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Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers

Synchrotron Light Sources and Free-Electron Lasers

Abstract

Third-generation synchrotron radiation (SR) X-rays have transformed structural biology research in the past decades with the advent of high-brilliance undulator X-ray beams. Combined with developments in microfocus beams, area detectors, and data analysis software, it is now possible to determine large complex structures from extremely small (microns in all directions) crystals, as exemplified by the structures of potassium channels, G-protein coupled receptors (GPCRs), ribosomes, and RNA polymerase complexes. The number of depositions in PDB (the Protein Data Bank) is already more than 100,000, the majority of which have been determined by X-rays. Almost all biology, biochemistry, and molecular biology textbooks now contain protein structures to explain their functions in the cell. Now, X-ray free-electron lasers (XFELs) promise to provide new opportunities in structural biology research. They produce X-ray beams with extraordinary properties: 9 to 10 orders of magnitude higher peak brilliance and 1000 times shorter pulse lengths, compared to existing synchrotron radiation beamlines around the world. Diffraction patterns can be recorded from micro and nanocrystals before radiation damage starts to destroy the samples. Using this “diffract-before-destroy” concept, a new area of XFEL biology has arisen, wherein biologically important questions are tackled beyond what is possible using traditional SR. Ultrashort XFEL pulses allow for frozen-in-time fluctuation X-ray scattering with a possibility of expanding isotropic solution scattering. New modes of XFEL pulses such as two-pulse/two-color are being developed for pump-probe femtosecond time-resolved experiments and phasing. Additionally, hybrid methods are increasingly used for challenging biological questions, in which SR and XFEL methods are combined with other methods such as cryo-electron microscopy, NMR, DEER, and optical and atomic force microscopes. Taken together, SR and XFELs provide a portfolio of structural biology tools which continue to enable cutting edge structural biology research of complex molecular machineries.

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Acknowledgements

The author is deeply indebted to Profs. Jochen Schneider and Jerome Hastings for their encouragements throughout the process, is grateful for fruitful discussions with the colleagues at SLAC and Stanford University, in particular to Marc Deller, Sebastien Boutet, Han Dao, Fatemeh Jabbarpour and Varun Bhadkamkar for their help with editing of the manuscript, and NIH-NIGMS, DOE BES and BER, SLAC and Stanford University for funding.

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Authors and Affiliations

  1. Department of Structural Biology, School of Medicine, Stanford University, 94305, Stanford, CA, USA

    Soichi Wakatsuki

  2. Biosciences Division, Science Directorate, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA

    Soichi Wakatsuki

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  1. Soichi Wakatsuki
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Correspondence to Soichi Wakatsuki .

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Editors and Affiliations

  1. Helmholtz-Zentrum Berlin, Berlin, Germany

    Eberhard Jaeschke

  2. Zentrum für Synchrotronstrahlung, TU Dortmund, Dortmund, Germany

    Shaukat Khan

  3. FS-CFEL-1, DESY, Hamburg, Germany

    Jochen R. Schneider

  4. SLAC National Accelerator Laboratory Linac Coherent Light Source, Stanford University, Menlo Park, California, USA

    Jerome B. Hastings

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Wakatsuki, S. (2015). Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers. In: Jaeschke, E., Khan, S., Schneider, J., Hastings, J. (eds) Synchrotron Light Sources and Free-Electron Lasers. Springer, Cham. https://doi.org/10.1007/978-3-319-04507-8_44-1

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  1. Latest

    The SACLA X-Ray Free-Electron Laser Based on Normal-Conducting C-Band Technology
    Published:
    25 January 2016

    DOI: https://doi.org/10.1007/978-3-319-04507-8_9-2

  2. Characterization of the Time Structure of Free-Electron Laser Radiation
    Published:
    23 January 2016

    DOI: https://doi.org/10.1007/978-3-319-04507-8_49-2

  3. Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers
    Published:
    16 September 2015

    DOI: https://doi.org/10.1007/978-3-319-04507-8_44-1

  4. Original

    The SACLA X-Ray FEL Based on Normal-Conducting C-Band Technology
    Published:
    09 May 2015

    DOI: https://doi.org/10.1007/978-3-319-04507-8_9-1

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