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

Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions.

[1]  Nicholas K. Sauter,et al.  Robust indexing for automatic data collection , 2004, Journal of applied crystallography.

[2]  Robert A. Grothe,et al.  Structure of the cross-β spine of amyloid-like fibrils , 2005, Nature.

[3]  R. Diaz-Avalos,et al.  Protein-only transmission of three yeast prion strains , 2004, Nature.

[4]  Pawel Sikorski,et al.  Molecular basis for amyloid fibril formation and stability. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[6]  J. Sipe,et al.  Review: history of the amyloid fibril. , 2000, Journal of structural biology.

[7]  David Eisenberg,et al.  Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide. , 2003, Journal of molecular biology.

[8]  R. Wickner,et al.  [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. , 1994, Science.

[9]  Robert A. Grothe,et al.  An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  S. Lindquist,et al.  Nucleated conformational conversion and the replication of conformational information by a prion determinant. , 2000, Science.

[11]  Zach DeVito,et al.  Opt , 2017 .

[12]  H. A. Levy,et al.  ANGLE CALCULATIONS FOR 3- AND 4-CIRCLE X-RAY AND NEUTRON DIFFRACTOMETERS. , 1967 .

[13]  Roger Cooke,et al.  Conformational variations in an infectious protein determine prion strain differences , 2004, Nature.

[14]  John A. Nelder,et al.  A Simplex Method for Function Minimization , 1965, Comput. J..

[15]  A G Leslie,et al.  Biological Crystallography Integration of Macromolecular Diffraction Data , 2022 .

[16]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[17]  Sébastien Boutet,et al.  Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers , 2014, Nature Methods.

[18]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[19]  Nicholas K. Sauter,et al.  Automated diffraction image analysis and spot searching for high-throughput crystal screening , 2006 .

[20]  Nicholas K. Sauter,et al.  The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework , 2002 .

[21]  Nicholas K. Sauter,et al.  New Python-based methods for data processing , 2013, Acta crystallographica. Section D, Biological crystallography.

[22]  Michael G. Rossmann,et al.  An Algorithm for Automatic Indexing of Oscillation Images using Fourier Analysis , 1997 .

[23]  C. Blake,et al.  From the globular to the fibrous state: protein structure and structural conversion in amyloid formation , 1998, Quarterly Reviews of Biophysics.

[24]  J R Glover,et al.  Support for the Prion Hypothesis for Inheritance of a Phenotypic Trait in Yeast , 1996, Science.

[25]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[26]  Nicholas K. Sauter,et al.  New methods for indexing multi-lattice diffraction data , 2014, Acta crystallographica. Section D, Biological crystallography.

[27]  Frédéric Cazals,et al.  A note on the problem of reporting maximal cliques , 2008, Theor. Comput. Sci..

[28]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[29]  H R Powell,et al.  The Rossmann Fourier autoindexing algorithm in MOSFLM. , 1999, Acta crystallographica. Section D, Biological crystallography.

[30]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[31]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[32]  Mauro Bortolotti,et al.  ReX.Cell: a user-friendly program for powder diffraction indexing , 2013 .

[33]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[34]  Victor H Hernandez,et al.  Nature Methods , 2007 .

[35]  U Weierstall,et al.  Injector for scattering measurements on fully solvated biospecies. , 2012, The Review of scientific instruments.

[36]  H. Chapman,et al.  Femtosecond protein nanocrystallography-data analysis methods. , 2010, Optics express.

[37]  Chao Yang,et al.  Compressive auto-indexing in femtosecond nanocrystallography. , 2010, Ultramicroscopy.

[38]  Carmelo Giacovazzo,et al.  Advances in powder diffraction pattern indexing: N-TREOR09 , 2009 .