51
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Wu L, Jiang J, Jin Y, Kallemeijn WW, Kuo CL, Artola M, Dai W, van Elk C, van Eijk M, van der Marel GA, Codée JDC, Florea BI, Aerts JMFG, Overkleeft HS, Davies GJ. Activity-based probes for functional interrogation of retaining β-glucuronidases. Nat Chem Biol 2017; 13:867-873. [PMID: 28581485 DOI: 10.1038/nchembio.2395] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/10/2017] [Indexed: 02/06/2023]
Abstract
Humans express at least two distinct β-glucuronidase enzymes that are involved in disease: exo-acting β-glucuronidase (GUSB), whose deficiency gives rise to mucopolysaccharidosis type VII, and endo-acting heparanase (HPSE), whose overexpression is implicated in inflammation and cancers. The medical importance of these enzymes necessitates reliable methods to assay their activities in tissues. Herein, we present a set of β-glucuronidase-specific activity-based probes (ABPs) that allow rapid and quantitative visualization of GUSB and HPSE in biological samples, providing a powerful tool for dissecting their activities in normal and disease states. Unexpectedly, we find that the supposedly inactive HPSE proenzyme proHPSE is also labeled by our ABPs, leading to surprising insights regarding structural relationships between proHPSE, mature HPSE, and their bacterial homologs. Our results demonstrate the application of β-glucuronidase ABPs in tracking pathologically relevant enzymes and provide a case study of how ABP-driven approaches can lead to discovery of unanticipated structural and biochemical functionality.
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Affiliation(s)
- Liang Wu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Jianbing Jiang
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Yi Jin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Wouter W Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Chi-Lin Kuo
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Marta Artola
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Wei Dai
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cas van Elk
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Marco van Eijk
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gijsbert A van der Marel
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Jeroen D C Codée
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bogdan I Florea
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Herman S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
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52
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Wang R, Wu J, Jin DK, Chen Y, Lv Z, Chen Q, Miao Q, Huo X, Wang F. Structure of NADP +-bound 7β-hydroxysteroid dehydrogenase reveals two cofactor-binding modes. Acta Crystallogr F Struct Biol Commun 2017; 73:246-252. [PMID: 28471355 PMCID: PMC5417313 DOI: 10.1107/s2053230x17004460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/21/2017] [Indexed: 03/27/2024] Open
Abstract
In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP+ bound to dimeric 7β-HSDH is presented. In one active site, NADP+ adopts a conventional binding mode similar to that displayed in related enzyme structures. However, in the other active site a unique binding mode is observed in which the orientation of the nicotinamide is different. Since 7β-HSDH has become an attractive target owing to the wide and important pharmaceutical use of its product ursodeoxycholic acid, this work provides a more detailed template to support rational protein engineering to improve the enzymatic activities of this useful biocatalyst, further improving the yield of ursodeoxycholic acid and its other applications.
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Affiliation(s)
- Rui Wang
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Jiaquan Wu
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - David Kin Jin
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Yali Chen
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Zhijia Lv
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Qian Chen
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Qiwei Miao
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Xiaoyu Huo
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
| | - Feng Wang
- Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People’s Republic of China
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53
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Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY. Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J Biol Chem 2017; 292:4789-4800. [PMID: 28179425 DOI: 10.1074/jbc.m116.763821] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/11/2017] [Indexed: 01/27/2023] Open
Abstract
Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases. The X-ray crystal structures of 103S_EGCase I alone and in complex with its substrates monosialodihexosylganglioside (GM3) and monosialotetrahexosylganglioside (GM1) enabled us to identify several structural features that may account for its broad specificity. Compared with EGCase II from Rhodococcus sp. M-777 (M777_EGCase II), which possesses strict substrate specificity, 103S_EGCase I possesses a longer α7-helix and a shorter loop 4, which forms a larger substrate-binding pocket that could accommodate more extended oligosaccharides. In addition, loop 2 and loop 8 of the enzyme adopt a more open conformation, which also enlarges the oligosaccharide-binding cavity. Based on this knowledge, a rationally designed experiment was performed to examine the substrate specificity of EGCase II. The truncation of loop 4 in M777_EGCase II increased its activity toward GM1 (163%). Remarkably, the S63G mutant of M777_EGCase II showed a broader substrate spectra and significantly increased activity toward bulky substrates (up to >1370-fold for fucosyl-GM1). Collectively, the results presented here reveal the exquisite substrate recognition mechanism of EGCases and provide an opportunity for further engineering of these enzymes.
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Affiliation(s)
- Yun-Bin Han
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,the Shanghai Institute for Advanced Immunological Studies, ShanghaiTech University, Shanghai 200031, China, and
| | - Liu-Qing Chen
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Li
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Meng Tan
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- From the State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China, .,the Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai 200237, China
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54
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Müller I. Guidelines for the successful generation of protein-ligand complex crystals. Acta Crystallogr D Struct Biol 2017; 73:79-92. [PMID: 28177304 PMCID: PMC5297911 DOI: 10.1107/s2059798316020271] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/21/2016] [Indexed: 11/23/2022] Open
Abstract
With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein-ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting.
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Affiliation(s)
- Ilka Müller
- Structural Biology, Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, England
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55
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Bindels DS, Haarbosch L, van Weeren L, Postma M, Wiese KE, Mastop M, Aumonier S, Gotthard G, Royant A, Hink MA, Gadella TWJ. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat Methods 2017; 14:53-56. [PMID: 27869816 DOI: 10.1038/nmeth.4074] [Citation(s) in RCA: 616] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/20/2016] [Indexed: 12/24/2022]
Abstract
We report the engineering of mScarlet, a truly monomeric red fluorescent protein with record brightness, quantum yield (70%) and fluorescence lifetime (3.9 ns). We developed mScarlet starting with a consensus synthetic template and using improved spectroscopic screening techniques; mScarlet's crystal structure reveals a planar and rigidified chromophore. mScarlet outperforms existing red fluorescent proteins as a fusion tag, and it is especially useful as a Förster resonance energy transfer (FRET) acceptor in ratiometric imaging.
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Affiliation(s)
- Daphne S Bindels
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Lindsay Haarbosch
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura van Weeren
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marten Postma
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Katrin E Wiese
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Mastop
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Guillaume Gotthard
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France
| | - Mark A Hink
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Theodorus W J Gadella
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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56
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Pernigo S, Fukuzawa A, Beedle AEM, Holt M, Round A, Pandini A, Garcia-Manyes S, Gautel M, Steiner RA. Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection. Structure 2016; 25:107-120. [PMID: 27989621 PMCID: PMC5222588 DOI: 10.1016/j.str.2016.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/16/2016] [Accepted: 11/18/2016] [Indexed: 12/03/2022]
Abstract
The sarcomeric cytoskeleton is a network of modular proteins that integrate mechanical and signaling roles. Obscurin, or its homolog obscurin-like-1, bridges the giant ruler titin and the myosin crosslinker myomesin at the M-band. Yet, the molecular mechanisms underlying the physical obscurin(-like-1):myomesin connection, important for mechanical integrity of the M-band, remained elusive. Here, using a combination of structural, cellular, and single-molecule force spectroscopy techniques, we decode the architectural and functional determinants defining the obscurin(-like-1):myomesin complex. The crystal structure reveals a trans-complementation mechanism whereby an incomplete immunoglobulin-like domain assimilates an isoform-specific myomesin interdomain sequence. Crucially, this unconventional architecture provides mechanical stability up to forces of ∼135 pN. A cellular competition assay in neonatal rat cardiomyocytes validates the complex and provides the rationale for the isoform specificity of the interaction. Altogether, our results reveal a novel binding strategy in sarcomere assembly, which might have implications on muscle nanomechanics and overall M-band organization. The structure of the human obscurin-like-1:myomesin complex has been determined A myomesin sequence complements an immunoglobulin fold of obscurin-like-1 This binding mechanism provides mechanical stability up to forces of ∼135 pN Possible implications on muscle nanomechanics and M-band organization are discussed
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Affiliation(s)
- Stefano Pernigo
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Atsushi Fukuzawa
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Cardiovascular Division, King's College London BHF Centre of Research Excellence, London SE1 1UL, UK
| | - Amy E M Beedle
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Department of Physics, King's College London, London WC2R 2LS, UK
| | - Mark Holt
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Cardiovascular Division, King's College London BHF Centre of Research Excellence, London SE1 1UL, UK
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France; School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, UK
| | - Alessandro Pandini
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Department of Computer Science and Synthetic Biology Theme, Brunel University London, London UB8 3PH, UK
| | - Sergi Garcia-Manyes
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Mathias Gautel
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Cardiovascular Division, King's College London BHF Centre of Research Excellence, London SE1 1UL, UK.
| | - Roberto A Steiner
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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57
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Hendrick AG, Müller I, Willems H, Leonard PM, Irving S, Davenport R, Ito T, Reeves J, Wright S, Allen V, Wilkinson S, Heffron H, Bazin R, Turney J, Mitchell PJ. Identification and Investigation of Novel Binding Fragments in the Fatty Acid Binding Protein 6 (FABP6). J Med Chem 2016; 59:8094-102. [PMID: 27500412 DOI: 10.1021/acs.jmedchem.6b00869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fatty acid binding protein 6 (FABP6) is a potential drug discovery target, which, if inhibited, may have a therapeutic benefit for the treatment of diabetes. Currently, there are no published inhibitors of FABP6, and with the target believed to be amenable to fragment-based drug discovery, a structurally enabled program was initiated. This program successfully identified fragment hits using the surface plasmon resonance (SPR) platform. Several hits were validated with SAR and were found to be displaced by the natural ligand taurocholate. We report the first crystal structure of human FABP6 in the unbound form, in complex with cholate, and with one of the key fragments.
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Affiliation(s)
- Alan G Hendrick
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Ilka Müller
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Henriëtte Willems
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Philip M Leonard
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Steve Irving
- Charles River , Ingram Building, Parkwood Road, Canterbury, Kent CT2 7NH, United Kingdom
| | - Richard Davenport
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Takashi Ito
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa 251-8555, Japan
| | - Jenny Reeves
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Susanne Wright
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Vivienne Allen
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Stephen Wilkinson
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Helen Heffron
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Richard Bazin
- Charles River , Ingram Building, Parkwood Road, Canterbury, Kent CT2 7NH, United Kingdom
| | - Jennifer Turney
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Philip J Mitchell
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
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58
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Anandapadamanaban M, Pilstål R, Andresen C, Trewhella J, Moche M, Wallner B, Sunnerhagen M. Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression. Structure 2016; 24:1311-1321. [DOI: 10.1016/j.str.2016.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/20/2016] [Accepted: 06/05/2016] [Indexed: 12/01/2022]
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59
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Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol 2016; 72:603-15. [PMID: 27139624 PMCID: PMC4854312 DOI: 10.1107/s2059798316001546] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.
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Affiliation(s)
- Hilary P. Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ieva Sutkeviciute
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shelley Reynolds
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ying Wu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | | | - Alexander M. Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Robert Lawrence
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Emily Lamm
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Lisa Clark
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Craig M. Ogata
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 60439, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Angela M. Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jean-Pierre Vilardaga
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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60
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Kolek SA, Bräuning B, Shaw Stewart PD. A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase. Acta Crystallogr F Struct Biol Commun 2016; 72:307-12. [PMID: 27050265 PMCID: PMC4822988 DOI: 10.1107/s2053230x16004118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/10/2016] [Indexed: 11/10/2022] Open
Abstract
Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crystallization. Seed crystals are grown directly in LCP and, as with conventional rMMS, a seeding experiment is combined with an additive experiment. The new method was used with the bacterial integral membrane protein OmpF, and it was found that it increased the number of crystallization hits by almost an order of magnitude: without microseeding one new hit was found, whereas with LCP-rMMS eight new hits were found. It is anticipated that this new method will lead to better diffracting crystals of membrane proteins. A method of generating seed gradients, which allows the LCP seed stock to be diluted and the number of crystals in each LCP bolus to be reduced, if required for optimization, is also demonstrated.
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Affiliation(s)
| | - Bastian Bräuning
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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61
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Rose JP, Wang BC. SAD phasing: History, current impact and future opportunities. Arch Biochem Biophys 2016; 602:80-94. [PMID: 27036852 DOI: 10.1016/j.abb.2016.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/17/2023]
Abstract
Single wavelength anomalous diffraction (SAD) can trace its beginnings to the early 1950s. Researchers at the time recognized that SAD offers some unique features that might be advantageous for crystallographic phasing, despite the fact that at that time recording accurate SAD data was problematic. In this review we will follow the trail from those early days, highlighting key advances in the field and interpreting them in terms on how they stimulated continued phasing development that produced the theoretical foundation for the routine macromolecular structure determination by SAD today. The technological advances over the past three decades in both hardware and software, which played a significant role in making SAD phasing a 'first choice method', will also be described.
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Affiliation(s)
- John P Rose
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R. NMR-Based Determination of the 3D Structure of the Ligand-Protein Interaction Site without Protein Resonance Assignment. J Am Chem Soc 2016; 138:4393-400. [PMID: 26943491 DOI: 10.1021/jacs.5b12391] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not available for NMR. Here, we establish a comparable method, called NMR molecular replacement (NMR(2)). The method requires experimentally measured ligand intramolecular NOEs and ligand-protein intermolecular NOEs as well as a previously known receptor structure or model. Our findings demonstrate that NMR(2) may open a new avenue for the fast and robust determination of the interaction site of ligand-protein complexes at atomic resolution.
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Affiliation(s)
- Julien Orts
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - May Marsh
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis AG , CH-4002 Basel, Switzerland
| | - Peter Güntert
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main , Frankfurt am Main 60323, Germany
| | - Roland Riek
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Dinç I, Pusey ML, Aygün RS. Optimizing Associative Experimental Design for Protein Crystallization Screening. IEEE Trans Nanobioscience 2016; 15:101-12. [PMID: 26955046 PMCID: PMC4898777 DOI: 10.1109/tnb.2016.2536030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The goal of protein crystallization screening is the determination of the main factors of importance to crystallizing the protein under investigation. One of the major issues about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for maximizing the chances of a successful (crystalline) outcome. In this paper, we propose an experimental design method called "Associative Experimental Design (AED)" and an optimization method includes eliminating prohibited combinations and prioritizing reagents based on AED analysis of results from protein crystallization experiments. AED generates candidate cocktails based on these initial screening results. These results are analyzed to determine those screening factors in chemical space that are most likely to lead to higher scoring outcomes, crystals. We have tested AED on three proteins derived from the hyperthermophile Thermococcus thioreducens, and we applied an optimization method to these proteins. Our AED method generated novel cocktails (count provided in parentheses) leading to crystals for three proteins as follows: Nucleoside diphosphate kinase (4), HAD superfamily hydrolase (2), Nucleoside kinase (1). After getting promising results, we have tested our optimization method on four different proteins. The AED method with optimization yielded 4, 3, and 20 crystalline conditions for holo Human Transferrin, archaeal exosome protein, and Nucleoside diphosphate kinase, respectively.
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Affiliation(s)
- Imren Dinç
- DataMedia Research Lab, Computer Science Department, University of Alabama in Huntsville, Huntsville, Alabama 35899 USA
| | - Marc L. Pusey
- iXpressGenes, Inc., 601 Genome Way, Huntsville, Alabama 35806 USA
| | - Ramazan S. Aygün
- DataMedia Research Lab, Computer Science Department, University of Alabama in Huntsville, Huntsville, Alabama 35899 USA
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64
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Gavira JA. Current trends in protein crystallization. Arch Biochem Biophys 2015; 602:3-11. [PMID: 26747744 DOI: 10.1016/j.abb.2015.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. SYNOPSIS Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda. de las Palmeras, 4. 18100 Armilla, Granada, Spain
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Rumpf T, Gerhardt S, Einsle O, Jung M. Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking. Acta Crystallogr F Struct Biol Commun 2015; 71:1498-510. [PMID: 26625292 PMCID: PMC4666478 DOI: 10.1107/s2053230x15019986] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/22/2015] [Indexed: 12/30/2022] Open
Abstract
Sirtuins constitute a family of NAD(+)-dependent enzymes that catalyse the cleavage of various acyl groups from the ℇ-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. To date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2-ADPR-indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.
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Affiliation(s)
- Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstrasse 25, 79104 Freiburg, Baden-Württemberg, Germany
| | - Stefan Gerhardt
- Institute of Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104 Freiburg, Baden-Württemberg, Germany
| | - Oliver Einsle
- Institute of Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Albertstrasse 21, 79104 Freiburg, Baden-Württemberg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstrasse 25, 79104 Freiburg, Baden-Württemberg, Germany
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66
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Successful generation of structural information for fragment-based drug discovery. Drug Discov Today 2015; 20:1104-11. [DOI: 10.1016/j.drudis.2015.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/12/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
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Rupp B. Origin and use of crystallization phase diagrams. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:247-60. [PMID: 25760697 DOI: 10.1107/s2053230x1500374x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/23/2015] [Indexed: 11/10/2022]
Abstract
Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably displayed in a phase diagram, and imagination may start to conflict with thermodynamic realities. Here, the commonly used `crystallization phase diagrams' are derived from thermodynamic excess properties and their limitations and appropriate use is discussed.
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Affiliation(s)
- Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
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Caffrey M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:3-18. [PMID: 25615961 PMCID: PMC4304740 DOI: 10.1107/s2053230x14026843] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/05/2014] [Indexed: 01/12/2023]
Abstract
A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.
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Affiliation(s)
- Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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McPherson A, Cudney B. Optimization of crystallization conditions for biological macromolecules. Acta Crystallogr F Struct Biol Commun 2014; 70:1445-67. [PMID: 25372810 PMCID: PMC4231845 DOI: 10.1107/s2053230x14019670] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 08/31/2014] [Indexed: 11/11/2022] Open
Abstract
For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Bob Cudney
- Hampton Research, 34 Journey, Aliso Viejo, CA 92656-3317, USA
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