 2012

Angle calculations for 3- and 4-circle X-ray and neutron diffractometers
journal, April 1967

A note on the problem of reporting maximal cliques
journal, November 2008

Cross-beta Order and Diversity in Nanocrystals of an Amyloid-forming Peptide
journal, July 2003

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

New methods for indexing multi-lattice diffraction data
journal, September 2014

  • Gildea, Richard J.; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10
  • DOI: 10.1107/S1399004714017039

The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002

  • Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
  • Journal of Applied Crystallography, Vol. 35, Issue 1
  • DOI: 10.1107/S0021889801017824

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
journal, March 2014

  • Hattne, Johan; Echols, Nathaniel; Tran, Rosalie
  • Nature Methods, Vol. 11, Issue 5
  • DOI: 10.1038/nmeth.2887

Protein-only transmission of three yeast prion strains
journal, March 2004

Femtosecond protein nanocrystallography—data analysis methods
journal, January 2010

  • Kirian, Richard A.; Wang, Xiaoyu; Weierstall, Uwe
  • Optics Express, Vol. 18, Issue 6
  • DOI: 10.1364/OE.18.005713

The integration of macromolecular diffraction data
journal, December 2005

  • Leslie, Andrew G. W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1
  • DOI: 10.1107/S0907444905039107

Compressive auto-indexing in femtosecond nanocrystallography
journal, June 2011

Molecular basis for amyloid fibril formation and stability
journal, January 2005

  • Makin, O. S.; Atkins, E.; Sikorski, P.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 2
  • DOI: 10.1073/pnas.0406847102

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

A Simplex Method for Function Minimization
journal, January 1965

Structure of the cross-β spine of amyloid-like fibrils
journal, June 2005

  • Nelson, Rebecca; Sawaya, Michael R.; Balbirnie, Melinda
  • Nature, Vol. 435, Issue 7043
  • DOI: 10.1038/nature03680

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Support for the Prion Hypothesis for Inheritance of a Phenotypic Trait in Yeast
journal, August 1996

The Rossmann Fourier autoindexing algorithm in MOSFLM
journal, October 1999

  • Powell, Harold R.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 10
  • DOI: 10.1107/S0907444999009506

Robust indexing for automatic data collection
journal, May 2004

  • Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 37, Issue 3
  • DOI: 10.1107/S0021889804005874

New Python-based methods for data processing
journal, June 2013

  • Sauter, Nicholas K.; Hattne, Johan; Grosse-Kunstleve, Ralf W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000863

Review: History of the Amyloid Fibril
journal, June 2000

  • Sipe, Jean D.; Cohen, Alan S.
  • Journal of Structural Biology, Vol. 130, Issue 2-3
  • DOI: 10.1006/jsbi.2000.4221

An Algorithm for Automatic Indexing of Oscillation Images using Fourier Analysis
journal, December 1997

  • Steller, I.; Bolotovsky, R.; Rossmann, M. G.
  • Journal of Applied Crystallography, Vol. 30, Issue 6
  • DOI: 10.1107/S0021889897008777

From the globular to the fibrous state: protein structure and structural conversion in amyloid formation
journal, February 1998

Conformational variations in an infectious protein determine prion strain differences
journal, March 2004

  • Tanaka, Motomasa; Chien, Peter; Naber, Nariman
  • Nature, Vol. 428, Issue 6980
  • DOI: 10.1038/nature02392

The NumPy Array: A Structure for Efficient Numerical Computation
journal, March 2011

  • van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël
  • Computing in Science & Engineering, Vol. 13, Issue 2
  • DOI: 10.1109/MCSE.2011.37

Injector for scattering measurements on fully solvated biospecies
journal, March 2012

  • Weierstall, U.; Spence, J. C. H.; Doak, R. B.
  • Review of Scientific Instruments, Vol. 83, Issue 3
  • DOI: 10.1063/1.3693040

Automated diffraction image analysis and spot searching for high-throughput crystal screening
journal, January 2006

  • Zhang, Zepu; Sauter, Nicholas K.; van den Bedem, Henry
  • Journal of Applied Crystallography, Vol. 39, Issue 1
  • DOI: 10.1107/S0021889805040677
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    Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED
    journal, September 2016

    • Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 40
    • DOI: 10.1073/pnas.1606287113

    SPIND : a reference-based auto-indexing algorithm for sparse serial crystallography data
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