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Yusuf M, Zhang F, Chen B, Bhartiya A, Cunnea K, Wagner U, Cacho-Nerin F, Schwenke J, Robinson IK. Procedures for cryogenic X-ray ptychographic imaging of biological samples. IUCRJ 2017; 4:147-151. [PMID: 28250953 PMCID: PMC5330525 DOI: 10.1107/s2052252516020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/16/2016] [Indexed: 05/15/2023]
Abstract
Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.
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Affiliation(s)
- M. Yusuf
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, England
| | - F. Zhang
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, 518055, People’s Republic of China
| | - B. Chen
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
| | - A. Bhartiya
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
| | - K. Cunnea
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
| | - U. Wagner
- Diamond Light Source, Didcot, Oxfordshire, England
| | | | - J. Schwenke
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
| | - I. K. Robinson
- London Centre for Nanotechnology, University College London, London, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, England
- Condensed Matter Physics and Materials Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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Giewekemeyer K, Hackenberg C, Aquila A, Wilke RN, Groves MR, Jordanova R, Lamzin VS, Borchers G, Saksl K, Zozulya AV, Sprung M, Mancuso AP. Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging. Biophys J 2016; 109:1986-95. [PMID: 26536275 PMCID: PMC4643197 DOI: 10.1016/j.bpj.2015.08.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/14/2015] [Accepted: 08/27/2015] [Indexed: 12/02/2022] Open
Abstract
The structural investigation of noncrystalline, soft biological matter using x-rays is of rapidly increasing interest. Large-scale x-ray sources, such as synchrotrons and x-ray free electron lasers, are becoming ever brighter and make the study of such weakly scattering materials more feasible. Variants of coherent diffractive imaging (CDI) are particularly attractive, as the absence of an objective lens between sample and detector ensures that no x-ray photons scattered by a sample are lost in a limited-efficiency imaging system. Furthermore, the reconstructed complex image contains quantitative density information, most directly accessible through its phase, which is proportional to the projected electron density of the sample. If applied in three dimensions, CDI can thus recover the sample's electron density distribution. As the extension to three dimensions is accompanied by a considerable dose applied to the sample, cryogenic cooling is necessary to optimize the structural preservation of a unique sample in the beam. This, however, imposes considerable technical challenges on the experimental realization. Here, we show a route toward the solution of these challenges using ptychographic CDI (PCDI), a scanning variant of coherent imaging. We present an experimental demonstration of the combination of three-dimensional structure determination through PCDI with a cryogenically cooled biological sample—a budding yeast cell (Saccharomyces cerevisiae)—using hard (7.9 keV) synchrotron x-rays. This proof-of-principle demonstration in particular illustrates the potential of PCDI for highly sensitive, quantitative three-dimensional density determination of cryogenically cooled, hydrated, and unstained biological matter and paves the way to future studies of unique, nonreproducible biological cells at higher resolution.
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Affiliation(s)
| | - C Hackenberg
- European Molecular Biology Laboratory Hamburg c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - A Aquila
- European XFEL GmbH, Hamburg, Germany
| | - R N Wilke
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - M R Groves
- European Molecular Biology Laboratory Hamburg c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - R Jordanova
- European Molecular Biology Laboratory Hamburg c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - V S Lamzin
- European Molecular Biology Laboratory Hamburg c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - K Saksl
- Institute of Materials Research, Slovak Academy of Sciences, Kosice, Slovak Republic
| | | | - M Sprung
- DESY Photon Science, Hamburg, Germany
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Lafumat B, Mueller-Dieckmann C, Leonard G, Colloc'h N, Prangé T, Giraud T, Dobias F, Royant A, van der Linden P, Carpentier P. Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716010992] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Molecular oxygen (O2) is a key player in many fundamental biological processes. However, the combination of the labile nature and poor affinity of O2 often makes this substrate difficult to introduce into crystals at sufficient concentrations to enable protein/O2 interactions to be deciphered in sufficient detail. To overcome this problem, a gas pressure cell has been developed specifically for the `soak-and-freeze' preparation of crystals of O2-dependent biological molecules. The `soak-and-freeze' method uses high pressure to introduce oxygen molecules or krypton atoms (O2 mimics) into crystals which, still under high pressure, are then cryocooled for X-ray data collection. Here, a proof of principle of the gas pressure cell and the methodology developed is demonstrated with crystals of enzymes (lysozyme, thermolysin and urate oxidase) that are known to absorb and bind molecular oxygen and/or krypton. The successful results of these experiments lead to the suggestion that the soak-and-freeze method could be extended to studies involving a wide range of gases of biological, medical and/or environmental interest, including carbon monoxide, ethylene, methane and many others.
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Huang Q, Gruner SM, Kim CU, Mao Y, Wu X, Szebenyi DME. Reduction of lattice disorder in protein crystals by high-pressure cryocooling. J Appl Crystallogr 2016; 49:149-157. [PMID: 26937238 PMCID: PMC4762570 DOI: 10.1107/s1600576715023195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
High-pressure cryocooling (HPC) has been developed as a technique for reducing the damage that frequently occurs when macromolecular crystals are cryocooled at ambient pressure. Crystals are typically pressurized at around 200 MPa and then cooled to liquid nitrogen temperature under pressure; this process reduces the need for penetrating cryoprotectants, as well as the damage due to cryocooling, but does not improve the diffraction quality of the as-grown crystals. Here it is reported that HPC using a pressure above 300 MPa can reduce lattice disorder, in the form of high mosaicity and/or nonmerohedral twinning, in crystals of three different proteins, namely human glutaminase C, the GTP pyrophosphokinase YjbM and the uncharacterized protein lpg1496. Pressure lower than 250 MPa does not induce this transformation, even with a prolonged pressurization time. These results indicate that HPC at elevated pressures can be a useful tool for improving crystal packing and hence the quality of the diffraction data collected from pressurized crystals.
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Affiliation(s)
| | - Sol M. Gruner
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Chae Un Kim
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Xiaochun Wu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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