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Hou H, Wang B, Xie PP, Guo YZ, Li J, Yin DC. Combined cross-diffusion microbatch method and seeding technique to enhance protein crystallization based on a common dispersing agent. CrystEngComm 2017. [DOI: 10.1039/c7ce00664k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hou H, Liu Y, Wang B, Jiang F, Tao HR, Hu SY, Yin DC. Recrystallization: a method to improve the quality of protein crystals. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715005129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.
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Pechkova E, Bragazzi NL, Nicolini C. Advances in nanocrystallography as a proteomic tool. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:163-91. [PMID: 24985772 DOI: 10.1016/b978-0-12-800453-1.00005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.
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Affiliation(s)
- Eugenia Pechkova
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy
| | - Nicola Luigi Bragazzi
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Claudio Nicolini
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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Crystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases. PLoS One 2013; 8:e56138. [PMID: 23457513 PMCID: PMC3573020 DOI: 10.1371/journal.pone.0056138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 01/05/2013] [Indexed: 11/19/2022] Open
Abstract
Background Ruminococcus flavefaciens is one of the predominant fiber-degrading bacteria found in the rumen of herbivores. Bioinformatic analysis of the recently sequenced genome indicated that this bacterium produces one of the most intricate cellulosome systems known to date. A distinct ORF, encoding for a multi-modular protein, RflaF_05439, was discovered during mining of the genome sequence. It is composed of two tandem modules of currently undefined function that share 45% identity and a C-terminal X-dockerin modular dyad. Gaining insight into the diversity, architecture and organization of different types of proteins in the cellulosome system is essential for broadening our understanding of a multi-enzyme complex, considered to be one of the most efficient systems for plant cell wall polysaccharide degradation in nature. Methodology/Principal Findings Following bioinformatic analysis, the second tandem module of RflaF_05439 was cloned and its selenium-labeled derivative was expressed and crystallized. The crystals belong to space group P21 with unit-cell parameters of a = 65.81, b = 60.61, c = 66.13 Å, β = 107.66° and contain two protein molecules in the asymmetric unit. The crystal structure was determined at 1.38-Å resolution by X-ray diffraction using the single-wavelength anomalous dispersion (SAD) method and was refined to Rfactor and Rfree of 0.127 and 0.152 respectively. The protein molecule mainly comprises a β-sheet flanked by short α-helixes, and a globular α-helical domain. The structure was found to be structurally similar to members of the NlpC/P60 superfamily of cysteine peptidases. Conclusions/Significance The 3D structure of the second repeat of the RflaF_05439 enabled us to propose a role for the currently undefined function of this protein. Its putative function as a cysteine peptidase is inferred from in silico structural homology studies. It is therefore apparent that cellulosomes integrate proteins with other functions in addition to the classic well-defined carbohydrate active enzymes.
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DeWalt EL, Begue VJ, Ronau JA, Sullivan SZ, Das C, Simpson GJ. Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:74-81. [PMID: 23275165 PMCID: PMC3532131 DOI: 10.1107/s0907444912042503] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/10/2012] [Indexed: 11/11/2022]
Abstract
Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals.
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Affiliation(s)
- Emma L. DeWalt
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Victoria J. Begue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Shane Z. Sullivan
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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Chayen NE. High-throughput protein crystallization. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 77:1-22. [PMID: 20663479 DOI: 10.1016/s1876-1623(09)77001-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Structural genomics projects have led to great progress in the field of structural biology. Considerable advances have been made in the automation of all stages of the pipeline from clone to structure. This chapter focuses on crystallization that is one of the major bottlenecks in this pipeline. It discusses new developments and describes a variety of techniques for high-throughput screening and optimizing of conditions for crystallization.
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Affiliation(s)
- Naomi E Chayen
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
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Brostromer E, Nan J, Li LF, Su XD. Solid-liquid interface method (SLIM): a new crystallization method for proteins. Biochem Biophys Res Commun 2009; 386:634-8. [PMID: 19545537 DOI: 10.1016/j.bbrc.2009.06.086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Accepted: 06/16/2009] [Indexed: 11/30/2022]
Abstract
Despite impressive advances in theories, methods and technologies, crystallization still remains a serious bottleneck in structural determination of macromolecules. Here we present a novel solid-liquid interface method (SLIM) for protein crystallization, based on the pre-adding and drying of a crystallization reagent, and thereafter the dispensing of a protein solution to the dried media to initiate crystallization from the solid-liquid interface. Not only quick and easy to perform, the method also allows for a less concentrated protein solution for setting up crystallization trials.
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Affiliation(s)
- Erik Brostromer
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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Fromme P, Grotjohann I. Chapter 9 Crystallization of Photosynthetic Membrane Proteins. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)63009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Chayen NE, Saridakis E. Protein crystallization: from purified protein to diffraction-quality crystal. Nat Methods 2008; 5:147-53. [DOI: 10.1038/nmeth.f.203] [Citation(s) in RCA: 262] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Benvenuti M, Mangani S. Crystallization of soluble proteins in vapor diffusion for x-ray crystallography. Nat Protoc 2007; 2:1633-51. [PMID: 17641629 DOI: 10.1038/nprot.2007.198] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The preparation of protein single crystals represents one of the major obstacles in obtaining the detailed 3D structure of a biological macromolecule. The complete automation of the crystallization procedures requires large investments in terms of money and labor, which are available only to large dedicated infrastructures and is mostly suited for genomic-scale projects. On the other hand, many research projects from departmental laboratories are devoted to the study of few specific proteins. Here, we try to provide a series of protocols for the crystallization of soluble proteins, especially the difficult ones, tailored for small-scale research groups. An estimate of the time needed to complete each of the steps described can be found at the end of each section.
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Affiliation(s)
- Manuela Benvenuti
- Dipartimento di Chimica, Università di Siena, Via Aldo Moro 2, Siena 53100, Italy
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Abstract
The main effort in the area of crystallization for structural genomics is currently being invested in automation of high-throughput screening procedures to identify potential crystallization conditions. However, screening in itself, even in massive quantities, is not enough; it has to be complemented by an equally important procedure in crystal production, namely crystal optimization. This chapter describes optimization methods for turning low-quality crystals into useful diffracting ones and presents practical ways of automating such methods and adapting them to high throughput. The methods enable the control of the crystallization environment as the trial takes place. They include the use of oils, gels, and the uncoupling of the nucleation and growth phases of crystallization.
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Affiliation(s)
- Naomi E Chayen
- Biological Structure and Function Section, Division of Biomedical Sciences, Imperial College, London, United Kingdom
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Williams SP, Kuyper LF, Pearce KH. Recent applications of protein crystallography and structure-guided drug design. Curr Opin Chem Biol 2005; 9:371-80. [PMID: 16006182 DOI: 10.1016/j.cbpa.2005.06.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/22/2005] [Indexed: 10/25/2022]
Abstract
Technological advances to increase the throughput of purified protein production and co-crystallization of target proteins with small molecules have helped to solidify the role that structure via crystallography has on drug discovery. Visualization of how drug-like molecules bind to the target protein is a key step in driving follow-up or preclinical chemistry to improve characteristics of the molecule. Using structural information to guide small-molecule design and generate new chemical ideas is now a mainstay in the drug discovery process.
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Affiliation(s)
- Shawn P Williams
- Department of Computational, Analytical and Structural Sciences, GlaxoSmithKline Discovery Research, Research Triangle Park, NC 27709, USA
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Mayo CJ, Diprose JM, Walter TS, Berry IM, Wilson J, Owens RJ, Jones EY, Harlos K, Stuart DI, Esnouf RM. Benefits of automated crystallization plate tracking, imaging, and analysis. Structure 2005; 13:175-82. [PMID: 15698562 DOI: 10.1016/j.str.2004.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 12/16/2004] [Accepted: 12/17/2004] [Indexed: 11/26/2022]
Abstract
We describe the design of a database and software for managing and organizing protein crystallization data. We also outline the considerations behind the design of a fast web interface linking protein production data, crystallization images, and automated image analysis. The database and associated interfaces underpin the Oxford Protein Production Facility (OPPF) crystallization laboratory, collecting, in a routine and automatic manner, up to 100,000 images per day. Over 17 million separate images are currently held in this database. We discuss the substantial scientific benefits automated tracking, imaging, and analysis of crystallizations offers to the structural biologist: analysis of the time course of the trial and easy analysis of trials with related crystallization conditions. Features of this system address requirements common to many crystallographic laboratories that are currently setting up (semi-)automated crystallization imaging systems.
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Affiliation(s)
- Christopher J Mayo
- The Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
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Schmid MB. Seeing is believing: the impact of structural genomics on antimicrobial drug discovery. Nat Rev Microbiol 2004; 2:739-46. [PMID: 15372084 DOI: 10.1038/nrmicro978] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, the availability of complete microbial genome sequences has led to changes in the strategies that are used to search for novel anti-infectives. However, despite the identification of many new potential drug targets, novel antimicrobial agents have been slow to emerge from these efforts. In part, this reflects the long discovery and development times that are needed to bring new drugs to market and the bottlenecks at the stages of identifying good lead compounds and optimizing these leads into drug candidates. Structural genomics will hopefully provide opportunities to overcome these bottlenecks and populate the antimicrobial pipeline.
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Affiliation(s)
- Molly B Schmid
- MBS Associates, 38 Avenue Road, Suite 601, Toronto, Ontario M5R 2G2, Canada.
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Stojanoff V. A novel approach to high-throughput screening; a solution for structural genomics? Structure 2004; 12:1127-8. [PMID: 15242588 DOI: 10.1016/j.str.2004.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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