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Stevenson HP, DePonte DP, Makhov AM, Conway JF, Zeldin OB, Boutet S, Calero G, Cohen AE. Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130322. [PMID: 24914151 DOI: 10.1098/rstb.2013.0322] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recent advancements at the Linac Coherent Light Source X-ray free-electron laser (XFEL) enabling successful serial femtosecond diffraction experiments using nanometre-sized crystals (NCs) have opened up the possibility of X-ray structure determination of proteins that produce only submicrometre crystals such as many membrane proteins. Careful crystal pre-characterization including compatibility testing of the sample delivery method is essential to ensure efficient use of the limited beamtime available at XFEL sources. This work demonstrates the utility of transmission electron microscopy for detecting and evaluating NCs within the carrier solutions of liquid injectors. The diffraction quality of these crystals may be assessed by examining the crystal lattice and by calculating the fast Fourier transform of the image. Injector reservoir solutions, as well as solutions collected post-injection, were evaluated for three types of protein NCs (i) the membrane protein PTHR1, (ii) the multi-protein complex Pol II-GFP and (iii) the soluble protein lysozyme. Our results indicate that the concentration and diffraction quality of NCs, particularly those with high solvent content and sensitivity to mechanical manipulation may be affected by the delivery process.
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Affiliation(s)
- H P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1040 Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - D P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - A M Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1040 Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1040 Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - O B Zeldin
- Department of Structural Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - S Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - G Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1040 Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - A E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Lunin VY, Grum-Grzhimailo AN, Gryzlova EV, Sinitsyn DO, Petrova TE, Lunina NL, Balabaev NK, Tereshkina KB, Stepanov AS, Krupyanskii YF. Efficient calculation of diffracted intensities in the case of nonstationary scattering by biological macromolecules under XFEL pulses. ACTA ACUST UNITED AC 2015; 71:293-303. [PMID: 25664739 DOI: 10.1107/s1399004714025450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022]
Abstract
The calculation of diffracted intensities from an atomic model is a routine step in the course of structure solution, and its efficiency may be crucial for the feasibility of the study. An intense X-ray free-electron laser (XFEL) pulse can change the electron configurations of atoms during its action. This results in time-dependence of the diffracted intensities and complicates their calculation. An algorithm is suggested that enables this calculation with a computational cost comparable to that for the time-independent case. The intensity is calculated as a sum of the `effective' intensity and a finite series of `correcting' intensities. These intensities are calculated in the conventional way but with modified atomic scattering factors that are specially derived for a particular XFEL experiment. The total number of members of the series does not exceed the number of chemically different elements present in the object under study. This number is small for biological molecules; in addition, the correcting terms are negligible within the parameter range and accuracy acceptable in biological crystallography. The time-dependent atomic scattering factors were estimated for different pulse fluence levels by solving the system of rate equations. The simulation showed that the changes in a diffraction pattern caused by the time-dependence of scattering factors are negligible if the pulse fluence does not exceed the limit that is currently achieved in experiments with biological macromolecular crystals (10(4) photons Å(-2) per pulse) but become significant with an increase in the fluence to 10(6) or 10(8) photons Å(-2) per pulse.
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Affiliation(s)
- Vladimir Y Lunin
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Alexei N Grum-Grzhimailo
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Elena V Gryzlova
- Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Dmitry O Sinitsyn
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Tatiana E Petrova
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Natalia L Lunina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Nikolai K Balabaev
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Ksenia B Tereshkina
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Alexei S Stepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Yurii F Krupyanskii
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygina Street, Moscow 119991, Russian Federation
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Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A 2014; 111:17122-7. [PMID: 25362050 PMCID: PMC4260607 DOI: 10.1073/pnas.1418733111] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.
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Affiliation(s)
| | | | | | | | | | - Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | | | | | | | | | | | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | | | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | | | | | | | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Artem Y Lyubimov
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | | | | | | | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Soichi Wakatsuki
- Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; Structural Biology, and
| | - William I Weis
- Molecular and Cellular Physiology, and Structural Biology, and
| | - Oleg A Zadvornyy
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715
| | - Oliver B Zeldin
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | | | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, Departments of Chemistry,
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Stevenson HP, Makhov AM, Calero M, Edwards AL, Zeldin OB, Mathews II, Lin G, Barnes CO, Santamaria H, Ross TM, Soltis SM, Khosla C, Nagarajan V, Conway JF, Cohen AE, Calero G. Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proc Natl Acad Sci U S A 2014; 111:8470-5. [PMID: 24872454 DOI: 10.1073/pnas.1400240111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The current practice for identifying crystal hits for X-ray crystallography relies on optical microscopy techniques that are limited to detecting crystals no smaller than 5 μm. Because of these limitations, nanometer-sized protein crystals cannot be distinguished from common amorphous precipitates, and therefore go unnoticed during screening. These crystals would be ideal candidates for further optimization or for femtosecond X-ray protein nanocrystallography. The latter technique offers the possibility to solve high-resolution structures using submicron crystals. Transmission electron microscopy (TEM) was used to visualize nanocrystals (NCs) found in crystallization drops that would classically not be considered as "hits." We found that protein NCs were readily detected in all samples tested, including multiprotein complexes and membrane proteins. NC quality was evaluated by TEM visualization of lattices, and diffraction quality was validated by experiments in an X-ray free electron laser.
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Kirian RA, White TA, Holton JM, Chapman HN, Fromme P, Barty A, Lomb L, Aquila A, Maia FRNC, Martin AV, Fromme R, Wang X, Hunter MS, Schmidt KE, Spence JCH. Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr A 2011; 67:131-40. [PMID: 21325716 PMCID: PMC3066792 DOI: 10.1107/s0108767310050981] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/05/2010] [Indexed: 11/10/2022] Open
Abstract
A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 µm, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.
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Affiliation(s)
- Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Thomas A. White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - James M. Holton
- Advanced Light Source, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry, University of California, San Francisco, CA 945158-2330, USA
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Department of Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lukas Lomb
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Filipe R. N. C. Maia
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Andrew V. Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Raimund Fromme
- Department of Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Xiaoyu Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Mark S. Hunter
- Department of Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Kevin E. Schmidt
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
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