Basic biochemical mechanisms fundamental to human health arise from understanding the structure of large biological molecules, both proteins and nucleic acids. X-ray crystallography has been a key method for uncovering their structure and function. This project will develop computational methods needed to enable the use of serial X-ray crystallography techniques. Serial crystallography, performed at either third generation synchrotron beamlines or X-ray free-electron lasers (XFEL), is emerging as a way to determine molecular structure using crystals that are probed once with a short X-ray pulse and then exchanged for a new sample. This a departure from traditional single-crystal experiments where the crystal is rotated in the beam to assemble a full data set, but which require large crystals, coupled with cryocooling to slow down the effects of radiation damage. Serial crystallography, in contrast, is performed with an extremely short X-ray pulse, which probes the structure before radiation damage occurs, and at normal physiological temperatures, where the full range of available molecular conformations can be revealed. The software toolkits DIALS (Diffraction Integration for Advanced Light Sources) and CCTBX (Computational Crystallography Toolbox) extract information from the diffraction pattern consisting of Bragg spots, the analysis of which eventually leads to molecular structure. This proposal re-examines the established data processing patterns that have existed for many decades, and favors new models that are specifically customized for serial crystallography, making systematic corrections to the measurements that have not previously been treated properly. This will lead to improved accuracy, even to the level of locating a single electron in a protein. Software will be deployed in cooperation with several XFEL lightsources worldwide including but not limited to LCLS (Stanford), EuXFEL (Germany), and SwissFEL (Switzerland), and at several synchrotron sources such as SSRL (Stanford), ESRF (France), and Diamond (UK). Code will be distributed in an open source, community-oriented software architecture that can be adapted by beamline scientists to accommodate new instrumentation, in a field where rapid hardware advances are expected to continue for many years.
Basic biochemical mechanisms fundamental to human health arise from understanding the structure of large biological molecules, both proteins and nucleic acids. X-ray crystallography is a key method for uncovering their function, and it continues to grow in importance as brighter X-ray sources and more sensitive detectors are developed. This is a computational technology project to provide a sharper picture than previously available, following chemical reactions as they progress over time, while avoiding X-ray damage that interfered with the measurement.
| Pande, Kanupriya; Donatelli, Jeffrey J; Malmerberg, Erik et al. (2018) Free-electron laser data for multiple-particle fluctuation scattering analysis. Sci Data 5:180201 |
| Duyvesteyn, Helen M E; Ginn, Helen M; Pietilä, Maija K et al. (2018) Towards in cellulo virus crystallography. Sci Rep 8:3771 |
| Winter, Graeme; Waterman, David G; Parkhurst, James M et al. (2018) DIALS: implementation and evaluation of a new integration package. Acta Crystallogr D Struct Biol 74:85-97 |
| Brewster, Aaron S; Waterman, David G; Parkhurst, James M et al. (2018) Improving signal strength in serial crystallography with DIALS geometry refinement. Acta Crystallogr D Struct Biol 74:877-894 |
| Kern, Jan; Chatterjee, Ruchira; Young, Iris D et al. (2018) Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature 563:421-425 |
| Fuller, Franklin D; Gul, Sheraz; Chatterjee, Ruchira et al. (2017) Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 14:443-449 |
| Roedig, Philip; Ginn, Helen M; Pakendorf, Tim et al. (2017) High-speed fixed-target serial virus crystallography. Nat Methods 14:805-810 |
| Thomaston, Jessica L; Woldeyes, Rahel A; Nakane, Takanori et al. (2017) XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proc Natl Acad Sci U S A 114:13357-13362 |
| Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira et al. (2016) Structure of photosystem II and substrate binding at room temperature. Nature 540:453-457 |
| Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Zeldin, Oliver B et al. (2016) Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Elife 5: |
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