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Crystallization screening: the influence of history on current practice

Published on Jul 1, 2014in Acta Crystallographica Section F-structural Biology and Crystallization Communications
· DOI :10.1107/S2053230X1401262X
Joseph R. Luft28
Estimated H-index: 28
(Hauptman-Woodward Medical Research Institute),
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Edward H. Snell23
Estimated H-index: 23
(UB: University at Buffalo)
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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.
  • References (134)
  • Citations (27)
Cite
References134
Newest
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 Dec 1, 2013in FEBS Journal4.74
Richard Giegé53
Estimated H-index: 53
(CNRS: Centre national de la recherche scientifique)
Protein crystallization has been known since 1840 and can prove to be straightforward but, in most cases, it constitutes a real bottleneck. This stimulated the birth of the biocrystallogenesis field with both ‘practical’ and ‘basic’ science aims. In the early years of biochemistry, crystallization was a tool for the preparation of biological substances. Today, biocrystallogenesis aims to provide efficient methods for crystal fabrication and a means to optimize crystal quality for X-ray crystallo...
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...
Published on Sep 1, 2012in Protein Science2.42
Joanne L. Parker12
Estimated H-index: 12
(University of Oxford),
Simon Newstead27
Estimated H-index: 27
(University of Oxford)
α-Helical membrane proteins (MPs) are the targets for many pharmaceutical drugs and play important roles in human physiology. In recent years, significant progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck in MP crystallography still remains, namely, the identification of conditions that give crystals that are suitable for structural determination. In 2008, we undertook an analysis of the crystallization conditions for 121 α-heli...
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
E. E. Bolton1
Estimated H-index: 1
+ 12 AuthorsRoger A. Sayle2
Estimated H-index: 2
When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange (XDX) workshop or...
Florine Dupeux10
Estimated H-index: 10
(Unit of Virus Host Cell Interactions),
Martin Röwer3
Estimated H-index: 3
(Unit of Virus Host Cell Interactions)
+ 2 AuthorsJosé A. Márquez18
Estimated H-index: 18
(Unit of Virus Host Cell Interactions)
The identification of crystallization conditions for biological molecules largely relies on a trial-and-error process in which a number of parameters are explored in large screening experiments. Currently, construct design and sample formulation are recognized as critical variables in this process and often a number of protein variants are assayed for crystallization either sequentially or in parallel, which adds complexity to the screening process. Significant effort is dedicated to sample char...
Published on May 1, 2011in Expert Opinion on Drug Discovery4.42
Luft1
Estimated H-index: 1
,
Edward H. Snell23
Estimated H-index: 23
,
George T. DeTitta25
Estimated H-index: 25
Introduction: X-ray crystallography provides the majority of our structural biological knowledge at a molecular level and, in terms of pharmaceutical design, is a valuable tool to accelerate discovery. It is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. It is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomi...
Published on Mar 2, 2011in Crystal Growth & Design4.15
Joseph R. Luft28
Estimated H-index: 28
,
Jennifer R. Wolfley9
Estimated H-index: 9
,
Edward H. Snell23
Estimated H-index: 23
Observations of crystallization experiments are classified as specific outcomes and integrated through a phase diagram to visualize solubility and thereby direct subsequent experiments. Specific examples are taken from our high-throughput crystallization laboratory which provided a broad scope of data from 20 million crystallization experiments on 12 500 different biological macromolecules. The methods and rationale are broadly and generally applicable in any crystallization laboratory. Through ...
Published on Feb 2, 2011in Nature43.07
Henry N. Chapman62
Estimated H-index: 62
,
Petra Fromme54
Estimated H-index: 54
+ 85 AuthorsUwe Weierstall37
Estimated H-index: 37
X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been dete...
Janet Newman26
Estimated H-index: 26
(CSIRO: Commonwealth Scientific and Industrial Research Organisation),
Lesley A. Pearce10
Estimated H-index: 10
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
+ 2 AuthorsThomas S. Peat22
Estimated H-index: 22
(CSIRO: Commonwealth Scientific and Industrial Research Organisation)
Arginase (EC 3.5.3.1) is an aminohydrolase that acts on l-arginine to produce urea and ornithine. Two isotypes of the enzyme are found in humans. Type I is predominantly produced in the liver and is a homotrimer of 35 kDa subunits. Human arginase (hArginase) I is seen to be up-regulated in many diseases and is a potential therapeutic target for many diverse indications. Previous reports of crystallization and structure determination of hArginase have always included inhibitors of the enzyme: her...
Cited By27
Newest
Published on Jul 16, 2019
Leonardo Lo Presti17
Estimated H-index: 17
,
Massimo Moret23
Estimated H-index: 23
,
Silvia Rizzato23
Estimated H-index: 23
A phenomenological study is carried out on a complex two-component diffusion-reacting system in gel, that is, the Cd-1,3-bis(4-pyridyl)propane (Cd-bpp) coordination polymer. The latter can exist in three solid forms, which exploit a 1:1 correspondence among the Cd/bpp ratio, the crystal structure and the crystal morphology (1/2: bipyramids; 2/3: needles; 1/3: plates). The aim was to clarify the role of key physicochemical variables (reactant concentrations, composition of the solvent and density...
Published on Apr 19, 2019in IUCrJ4.76
R. de Wijn (UDS: University of Strasbourg), Raphaël de Wijn1
Estimated H-index: 1
+ 14 AuthorsKarl Brillet
Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine `non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard te...
Published on Jan 1, 2019
Christopher J. Watkins1
Estimated H-index: 1
,
Nicholas Rosa2
Estimated H-index: 2
+ 6 AuthorsJanet Newman26
Estimated H-index: 26
Many long-standing image processing problems in applied science domains are finding solutions through the application of deep learning approaches to image processing. Here we present one such application; the case of classifying images of protein crystallisation droplets. The Collaborative Crystallisation Centre in Melbourne, Australia is a medium throughput service facility that produces between five and twenty thousand images per day. This submission outlines a reliable and robust machine lear...
Published on Dec 1, 2018in Journal of Agronomy and Crop Science2.96
V. Kumari (U of S: University of Saskatchewan), J. Germida (U of S: University of Saskatchewan), Vladimir Vujanovic16
Estimated H-index: 16
(U of S: University of Saskatchewan)
Published on Jan 1, 2018
Oksana Degtjarik4
Estimated H-index: 4
(Weizmann Institute of Science),
Gabriel Demo5
Estimated H-index: 5
(UMMS: University of Massachusetts Medical School)
+ 1 AuthorsIvana Kuta Smatanova11
Estimated H-index: 11
(Sewanee: The University of the South)
This chapter describes the fundamentals of the X-ray crystallography method and its application for studies of tertiary protein structures. A brief introduction to the theory of X-ray diffraction is given, followed by more detailed explanations of all protein structure determination stages, starting from crystal growth up to the final validation of protein structure. We emphasize the theoretical and practical aspects of the protein crystallization process which is the most crucial step of X-ray ...
Published on Jan 1, 2018
Qiang Chen17
Estimated H-index: 17
(University of Pittsburgh),
Yan Xu30
Estimated H-index: 30
(University of Pittsburgh),
Pei Tang28
Estimated H-index: 28
(University of Pittsburgh)
Abstract X-ray crystallography is a powerful tool in structural biology and can offer insight into structured-based understanding of general anesthetic action on various relevant molecular targets, including pentameric ligand-gated ion channels (pLGICs). In this chapter, we outline the procedures for expression and purification of pLGICs. Optimization of crystallization conditions, especially to achieve high-resolution structures of pLGICs bound with general anesthetics, is also presented. Case ...
Published on Dec 6, 2017in Crystal Growth & Design4.15
Luis Antonio González-Ramírez8
Estimated H-index: 8
(CSIC: Spanish National Research Council),
Carlos R. Ruiz-Martínez2
Estimated H-index: 2
(UPR: University of Puerto Rico)
+ 5 AuthorsJuan Manuel García-Ruiz32
Estimated H-index: 32
(CSIC: Spanish National Research Council)
We report an efficient screening methodology based on the capillary counter-diffusion technique (CCD), which was evaluated using two different practical approaches. The first consisted of kits prepared with the most successful crystallizing agents (PEG and ammonium sulfate) buffered at different pHs ranging from 4 to 9 and tested on 14 samples, including commercial and research target proteins. The second approach was based on the previously identified and highly effective 24 crystallization coc...
Published on Nov 1, 2017in Crystallography Reports0.75
A. S. Boikova2
Estimated H-index: 2
(RAS: Russian Academy of Sciences),
Yu. A. D’yakova3
Estimated H-index: 3
(RAS: Russian Academy of Sciences)
+ 6 AuthorsM. V. Koval’chuk1
Estimated H-index: 1
(SPbU: Saint Petersburg State University)
The composition of lysozyme solutions in D2O under conditions favorable for the formation of tetragonal crystals has been investigated at different protein concentrations by small-angle X-ray scattering using the synchrotron radiation. In addition to lysozyme monomers, dimeric and octameric species are found in the crystallization solutions; the octamer content increases with an increase in the protein concentration. A comparison of the data with those obtained under similar conditions but with ...
Published on Oct 4, 2017in Journal of the American Chemical Society14.70
Yigit Altay4
Estimated H-index: 4
,
Meniz Tezcan4
Estimated H-index: 4
,
Sijbren Otto46
Estimated H-index: 46
Our knowledge regarding the early steps in the formation of evolvable life and what constitutes the minimal molecular basis of life remains far from complete. The recent emergence of systems chemistry reinvigorated the investigation of systems of self-replicating molecules to address these questions. Most of these studies focus on single replicators and the effects of replicators on the emergence of other replicators remains under-investigated. Here we show the cross-catalyzed emergence of a nov...
View next paperOptimization of crystallization conditions for biological macromolecules