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Ye Y, Zheng L, Hong L, García Sakai V, de Souza NR, Teng D, Wu B, Xu Y, Cai J, Liu Z. Direct Observation of the Mutual Coupling Effect in the Protein-Water-Glycerol Mixture by Combining Neutron Scattering and Selective Deuteration. J Phys Chem B 2024; 128:405-414. [PMID: 38183282 DOI: 10.1021/acs.jpcb.3c05135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Numerous studies have discussed the impact of cosolvents on the structure, dynamics, and stability of proteins in aqueous solutions. However, the dynamics of cosolvents in the protein-water-cosolvent ternary system is largely unexplored in experiments due to technical difficulty. Consequently, a comprehensive understanding of the interplay among proteins, water, and cosolvents is still lacking. Here, we employed selective deuteration and neutron scattering techniques to characterize the individual motions of each component in the protein/water/glycerol (GLY) mixture across various temperatures. The consistent dynamic onset temperatures and the correlation between the MSD of the protein and the viscosity of solvents revealed the mutual coupling effects among the three components. Furthermore, our experimental and simulation results showed that the hydrogen bond relaxation energy barrier in the ternary system is ∼43 kJ/mol, whereas in the protein-water binary system it is merely ∼35 kJ/mol. Therefore, we suggest that GLY can enhance hydrogen bond interactions in the ternary system through the mutual coupling effect, thereby serving as one of the protective mechanisms of protein preservation by GLY.
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Affiliation(s)
- Yongfeng Ye
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lirong Zheng
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Centre for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, U.K
| | - Nicolas R de Souza
- Australian Nuclear Science and Technology (ANSTO), Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
| | - Dahong Teng
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Bin Wu
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Yichao Xu
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Jinzhen Cai
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Centre for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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2
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Abstract
The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.
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3
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Moreau DW, Atakisi H, Thorne RE. Ice in biomolecular cryocrystallography. Acta Crystallogr D Struct Biol 2021; 77:540-554. [PMID: 33825714 PMCID: PMC8025888 DOI: 10.1107/s2059798321001170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/01/2021] [Indexed: 12/05/2022] Open
Abstract
Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729-727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.
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Affiliation(s)
- David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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4
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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5
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Harrison K, Wu Z, Juers DH. A comparison of gas stream cooling and plunge cooling of macromolecular crystals. J Appl Crystallogr 2019; 52:1222-1232. [PMID: 31636524 PMCID: PMC6782077 DOI: 10.1107/s1600576719010318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/18/2019] [Indexed: 01/17/2023] Open
Abstract
Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.
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Affiliation(s)
- Kaitlin Harrison
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Zhenguo Wu
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Douglas H Juers
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
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6
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Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli. Sci Rep 2019; 9:7087. [PMID: 31068633 PMCID: PMC6506529 DOI: 10.1038/s41598-019-43577-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/27/2019] [Indexed: 01/07/2023] Open
Abstract
4-Hydroxyphenylacetate 3-hydroxylase (EcHpaB) from Escherichia coli is capable of efficient ortho-hydroxylation of a wide range of phenolic compounds and demonstrates great potential for broad chemoenzymatic applications. To understand the structural and mechanistic basis of its catalytic versatility, we elucidated the crystal structure of EcHpaB by X-ray crystallography, which revealed a unique loop structure covering the active site. We further performed mutagenesis studies of this loop to probe its role in substrate specificity and catalytic activity. Our results not only showed the loop has great plasticity and strong tolerance towards extensive mutagenesis, but also suggested a flexible loop that enables the entrance and stable binding of substrates into the active site is the key factor to the enzyme catalytic versatility. These findings lay the groundwork for editing the loop sequence and structure for generation of EcHpaB mutants with improved performance for broader laboratory and industrial use.
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7
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Abstract
Radiation damage inflicted on macromolecular crystals during X-ray diffraction experiments remains a limiting factor for structure solution, even when samples are cooled to cryotemperatures (~100 K). Efforts to establish mitigation strategies are ongoing and various approaches, summarized below, have been investigated over the last 15 years, resulting in a deeper understanding of the physical and chemical factors affecting damage rates. The recent advent of X-ray free electron lasers permits "diffraction-before-destruction" by providing highly brilliant and short (a few tens of fs) X-ray pulses. New fourth generation synchrotron sources now coming on line with higher X-ray flux densities than those available from third generation synchrotrons will bring the issue of radiation damage once more to the fore for structural biologists.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Institut de Biologie Structurale, University of Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38044, Grenoble, France.
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8
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Shen C, Julius EF, Tyree TJ, Moreau DW, Atakisi H, Thorne RE. Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection. Acta Crystallogr D Struct Biol 2016; 72:742-52. [PMID: 27303794 PMCID: PMC8493611 DOI: 10.1107/s2059798316005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/01/2016] [Indexed: 11/10/2022] Open
Abstract
The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%(w/v) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen-argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals.
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Affiliation(s)
- Chen Shen
- Cornell University, Ithaca, NY 14853, USA
| | | | | | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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9
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Pflugrath JW. Practical macromolecular cryocrystallography. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:622-42. [PMID: 26057787 PMCID: PMC4461322 DOI: 10.1107/s2053230x15008304] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022]
Abstract
Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.
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Affiliation(s)
- J W Pflugrath
- Rigaku Americas Corp., 9009 New Trails Drive, The Woodlands, TX 77381, USA
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10
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Ng JD, Baird JK, Coates L, Garcia-Ruiz JM, Hodge TA, Huang S. Large-volume protein crystal growth for neutron macromolecular crystallography. Acta Crystallogr F Struct Biol Commun 2015; 71:358-70. [PMID: 25849493 PMCID: PMC4388167 DOI: 10.1107/s2053230x15005348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/15/2015] [Indexed: 11/10/2022] Open
Abstract
Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.
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Affiliation(s)
- Joseph D. Ng
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- iXpressGenes Inc., Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - James K. Baird
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, MS6475, Oak Ridge, TN 37831, USA
| | - Juan M. Garcia-Ruiz
- Laboratorio de Estudios Cristalográficos (IACT), CSIC–Universidad de Granada, Avenida de la Innovación s/n, Armilla (Granada), Spain
| | - Teresa A. Hodge
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Sijay Huang
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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11
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Luo YC, Wang CH, Wu YM, Liu W, Lu MW, Lin CS. Crystallization and X-ray diffraction of virus-like particles from a piscine betanodavirus. Acta Crystallogr F Struct Biol Commun 2014; 70:1080-6. [PMID: 25084387 PMCID: PMC4118809 DOI: 10.1107/s2053230x14013703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
Dragon grouper nervous necrosis virus (DGNNV), a member of the genus Betanodavirus, causes high mortality of larvae and juveniles of the grouper fish Epinephelus lanceolatus. Currently, there is no reported crystal structure of a fish nodavirus. The DGNNV virion capsid is derived from a single open reading frame that encodes a 338-amino-acid protein of approximately 37 kDa. The capsid protein of DGNNV was expressed to form virus-like particles (VLPs) in Escherichia coli. The VLP shape is T = 3 quasi-symmetric with a diameter of ∼38 nm in cryo-electron microscopy images and is highly similar to the native virion. In this report, crystals of DGNNV VLPs were grown to a size of 0.27 mm within two weeks by the hanging-drop vapour-diffusion method at 283 K and diffracted X-rays to ∼7.5 Å resolution. In-house X-ray diffraction data of the DGNNV VLP crystals showed that the crystals belonged to space group R32, with unit-cell parameters a = b = 353.00, c = 800.40 Å, α = β = 90, γ = 120°. 23 268 unique reflections were acquired with an overall Rmerge of 18.2% and a completeness of 93.2%. Self-rotation function maps confirmed the fivefold, threefold and twofold symmetries of the icosahedron of DGNNV VLPs.
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Affiliation(s)
- Yu-Chun Luo
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chun-Hsiung Wang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yi-Min Wu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Wangta Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Ming-Wei Lu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chan-Shing Lin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
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12
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Wierman JL, Alden JS, Kim CU, McEuen PL, Gruner SM. Graphene as a protein crystal mounting material to reduce background scatter. J Appl Crystallogr 2013; 46:1501-1507. [PMID: 24068843 PMCID: PMC3778323 DOI: 10.1107/s002188981301786x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/28/2013] [Indexed: 11/11/2022] Open
Abstract
The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. This article demonstrates a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects.
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Affiliation(s)
| | - Jonathan S. Alden
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Chae Un Kim
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
| | - Paul L. McEuen
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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13
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Aggarwal M, Boone CD, Kondeti B, Tu C, Silverman DN, McKenna R. Effects of cryoprotectants on the structure and thermostability of the human carbonic anhydrase II-acetazolamide complex. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:860-5. [PMID: 23633596 PMCID: PMC3640473 DOI: 10.1107/s0907444913002771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022]
Abstract
Protein X-ray crystallography has seen a progressive shift from data collection at cool/room temperature (277-298 K) to data collection at cryotemperature (100 K) because of its ease of crystal preparation and the lessening of the detrimental effects of radiation-induced crystal damage, with 20-25%(v/v) glycerol (GOL) being the preferred choice of cryoprotectant. Here, a case study of the effects of cryoprotectants on the kinetics of carbonic anhydrase II (CA II) and its inhibition by the clinically used inhibitor acetazolamide (AZM) is presented. Comparative studies of crystal structure, kinetics, inhibition and thermostability were performed on CA II and its complex with AZM in the presence of either GOL or sucrose. These results suggest that even though the cryoprotectant GOL was previously shown to be directly bound in the active site and to interact with AZM, it affects neither the thermostability of CA II nor the binding of AZM in the crystal structure or in solution. However, addition of GOL does affect the kinetics of CA II, presumably as it displaces the water proton-transfer network in the active site.
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Affiliation(s)
- Mayank Aggarwal
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Christopher D. Boone
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Bhargav Kondeti
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Chingkuang Tu
- Department of Pharmacology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
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14
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Kim CU, Wierman JL, Gillilan R, Lima E, Gruner SM. A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter. J Appl Crystallogr 2012; 46:234-241. [PMID: 23396891 DOI: 10.1107/s0021889812045013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/30/2012] [Indexed: 11/11/2022] Open
Abstract
High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydrated via vapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryo-cooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.
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Affiliation(s)
- Chae Un Kim
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
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15
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Lippa GM, Liberman JA, Jenkins JL, Krucinska J, Salim M, Wedekind JE. Crystallographic analysis of small ribozymes and riboswitches. Methods Mol Biol 2012; 848:159-84. [PMID: 22315069 PMCID: PMC5008910 DOI: 10.1007/978-1-61779-545-9_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribozymes and riboswitches are RNA motifs that accelerate biological reactions and regulate gene expression in response to metabolite recognition, respectively. These RNA molecules gain functionality via complex folding that cannot be predicted a priori, and thus requires high-resolution three-dimensional structure determination to locate key functional attributes. Herein, we present an overview of the methods used to determine small RNA structures with an emphasis on RNA preparation, crystallization, and structure refinement. We draw upon examples from our own research in the analysis of the leadzyme ribozyme, the hairpin ribozyme, a class I preQ(1) riboswitch, and variants of a larger class II preQ(1) riboswitch. The methods presented provide a guide for comparable investigations of noncoding RNA molecules including a 48-solution, "first choice" RNA crystal screen compiled from our prior successes with commercially available screens.
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Affiliation(s)
- Geoffrey M Lippa
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
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16
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Mueller-Dieckmann C, Kauffmann B, Weiss MS. TrimethylamineN-oxide as a versatile cryoprotective agent in macromolecular crystallography. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811000045] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The surge of macromolecular crystallography is intimately linked to the advent of methods for cryoprotecting macromolecular crystals. Only if crystals are kept cold during data collection can they withstand the effects of radiation damage during a diffraction experiment, especially at third-generation synchrotron sources. While a number of different cryoprotective agents and procedures have been described in the literature over the past three decades, it is still a time- and crystal-consuming process to establish and optimize a good cryo-condition for a specific crystal. In this study, trimethylamineN-oxide (TMAO) has been identified as a very versatile cryoprotectant for macromolecular crystals. In a few test cases it was shown that diffraction data collected from crystals treated with TMAO are of very good quality.
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17
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Alcorn T, Juers DH. Progress in rational methods of cryoprotection in macromolecular crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:366-73. [PMID: 20382989 PMCID: PMC2852300 DOI: 10.1107/s090744490903995x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 10/01/2009] [Indexed: 11/11/2022]
Abstract
Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2-13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed.
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Affiliation(s)
- Thomas Alcorn
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Douglas H. Juers
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, WA 99362, USA
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
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Xu J, Xue Y, Skrynnikov NR. Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent. JOURNAL OF BIOMOLECULAR NMR 2009; 45:57-72. [PMID: 19582374 DOI: 10.1007/s10858-009-9336-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 06/06/2009] [Indexed: 05/28/2023]
Abstract
In solution, the correlation time of the overall protein tumbling, tau(R), plays a role of a natural dynamics cutoff-internal motions with correlation times on the order of tau ( R ) or longer cannot be reliably identified on the basis of spin relaxation data. It has been proposed some time ago that the 'observation window' of solution experiments can be expanded by changing the viscosity of solvent to raise the value of tau(R). To further explore this concept, we prepared a series of samples of alpha-spectrin SH3 domain in solvent with increasing concentration of glycerol. In addition to the conventional (15)N labeling, the protein was labeled in the Val, Leu methyl positions ((13)CHD(2) on a deuterated background). The collected relaxation data were used in asymmetric fashion: backbone (15)N relaxation rates were used to determine tau(R) across the series of samples, while methyl (13)C data were used to probe local dynamics (side-chain motions). In interpreting the results, it has been initially suggested that addition of glycerol leads only to increases in tau(R), whereas local motional parameters remain unchanged. Thus the data from multiple samples can be analyzed jointly, with tau(R) playing the role of experimentally controlled variable. Based on this concept, the extended model-free model was constructed with the intent to capture the effect of ns time-scale rotameric jumps in valine and leucine side chains. Using this model, we made a positive identification of nanosecond dynamics in Val-23 where ns motions were already observed earlier. In several other cases, however, only tentative identification was possible. The lack of definitive results was due to the approximate character of the model-contrary to what has been assumed, addition of glycerol led to a gradual 'stiffening' of the protein. This and other observations also shed light on the interaction of the protein with glycerol, which is one of the naturally occurring osmoprotectants. In particular, it has been found that the overall protein tumbling is controlled by the bulk solvent, and not by a thin solvation layer which contains a higher proportion of water.
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Affiliation(s)
- Jun Xu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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Barnard TJ, Wally JL, Buchanan SK. Crystallization of integral membrane proteins. ACTA ACUST UNITED AC 2008; Chapter 17:Unit 17.9. [PMID: 18429311 DOI: 10.1002/0471140864.ps1709s47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Over the last 20 years, the use of X-ray crystallography has become a viable technique for the structure determination of integral membrane proteins. However, standard crystallizaton protocols must be modified to account for difficulties involved in handling membrane proteins, which arise primarily from having detergent present. This unit provides protocols that can be used to crystallize a purified membrane protein, including detergent exchange, sample concentration, initial screening using a crystallization robot, and finally, optimization of crystallization conditions to obtain diffraction-quality crystals. These protocols were established for outer membrane proteins, but can be used for inner membrane proteins as well. Advice on alternative protocols, detergent selection, and optimization of crystallization conditions is provided.
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Abstract
The physical chemistry of crystal growth can help to identify directions in which to look for improved crystal properties. In this chapter, we summarize how crystal growth depends on parameters that can be controlled experimentally, and relate them to the tools available for optimizing a particular crystal form for crystal shape, volume, and diffraction quality. Our purpose is to sketch the conceptual basis of optimization and to provide sample protocols derived from those foundations. We hope to assist even those who chose not to use systematic methods by enabling them to carry out rudimentary optimization searches armed with a better understanding of how the underlying physical chemistry operates.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Brüx C, Niefind K, Ben-David A, Leon M, Shoham G, Shoham Y, Schomburg D. Crystallization and preliminary crystallographic analysis of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1054-7. [PMID: 16511233 PMCID: PMC1978154 DOI: 10.1107/s1744309105036262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 11/04/2005] [Indexed: 11/10/2022]
Abstract
Beta-D-Xylosidases (EC 3.2.1.37) are hemicellulases that cleave single xylose units from the nonreducing end of xylooligomers. In this study, the crystallization and preliminary X-ray analysis of a beta-D-xylosidase from Geobacillus stearothermophilus T-6 (XynB3), a family 43 glycoside hydrolase, is described. XynB3 is a 535-amino-acid protein with a calculated molecular weight of 61 891 Da. Purified recombinant native and catalytic inactive mutant proteins were crystallized and cocrystallized with xylobiose in two different space groups, P2(1)2(1)2 (unit-cell parameters a = 98.32, b = 99.36, c = 258.64 A) and P4(1)2(1)2 (or the enantiomorphic space group P4(3)2(1)2; unit-cell parameters a = b = 140.15, c = 233.11 A), depending on the detergent. Transferring crystals to cryoconditions required a very careful protocol. Orthorhombic crystals diffract to 2.5 A and tetragonal crystals to 2.2 A.
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Affiliation(s)
- Christian Brüx
- Institute for Biochemistry, University of Cologne, Germany
| | | | - Alon Ben-David
- Department of Biotechnology and Food Engineering and Institute of Catalysis Science and Technology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Maya Leon
- Department of Biotechnology and Food Engineering and Institute of Catalysis Science and Technology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Gil Shoham
- Department of Inorganic Chemistry and The Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering and Institute of Catalysis Science and Technology, Technion–Israel Institute of Technology, Haifa, Israel
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Abrahams JP, Ban N. X-Ray Crystallographic Structure Determination of Large Asymmetric Macromolecular Assemblies. Methods Enzymol 2003; 374:163-88. [PMID: 14696373 DOI: 10.1016/s0076-6879(03)74008-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
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