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Stagno JR. Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments. Methods Mol Biol 2023; 2568:233-242. [PMID: 36227572 DOI: 10.1007/978-1-0716-2687-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serial femtosecond crystallography (SFX) experiments using an X-ray free electron laser (XFEL) is a burgeoning method for time-resolved structural studies of biomacromolecules. As with any crystallography experiment, the most important component is quality sample preparation. Whereas dozens of SFX experiments, including batch crystallization methods, have been reported for proteins, very few have been reported for RNA. This chapter outlines standard procedures for preparing RNA microcrystalline samples suitable for SFX studies.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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2
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Cheng QD, Chung HY, Schubert R, Chia SH, Falke S, Mudogo CN, Kärtner FX, Chang G, Betzel C. Protein-crystal detection with a compact multimodal multiphoton microscope. Commun Biol 2020; 3:569. [PMID: 33051587 PMCID: PMC7553921 DOI: 10.1038/s42003-020-01275-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/01/2020] [Indexed: 11/28/2022] Open
Abstract
There is an increasing demand for rapid, effective methods to identify and detect protein micro- and nano-crystal suspensions for serial diffraction data collection at X-ray free-electron lasers or high-intensity micro-focus synchrotron radiation sources. Here, we demonstrate a compact multimodal, multiphoton microscope, driven by a fiber-based ultrafast laser, enabling excitation wavelengths at 775 nm and 1300 nm for nonlinear optical imaging, which simultaneously records second-harmonic generation, third-harmonic generation and three-photon excited ultraviolet fluorescence to identify and detect protein crystals with high sensitivity. The instrument serves as a valuable and important tool supporting sample scoring and sample optimization in biomolecular crystallography, which we hope will increase the capabilities and productivity of serial diffraction data collection in the future.
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Affiliation(s)
- Qing-di Cheng
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Hsiang-Yu Chung
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Schubert
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- XFEL Biological Infrastructure Laboratory at the European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Shih-Hsuan Chia
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Celestin Nzanzu Mudogo
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany
| | - Franz X Kärtner
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Physics Department, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Guoqing Chang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a Notkestrasse 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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3
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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4
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Smith CJ, Dinh J, Schmitt PD, Stroud PA, Hinds J, Johnson MJ, Simpson GJ. Calibration-Free Second Harmonic Generation (SHG) Image Analysis for Quantification of Trace Crystallinity Within Final Dosage Forms of Amorphous Solid Dispersions. APPLIED SPECTROSCOPY 2018; 72:1594-1605. [PMID: 29896972 DOI: 10.1177/0003702818786506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A statistical model enables auto-calibration of second harmonic generation (SHG) images for quantifying trace crystallinity within amorphous solid dispersions (ASDs) over a wide dynamic range of crystallinity. In this paper, we demonstrate particle-counting approaches for quantifying trace crystallinity, combined with analytical expressions correcting for particle overlap bias in higher crystallinity regimes to extend the continuous dynamic range of standard particle-counting algorithms through to the signal averaging regime. The reliability of the values recovered by these expressions was demonstrated with simulated data as well as experimental data obtained for an amorphous solid dispersion formulation containing evacetrapib, an Eli Lilly and Company compound. Since particle counting independently recovers the crystalline volume and the SHG intensity, the average SHG intensity per unit volume can be used as an internal calibrant for quantifying crystallinity at higher volume fractions, for which particle counting is no longer applicable.
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Affiliation(s)
- Casey J Smith
- 1 Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Janny Dinh
- 1 Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Paul D Schmitt
- 3 Department of Chemistry, Wabash College, Crawfordsville, IN, USA
| | | | | | | | - Garth J Simpson
- 1 Department of Chemistry, Purdue University, West Lafayette, IN, USA
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5
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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6
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Arzumanyan GM, Doroshkevich NV, Mamatkulov KZ, Shashkov SN, Zinovev EV, Vlasov AV, Round ES, Gordeliy VI. Highly Sensitive Coherent Anti-Stokes Raman Scattering Imaging of Protein Crystals. J Am Chem Soc 2016; 138:13457-13460. [PMID: 27636908 DOI: 10.1021/jacs.6b04464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serial crystallography at last generation X-ray synchrotron sources and free electron lasers enabled data collection with micrometer and even submicrometer size crystals, which have resulted in amazing progress in structural biology. However, imaging of small crystals, which although is highly demanded, remains a challenge, especially in the case of membrane protein crystals. Here we describe a new extremely sensitive method of the imaging of protein crystals that is based on coherent anti-Stokes Raman scattering.
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Affiliation(s)
- Grigory M Arzumanyan
- Joint Institute for Nuclear Research , 141980 Dubna, Russia.,Dubna State University , 19 Universitetskaya st., Dubna 141982, Russia
| | | | | | - Sergey N Shashkov
- SOL Instruments , 220005 BY P.O. Box 235, Minsk, Republic of Belarus
| | - Egor V Zinovev
- Moscow Institute of Physics and Technology , 141700 Dolgoprudny, Moscow region, Russia
| | - Alexey V Vlasov
- Moscow Institute of Physics and Technology , 141700 Dolgoprudny, Moscow region, Russia
| | - Ekaterina S Round
- Moscow Institute of Physics and Technology , 141700 Dolgoprudny, Moscow region, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS , F-38000 Grenoble, France.,Institute of Complex Systems: Structural Biochemistry (ICS-6), Research Centre Jülich , 52425 Jülich, Germany
| | - Valentin I Gordeliy
- Moscow Institute of Physics and Technology , 141700 Dolgoprudny, Moscow region, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS , F-38000 Grenoble, France.,Institute of Complex Systems: Structural Biochemistry (ICS-6), Research Centre Jülich , 52425 Jülich, Germany
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7
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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8
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Dörner K, Martin-Garcia JM, Kupitz C, Gong Z, Mallet TC, Chen L, Wachter RM, Fromme P. Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization. CRYSTAL GROWTH & DESIGN 2016; 16:3838-3845. [PMID: 29056873 PMCID: PMC5649632 DOI: 10.1021/acs.cgd.6b00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A new approach is described to screen for protein nanocrystals based on the reversibility of crystallization. Methods to characterize nanocrystals are in strong need to facilitate sample preparation for serial femtosecond X-ray nanocrystallography (SFX). SFX enables protein structure determination by collecting X-ray diffraction from nano- and microcrystals using a free electron laser. This technique is especially valuable for challenging proteins as for example membrane proteins and is in general a powerful method to overcome the radiation damage problem and to perform time-resolved structure analysis. Nanocrystal growth cannot be monitored with common methods used in protein crystallography, as the resolution of bright field microscopy is not sufficient. A high-performance method to screen for nanocrystals is second order nonlinear imaging of chiral crystals (SONICC). However, the high cost prevents its use in every laboratory, and some protein nanocrystals may be "invisible" to SONICC. In this work using a crystallization robot and a common imaging system precipitation comprised of nanocrystals and precipitation caused by aggregated protein can be distinguished.
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Affiliation(s)
- Katerina Dörner
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
| | - Christopher Kupitz
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Zhen Gong
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - T Conn Mallet
- Life Science, Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, Texas 77381, United States
| | - Liqing Chen
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Rebekka M Wachter
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
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9
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Exploiting Microbeams for Membrane Protein Structure Determination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:105-117. [PMID: 27553238 PMCID: PMC6126528 DOI: 10.1007/978-3-319-35072-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography.
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10
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Lukk T, Gillilan RE, Szebenyi DME, Zipfel WR. A visible-light-excited fluorescence method for imaging protein crystals without added dyes. J Appl Crystallogr 2016; 49:234-240. [PMID: 26937240 PMCID: PMC4762565 DOI: 10.1107/s160057671502419x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/16/2015] [Indexed: 11/10/2022] Open
Abstract
Fluorescence microscopy methods have seen an increase in popularity in recent years for detecting protein crystals in screening trays. The fluorescence-based crystal detection methods have thus far relied on intrinsic UV-inducible tryptophan fluorescence, nonlinear optics or fluorescence in the visible light range dependent on crystals soaked with fluorescent dyes. In this paper data are presented on a novel visible-light-inducible autofluorescence arising from protein crystals as a result of general stabilization of conjugated double-bond systems and increased charge delocalization due to crystal packing. The visible-light-inducible autofluorescence serves as a complementary method to bright-field microscopy in beamline applications where accurate crystal centering about the rotation axis is essential. Owing to temperature-dependent chromophore stabilization, protein crystals exhibit tenfold higher fluorescence intensity at cryogenic temperatures, making the method ideal for experiments where crystals are cooled to 100 K with a cryostream. In addition to the non-damaging excitation wavelength and low laser power required for imaging, the method can also serve a useful role for differentiating protein crystals from salt crystals in screening trays.
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Affiliation(s)
- Tiit Lukk
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Doletha M. E. Szebenyi
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Department of Biomedical Engineering, Cornell University, B41 Weill Hall, Ithaca, NY 14853, USA
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11
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Nonlinear Optical Characterization of Membrane Protein Microcrystals and Nanocrystals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:91-103. [DOI: 10.1007/978-3-319-35072-1_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Luft JR, Wolfley JR, Franks EC, Lauricella AM, Gualtieri EJ, Snell EH, Xiao R, Everett JK, Montelione GT. The detection and subsequent volume optimization of biological nanocrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041710. [PMID: 26798809 PMCID: PMC4711624 DOI: 10.1063/1.4921199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/05/2015] [Indexed: 06/05/2023]
Abstract
Identifying and then optimizing initial crystallization conditions is a prerequisite for macromolecular structure determination by crystallography. Improved technologies enable data collection on crystals that are difficult if not impossible to detect using visible imaging. The application of second-order nonlinear imaging of chiral crystals and ultraviolet two-photon excited fluorescence detection is shown to be applicable in a high-throughput manner to rapidly verify the presence of nanocrystals in crystallization screening conditions. It is noted that the nanocrystals are rarely seen without also producing microcrystals from other chemical conditions. A crystal volume optimization method is described and associated with a phase diagram for crystallization.
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Affiliation(s)
| | - Jennifer R Wolfley
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Eleanor Cook Franks
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Angela M Lauricella
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Ellen J Gualtieri
- Formulatrix, Inc. , 10 DeAngelo Drive, Bedford, Massachusetts 01730, USA
| | | | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
| | - John K Everett
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
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13
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Schmitt PD, Trasi NS, Taylor LS, Simpson GJ. Finding the Needle in the Haystack: Characterization of Trace Crystallinity in a Commercial Formulation of Paclitaxel Protein-Bound Particles by Raman Spectroscopy Enabled by Second Harmonic Generation Microscopy. Mol Pharm 2015; 12:2378-83. [PMID: 26066072 DOI: 10.1021/acs.molpharmaceut.5b00065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Paul D. Schmitt
- Department of Chemistry and ‡Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Niraj S. Trasi
- Department of Chemistry and ‡Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lynne S. Taylor
- Department of Chemistry and ‡Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Garth J. Simpson
- Department of Chemistry and ‡Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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14
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Palczewska G, Salom D. Imaging of rhodopsin crystals with two-photon microscopy. Methods Mol Biol 2015; 1271:55-64. [PMID: 25697516 DOI: 10.1007/978-1-4939-2330-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Two-photon microscopy has been shown to be an invaluable tool for detecting and monitoring protein crystallization trials and characterizing membrane protein crystals. This imaging method has proven especially useful for rhodopsin, because of the dependence of rhodopsin's fluorescence spectra on the isomerization state of its intrinsic chromophore (retinylidene) and, as such, it can provide additional information about the identity and functional state of rhodopsin in crystals. Here, we describe the acquisition of images and two-photon excitation and emission spectra using a commercial two-photon microscope, along with detailed instructions for the handling of rhodopsin crystals and specific examples of rhodopsin data.
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15
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Calero G, Cohen AE, Luft JR, Newman J, Snell EH. Identifying, studying and making good use of macromolecular crystals. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:993-1008. [PMID: 25084371 PMCID: PMC4118793 DOI: 10.1107/s2053230x14016574] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/16/2014] [Indexed: 11/30/2022]
Abstract
As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.
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Affiliation(s)
- Guillermo Calero
- Department of Structural Biology, University of Pittsburgh Medical School, Pittsburgh, PA 15261, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Joseph R Luft
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Janet Newman
- CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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