1
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Mehr A, Henneberg F, Chari A, Görlich D, Huyton T. The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography. Acta Crystallogr D Struct Biol 2020; 76:1222-1232. [PMID: 33263328 PMCID: PMC7709198 DOI: 10.1107/s2059798320013741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
The growth of diffraction-quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high-affinity copper(II)-binding tripeptide GHK was fused to the N-terminus of a GFP variant and an MBP-FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square-pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S-atom positions could also be located in log-likelihood-gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR-SAD phasing.
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Affiliation(s)
- Alexander Mehr
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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2
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High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur. Molecules 2019; 24:molecules24244451. [PMID: 31817305 PMCID: PMC6943606 DOI: 10.3390/molecules24244451] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022] Open
Abstract
The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.
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3
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Tsakiridou G, Reppas C, Kuentz M, Kalantzi L. A Novel Rheological Method to Assess Drug-Polymer Interactions Regarding Miscibility and Crystallization of Drug in Amorphous Solid Dispersions for Oral Drug Delivery. Pharmaceutics 2019; 11:pharmaceutics11120625. [PMID: 31766731 PMCID: PMC6955678 DOI: 10.3390/pharmaceutics11120625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/19/2019] [Indexed: 01/18/2023] Open
Abstract
Solid dispersions provide a key technology to formulate poorly water-soluble drugs, and a main task of early development is appropriate selection of polymer. This study investigates the use of a novel rheology-based approach to evaluate miscibility and interactions of drugs with polymers regarding amorphous solid drug dispersions for oral administration. Tacrolimus was used as model drug and hydroxypropyl cellulose, ethylcellulose, Soluplus®, polyethyleneglycol 6000, Poloxamer-188 (Koliphor-188), and Eudragit® S100 were used as excipients. Solvent-based evaporation methods were used to prepare binary solid dispersions of drug and polymer. Data of the dilute solution viscosimetry were compared with in silico calculations of the Hansen solubility parameter (HSP), as well as phase separation/crystallization data obtained from X-ray diffraction and differential scanning calorimetry. HSP calculations in some cases led to false positive predictions of tacrolimus miscibility with the tested polymers. The novel rheology-based method provided valuable insights into drug-polymer interactions and likely miscibility with polymer. It is a rather fast, inexpensive, and robust analytical approach, which could be used complementary to in silico-based evaluation of polymers in early formulation development, especially in cases of rather large active pharmaceutical ingredients.
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Affiliation(s)
- Georgia Tsakiridou
- Department of Scientific Affairs, Pharmathen S/A, 15125 Marousi, Greece;
- Department of Pharmaceutical Sciences, National and Kapodistrian University of Athens, 15784 Zografou, Greece;
| | - Christos Reppas
- Department of Pharmaceutical Sciences, National and Kapodistrian University of Athens, 15784 Zografou, Greece;
| | - Martin Kuentz
- Institute of Pharmaceutical Technology, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland;
| | - Lida Kalantzi
- Department of Scientific Affairs, Pharmathen S/A, 15125 Marousi, Greece;
- Correspondence: ; Tel.: +30-210-66-04-300
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4
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Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCRJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
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5
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Abrahams GJ, Newman J. BLASTing away preconceptions in crystallization trials. Acta Crystallogr F Struct Biol Commun 2019; 75:184-192. [PMID: 30839293 PMCID: PMC6404862 DOI: 10.1107/s2053230x19000141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/04/2019] [Indexed: 11/10/2022] Open
Abstract
Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption. This research investigates whether, given current information, one can detect any correlation between sequence similarity and crystallization cocktails. BLAST was used to quantitate the similarity between protein sequences in the Protein Data Bank, and this was compared with three estimations of the chemical similarities of the respective crystallization cocktails. No correlation was detected between proteins of similar (but not identical) sequence and their crystallization cocktails, suggesting that methods of determining screens based on this assumption are unlikely to result in screens that are better than those currently in use.
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Affiliation(s)
- Gabriel Jan Abrahams
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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6
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Rosa N, Ristic M, Marshall B, Newman J. Cinder: keeping crystallographers app-y. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:410-418. [PMID: 29969104 DOI: 10.1107/s2053230x18008038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 11/10/2022]
Abstract
The process of producing suitable crystals for X-ray diffraction analysis most often involves the setting up of hundreds (or thousands) of individual crystallization trials, each of which must be repeatedly examined for crystals or hints of crystallinity. Currently, the only real way to address this bottleneck is to use an automated imager to capture images of the trials. However, the images still need to be assessed for crystals or other outcomes. Ideally, there would exist some rapid and reliable machine-analysis tool to translate the images into a quantitative result. However, as yet no such tool exists in wide usage, despite this being a well recognized problem. One of the issues in creating robust automatic image-analysis software is the lack of reliable data for training machine-learning algorithms. Here, a mobile application, Cinder, has been developed which allows crystallization images to be scored quickly on a smartphone or tablet. The Cinder scores are inserted into the appropriate table in a crystallization database and are immediately available to the user through a more sophisticated web interface, allowing more detailed analyses. A sharp increase in the number of scored images was observed after Cinder was released, which in turn provides more data for training machine-learning tools.
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Affiliation(s)
- Nicholas Rosa
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Marko Ristic
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Bevan Marshall
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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7
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Bruno AE, Charbonneau P, Newman J, Snell EH, So DR, Vanhoucke V, Watkins CJ, Williams S, Wilson J. Classification of crystallization outcomes using deep convolutional neural networks. PLoS One 2018; 13:e0198883. [PMID: 29924841 PMCID: PMC6010233 DOI: 10.1371/journal.pone.0198883] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
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Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, University at Buffalo, Buffalo, New York, United States of America
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
| | - Janet Newman
- Collaborative Crystallisation Centre, CSIRO, Parkville, Victoria, Australia
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo, Department of Materials, Design, and Innovation, Buffalo, New York, United States of America
| | - David R. So
- Google Brain, Google Inc., Mountain View, California, United States of America
| | - Vincent Vanhoucke
- Google Brain, Google Inc., Mountain View, California, United States of America
| | | | - Shawn Williams
- Platform Technology and Sciences, GlaxoSmithKline Inc., Collegeville, Pennsylvania, United States of America
| | - Julie Wilson
- Department of Mathematics, University of York, York, United Kingdom
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8
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Previtali V, Trujillo C, Boisson JC, Khartabil H, Hénon E, Rozas I. Development of the first model of a phosphorylated, ATP/Mg 2+-containing B-Raf monomer by molecular dynamics simulations: a tool for structure-based design. Phys Chem Chem Phys 2017; 19:31177-31185. [PMID: 29139502 DOI: 10.1039/c7cp05038k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i.e. DFG motif, Mg2+ binding loop, activation loop, phosphorylation site and αC-helix region) were analysed for each trajectory to validate the aimed 2pBRAF_ATP model. Moreover, the structure and activating interactions of this 2pBRAF_ATP model were found to be in agreement with previously reported information. Finally, the model was further validated by means of a molecular docking study with our previously developed lead compound I confirming that this ATP-containing, phosphorylated protein model is suitable for further structure-based design studies.
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Affiliation(s)
- Viola Previtali
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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9
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Altan I, Charbonneau P, Snell EH. Computational crystallization. Arch Biochem Biophys 2016; 602:12-20. [PMID: 26792536 DOI: 10.1016/j.abb.2016.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/22/2015] [Accepted: 01/07/2016] [Indexed: 11/28/2022]
Abstract
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.
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Affiliation(s)
- Irem Altan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Physics, Duke University, Durham, NC 27708, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., NY 14203, USA; Department of Structural Biology, SUNY University of Buffalo, 700 Ellicott St., NY 14203, USA.
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10
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Fusco D, Charbonneau P. Soft matter perspective on protein crystal assembly. Colloids Surf B Biointerfaces 2016; 137:22-31. [DOI: 10.1016/j.colsurfb.2015.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/24/2023]
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11
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Kirkwood J, Hargreaves D, O’Keefe S, Wilson J. Analysis of crystallization data in the Protein Data Bank. Acta Crystallogr F Struct Biol Commun 2015; 71:1228-34. [PMID: 26457511 PMCID: PMC4601584 DOI: 10.1107/s2053230x15014892] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein was investigated and the possibility of predicting whether a protein will crystallize was explored.
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Affiliation(s)
- Jobie Kirkwood
- Department of Chemistry, University of York, York YO10 5DD, England
| | - David Hargreaves
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge CB4 0WG, England
| | - Simon O’Keefe
- Department of Computer Science, University of York, York YO10 5DD, England
| | - Julie Wilson
- Department of Chemistry, University of York, York YO10 5DD, England
- Department of Mathematics, University of York, York YO10 5DD, England
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12
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Malito E, Carfi A, Bottomley MJ. Protein Crystallography in Vaccine Research and Development. Int J Mol Sci 2015; 16:13106-40. [PMID: 26068237 PMCID: PMC4490488 DOI: 10.3390/ijms160613106] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
Abstract
The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.
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Affiliation(s)
- Enrico Malito
- Protein Biochemistry Department, Novartis Vaccines & Diagnostics s.r.l. (a GSK Company), Via Fiorentina 1, 53100 Siena, Italy.
| | - Andrea Carfi
- Protein Biochemistry Department, GSK Vaccines, Cambridge, MA 02139, USA.
| | - Matthew J Bottomley
- Protein Biochemistry Department, Novartis Vaccines & Diagnostics s.r.l. (a GSK Company), Via Fiorentina 1, 53100 Siena, Italy.
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13
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Liu Y, Zhang XF, Zhang CY, Guo YZ, Xie SX, Zhou RB, Cheng QD, Yan EK, Liu YL, Lu XL, Lu QQ, Lu HM, Ye YJ, Yin DC. A protein crystallisation screening kit designed using polyethylene glycol as major precipitant. CrystEngComm 2015. [DOI: 10.1039/c5ce00779h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Ng JT, Dekker C, Kroemer M, Osborne M, von Delft F. Using textons to rank crystallization droplets by the likely presence of crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2702-18. [PMID: 25286854 PMCID: PMC4188010 DOI: 10.1107/s1399004714017581] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/30/2014] [Indexed: 11/10/2022]
Abstract
The visual inspection of crystallization experiments is an important yet time-consuming and subjective step in X-ray crystallography. Previously published studies have focused on automatically classifying crystallization droplets into distinct but ultimately arbitrary experiment outcomes; here, a method is described that instead ranks droplets by their likelihood of containing crystals or microcrystals, thereby prioritizing for visual inspection those images that are most likely to contain useful information. The use of textons is introduced to describe crystallization droplets objectively, allowing them to be scored with the posterior probability of a random forest classifier trained against droplets manually annotated for the presence or absence of crystals or microcrystals. Unlike multi-class classification, this two-class system lends itself naturally to unidirectional ranking, which is most useful for assisting sequential viewing because images can be arranged simply by using these scores: this places droplets with probable crystalline behaviour early in the viewing order. Using this approach, the top ten wells included at least one human-annotated crystal or microcrystal for 94% of the plates in a data set of 196 plates imaged with a Minstrel HT system. The algorithm is robustly transferable to at least one other imaging system: when the parameters trained from Minstrel HT images are applied to a data set imaged by the Rock Imager system, human-annotated crystals ranked in the top ten wells for 90% of the plates. Because rearranging images is fundamental to the approach, a custom viewer was written to seamlessly support such ranked viewing, along with another important output of the algorithm, namely the shape of the curve of scores, which is itself a useful overview of the behaviour of the plate; additional features with known usefulness were adopted from existing viewers. Evidence is presented that such ranked viewing of images allows faster but more accurate evaluation of drops, in particular for the identification of microcrystals.
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Affiliation(s)
- Jia Tsing Ng
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Carien Dekker
- Novartis Institute for Biomedical Research, Novartis Campus, Postfach, CH-4056 Basel, Switzerland
| | - Markus Kroemer
- Novartis Institute for Biomedical Research, Novartis Campus, Postfach, CH-4056 Basel, Switzerland
| | - Michael Osborne
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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15
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Fazio VJ, Peat TS, Newman J. A drunken search in crystallization space. Acta Crystallogr F Struct Biol Commun 2014; 70:1303-11. [PMID: 25286930 PMCID: PMC4188070 DOI: 10.1107/s2053230x1401841x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022] Open
Abstract
The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition.
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Affiliation(s)
- Vincent J. Fazio
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S. Peat
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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16
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Fusco D, Barnum TJ, Bruno AE, Luft JR, Snell EH, Mukherjee S, Charbonneau P. Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. PLoS One 2014; 9:e101123. [PMID: 24988076 PMCID: PMC4079662 DOI: 10.1371/journal.pone.0101123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.
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Affiliation(s)
- Diana Fusco
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
| | - Timothy J. Barnum
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew E. Bruno
- Center for Computational Research, State University of New York, Buffalo, New York, United States of America
| | - Joseph R. Luft
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
| | - Sayan Mukherjee
- Department of Statistical Science, Department of Computer Science and Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
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17
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Luft JR, Newman J, Snell EH. Crystallization screening: the influence of history on current practice. Acta Crystallogr F Struct Biol Commun 2014; 70:835-53. [PMID: 25005076 PMCID: PMC4089519 DOI: 10.1107/s2053230x1401262x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/30/2014] [Indexed: 11/17/2022] Open
Abstract
While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.
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Affiliation(s)
- Joseph R. Luft
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Janet Newman
- CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, SUNY Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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18
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Bruno AE, Ruby AM, Luft JR, Grant TD, Seetharaman J, Montelione GT, Hunt JF, Snell EH. Comparing chemistry to outcome: the development of a chemical distance metric, coupled with clustering and hierarchal visualization applied to macromolecular crystallography. PLoS One 2014; 9:e100782. [PMID: 24971458 PMCID: PMC4074061 DOI: 10.1371/journal.pone.0100782] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/28/2014] [Indexed: 11/18/2022] Open
Abstract
Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields.
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Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, State University of New York (SUNY), Buffalo, New York, United States of America
| | - Amanda M. Ruby
- Center for Computational Research, State University of New York (SUNY), Buffalo, New York, United States of America
| | - Joseph R. Luft
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo Dept. of Structural Biology, Buffalo, New York, United States of America
| | - Thomas D. Grant
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Jayaraman Seetharaman
- Department of Biological Sciences, The Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - John F. Hunt
- Department of Biological Sciences, The Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo Dept. of Structural Biology, Buffalo, New York, United States of America
- * E-mail:
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19
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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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20
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Newman J, Burton DR, Caria S, Desbois S, Gee CL, Fazio VJ, Kvansakul M, Marshall B, Mills G, Richter V, Seabrook SA, Wu M, Peat TS. Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine? Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:712-8. [PMID: 23832194 PMCID: PMC3702311 DOI: 10.1107/s1744309113014152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/21/2013] [Indexed: 11/10/2022]
Abstract
Crystallization of macromolecules is famously difficult. By knowing what has worked for others, researchers can ease the process, both in the case where the protein has already been crystallized and in the situation where more general guidelines are needed. The 264 crystallization communications published in Acta Crystallographica Section F in 2012 have been reviewed, and from this analysis some information about trends in crystallization has been gleaned. More importantly, it was found that there are several ways in which the utility of these communications could be increased: to make each individual paper a more complete crystallization record; and to provide a means for taking a snapshot of what the current `best practices' are in the field.
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Affiliation(s)
- Janet Newman
- Materials, Science and Engineering Division, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.
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21
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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22
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Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ. The role of structural bioinformatics resources in the era of integrative structural biology. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:710-21. [PMID: 23633580 PMCID: PMC3640467 DOI: 10.1107/s0907444913001157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/11/2013] [Indexed: 11/10/2022]
Abstract
The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that the role of structural biology archives will change from being a pure repository of historic data into becoming an indispensable resource for the wider biomedical community. As part of this transformation, it will be necessary to validate the biomacromolecular structure data and ensure the highest possible quality for the archive holdings, to combine structural data from different spatial scales into a unified resource and to integrate structural data with functional, genetic and taxonomic data as well as other information available in bioinformatics resources. Some recent developments and plans to address these challenges at PDBe are presented.
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Affiliation(s)
- Aleksandras Gutmanas
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Thomas J. Oldfield
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Ardan Patwardhan
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Sanchayita Sen
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Sameer Velankar
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Gerard J. Kleywegt
- Protein Data Bank in Europe, EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
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Desbois S, Seabrook SA, Newman J. Some practical guidelines for UV imaging in the protein crystallization laboratory. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:201-8. [PMID: 23385768 PMCID: PMC3564629 DOI: 10.1107/s1744309112048634] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/27/2012] [Indexed: 04/24/2023]
Abstract
High-throughput imaging of protein crystallization experiments with ultraviolet (UV) light has recently become commercially available and can enable crystallographers to differentiate between crystals of protein and those of salt, as the visualization of protein crystals is based on intrinsic tryptophan fluorescence. Unfortunately, UV imaging is not a panacea, as some protein crystals will not fluoresce under UV excitation and some salt crystals are UV-fluorescently active. As a new technology, there is little experience within the general community on how to use this technology effectively and what caveats to look out for. Here, an attempt is made to identify some of the common problems that may arise using UV-imaging technology by examining test proteins, common crystallization reagents and a range of proteins by assessing their UV-Vis absorbance spectra. Some pointers are offered as to which systems may not be appropriate for this methodology.
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Affiliation(s)
- Sebastien Desbois
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Shane A. Seabrook
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- CSIRO Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia
- Correspondence e-mail:
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24
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Einspahr H, Weiss MS. Call for a crystallization ontology. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:252. [PMID: 22442215 PMCID: PMC3310523 DOI: 10.1107/s174430911200680x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 11/17/2022]
Abstract
Editorial.
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Affiliation(s)
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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