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Crystallization: Digging into the Past to Learn Lessons for the Future

Published on Jan 1, 2015in Methods of Molecular Biology
· DOI :10.1007/978-1-4939-2230-7_8
Vincent J. Fazio7
Estimated H-index: 7
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Thomas S. Peat22
Estimated H-index: 22
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
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  • References (52)
  • Citations (2)
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References52
Newest
Vincent J. Fazio7
Estimated H-index: 7
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Thomas S. Peat22
Estimated H-index: 22
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
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 abou...
A. D'Arcy10
Estimated H-index: 10
(Actelion),
Terese Bergfors19
Estimated H-index: 19
(Uppsala University)
+ 1 AuthorsMay Marsh13
Estimated H-index: 13
(Paul Scherrer Institute)
Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications fro...
Samad Jahandideh12
Estimated H-index: 12
(Sanford-Burnham Institute for Medical Research),
Lukasz Jaroszewski21
Estimated H-index: 21
(UCSD: University of California, San Diego),
Adam Godzik57
Estimated H-index: 57
(UCSD: University of California, San Diego)
Obtaining diffraction quality crystals remains one of the major bottlenecks in structural biology. The ability to predict the chances of crystallization from the amino-acid sequence of the protein can, at least partly, address this problem by allowing a crystallographer to select homologs that are more likely to succeed and/or to modify the sequence of the target to avoid features that are detrimental to successful crystallization. In 2007, the now widely used XtalPred algorithm [Slabinski et al...
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine),
Jose A. Gavira23
Estimated H-index: 23
(CSIC: Spanish National Research Council)
Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild p...
Published on Aug 31, 2013in Journal of Visualized Experiments1.11
Marisa Till4
Estimated H-index: 4
(UoB: University of Bristol),
Alice Robson11
Estimated H-index: 11
+ 4 AuthorsPaul R. Race6
Estimated H-index: 6
Random microseed matrix screening (rMMS) is a protein crystallization technique in which seed crystals are added to random screens. By increasing the likelihood that crystals will grow in the metastable zone of a protein's phase diagram, extra crystallization leads are often obtained, the quality of crystals produced may be increased, and a good supply of crystals for data collection and soaking experiments is provided. Here we describe a general method for rMMS that may be applied to either sit...
Published on Aug 12, 2013in ACS Combinatorial Science3.20
Shane A. Seabrook13
Estimated H-index: 13
,
Janet Newman26
Estimated H-index: 26
We present a high-throughput approach to help define experimental formulations that enhance protein stability, which is based on differential scanning fluorimetry (DSF). The method involves defining the thermal stability of a protein against a screen of 13 buffer systems, systematically sampling pH from 5.0 to 9.0 at high and low salt concentrations, using both redundancy and extensive controls to make the method robust. The screen allows rapid determination of a suitable base formulation for pr...
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Denis R. Burton2
Estimated H-index: 2
(La Trobe University)
+ 10 AuthorsViviane Richter4
Estimated H-index: 4
(La Trobe University)
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 the...
Chen-Yan Zhang8
Estimated H-index: 8
(NPU: Northwestern Polytechnical University),
Zi-Qing Wu4
Estimated H-index: 4
(NPU: Northwestern Polytechnical University)
+ 5 AuthorsPeng Shang20
Estimated H-index: 20
(NPU: Northwestern Polytechnical University)
The pH of a solution is an important parameter in crystallization that needs to be controlled in order to ensure success. The actual pH of the crystallization droplet is determined by the combined contribution of the buffers in the screening and protein solutions, although the contribution of the latter to the pH is often ignored. In this study, the effects of the buffer and protein solution pH values on the results of screening are systematically investigated. It was found that these parameters...
Published on Jun 1, 2013in Journal of Applied Crystallography
F. Gorrec6
Estimated H-index: 6
(LMB: Laboratory of Molecular Biology)
Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall ...
Published on Nov 1, 2012in Biochemistry and Molecular Biology Education0.95
Bernard Lorber28
Estimated H-index: 28
(UDS: University of Strasbourg),
Frédéric Fischer5
Estimated H-index: 5
(UDS: University of Strasbourg)
+ 2 AuthorsDaniel Kern33
Estimated H-index: 33
(UDS: University of Strasbourg)
Dynamic light scattering (DLS) analyses are routinely used in biology laboratories to detect aggregates in macromolecular solutions, to determine the size of proteins, nucleic acids, and complexes or to monitor the binding of ligands. This article is written for graduate and undergraduate students with access to DLS and for faculty members who wish to incorporate DLS into a lab activity, a practical course or research. It reviews the basic concepts of light scattering measurements and addresses ...
Cited By2
Newest
Published on Jun 20, 2018in PLOS ONE2.78
Andrew E. Bruno8
Estimated H-index: 8
(UB: University at Buffalo),
Patrick Charbonneau24
Estimated H-index: 24
(Duke University)
+ 6 AuthorsJulie Wilson23
Estimated H-index: 23
(Ebor: University of York)
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 s...
Published on Jan 1, 2016in Advances in Experimental Medicine and Biology2.13
Joanne L. Parker12
Estimated H-index: 12
(University of Oxford),
Simon Newstead27
Estimated H-index: 27
(University of Oxford)
Alpha helical membrane proteins are the targets for many pharmaceutical drugs and play important roles in physiology and disease processes. In recent years, substantial progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck still remains; the identification of conditions that give crystals that are suitable for structure determination. Over the past 10 years we have been analysing the crystallisation conditions reported for alpha hel...