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Large‐volume protein crystal growth for neutron macromolecular crystallography

Published on Apr 1, 2015in Acta Crystallographica Section F-structural Biology and Crystallization Communications
· DOI :10.1107/S2053230X15005348
Joseph D. Ng13
Estimated H-index: 13
(UAH: University of Alabama in Huntsville),
James K. Baird14
Estimated H-index: 14
(UAH: University of Alabama in Huntsville)
+ 3 AuthorsSijay Huang1
Estimated H-index: 1
(UAH: University of Alabama in Huntsville)
Cite
Abstract
Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.
  • References (77)
  • Citations (10)
Cite
References77
Newest
Bernhard Rupp30
Estimated H-index: 30
(Innsbruck Medical University)
Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably display...
Patrick J. Loll23
Estimated H-index: 23
(Drexel University)
At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures p...
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine),
Bob Cudney3
Estimated H-index: 3
© 2014 International Union of Crystallography. For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for ...
Published on Sep 1, 2014in Biotechnology Progress2.41
Natalie Rakel3
Estimated H-index: 3
,
Miriam Baum1
Estimated H-index: 1
,
Jürgen Hubbuch31
Estimated H-index: 31
Protein phase behavior characterization is a multivariate problem due to the high amount of influencing parameters and the diversity of the proteins. Single influences on the protein are not understood and fundamental knowledge remains to be obtained. For this purpose, a systematic screening method was developed to characterize the influence of fluid phase conditions on the phase behavior of proteins in three-dimensional phase diagrams. This approach was applied to three monoclonal antibodies to...
Published on Aug 1, 2014in Journal of Applied Crystallography
Leighton Coates22
Estimated H-index: 22
,
Stephen J. Tomanicek10
Estimated H-index: 10
+ 4 AuthorsAndreas Ostermann18
Estimated H-index: 18
The use of cryocooling in neutron diffraction has been hampered by several technical challenges such as the need for specialized equipment and techniques. Recently we have developed and deployed equipment and strategies that allow for routine neutron data collection on cryocooled crystals using off the shelf components. This system has several advantages, compared to a closed displex cooling system such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely ...
Published on Jul 11, 2014in Science41.04
Cecilia M. Casadei3
Estimated H-index: 3
(University of Leicester),
A. Gumiero5
Estimated H-index: 5
(University of Leicester)
+ 10 AuthorsAndreas Ostermann18
Estimated H-index: 18
(TUM: Technische Universität München)
Heme enzymes activate oxygen through formation of transient iron-oxo (ferryl) intermediates of the heme iron. A long-standing question has been the nature of the iron-oxygen bond and, in particular, the protonation state. We present neutron structures of the ferric derivative of cytochrome c peroxidase and its ferryl intermediate; these allow direct visualization of protonation states. We demonstrate that the ferryl heme is an Fe(IV)=O species and is not protonated. Comparison of the structures ...
Flora Meilleur18
Estimated H-index: 18
(NCSU: North Carolina State University),
P. Munshi3
Estimated H-index: 3
(ORNL: Oak Ridge National Laboratory)
+ 7 AuthorsDean A. A. Myles24
Estimated H-index: 24
(ORNL: Oak Ridge National Laboratory)
The first high-resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 A resolution were collected from a relatively small 0.7 mm3 PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecu...
Published on Jul 11, 2013in Journal of Medicinal Chemistry1.51
Irene T. Weber48
Estimated H-index: 48
,
Mary Jo Waltman9
Estimated H-index: 9
+ 5 AuthorsAndrey Kovalevsky33
Estimated H-index: 33
HIV-1 protease is an important target for the development of antiviral inhibitors to treat AIDS. A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined at 2.0 A resolution. The structure provides direct determination of hydrogen atom positions in the enzyme active site. Analysis of the enzyme–drug interactions suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances. This inform...
Ronny C. Hughes5
Estimated H-index: 5
(UAH: University of Alabama in Huntsville),
Leighton Coates22
Estimated H-index: 22
(ORNL: Oak Ridge National Laboratory)
+ 5 AuthorsJoseph D. Ng13
Estimated H-index: 13
(UAH: University of Alabama in Huntsville)
Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and n...
Published on Jun 22, 2011in Journal of Molecular Recognition1.92
Eduardo Howard6
Estimated H-index: 6
(CONICET: National Scientific and Technical Research Council),
M.P. Blakeley20
Estimated H-index: 20
+ 9 AuthorsC. Muller-Dieckmann2
Estimated H-index: 2
(European Synchrotron Radiation Facility)
Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been ...
Cited By10
Newest
Published on Dec 1, 2018
Jose A. Gavira23
Estimated H-index: 23
,
Mayte Conejero-Muriel3
Estimated H-index: 3
,
José Manuel Delgado-López14
Estimated H-index: 14
Published on Sep 1, 2018in Journal of Crystal Growth1.57
Xi H. Tang1
Estimated H-index: 1
(SCUT: South China University of Technology),
Jing J. Liu6
Estimated H-index: 6
(University of Leeds)
+ 1 AuthorsXue Z. Wang28
Estimated H-index: 28
(SCUT: South China University of Technology)
Abstract In this work, crystallization experiments were conducted in three different sizes of crystallizers (5 and 100 ml, and 1 L) to study the influence of temperature on the crystallization of lysozyme. Lysozyme solutions with concentrations of 40 and 30 g L −1 and 10% (w/w) NaCl were used. The temperature was reduced from 20 to 0 °C with various cooling rate and stirring speed. The data indicated that crystallization with cooling but without agitation or with agitation but without cooling le...
Dorothee Liebschner2
Estimated H-index: 2
(LBNL: Lawrence Berkeley National Laboratory),
Pavel V. Afonine29
Estimated H-index: 29
(SHU: Shanghai University)
+ 2 AuthorsPaul D. Adams78
Estimated H-index: 78
(University of California, Berkeley)
The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by ...
Published on Aug 1, 2018in Journal of Pharmaceutical Sciences3.20
Marieke E. Klijn1
Estimated H-index: 1
(KIT: Karlsruhe Institute of Technology),
Jürgen Hubbuch31
Estimated H-index: 31
(KIT: Karlsruhe Institute of Technology)
Abstract Protein phase diagrams are a tool to investigate the cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphologic features, such as crystal size, as well as kinetic features, such as crystal growth time. Commonly used data visualization techniques include individual line graphs or phase diagrams based on symbols. These techniques have...
Published on Apr 20, 2018
M.P. Blakeley20
Estimated H-index: 20
,
A. Podjarny10
Estimated H-index: 10
(UDS: University of Strasbourg)
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 A, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biolo...
Published on Sep 20, 2017
Ayana Sato-Tomita3
Estimated H-index: 3
,
Naoya Shibayama20
Estimated H-index: 20
While high-throughput screening for protein crystallization conditions have rapidly evolved in the last few decades, it is also becoming increasingly necessary for the control of crystal size and shape as increasing diversity of protein crystallographic experiments. For example, X-ray crystallography (XRC) combined with photoexcitation and/or spectrophotometry requires optically thin but well diffracting crystals. By contrast, large-volume crystals are needed for weak signal experiments, such as...
Published on Jul 1, 2016in Archives of Biochemistry and Biophysics3.56
Jose A. Gavira23
Estimated H-index: 23
(CSIC: Spanish National Research Council)
Abstract Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fiel...
Published on Jul 1, 2016in Archives of Biochemistry and Biophysics3.56
William B. O'Dell8
Estimated H-index: 8
(NCSU: North Carolina State University),
Annette M. Bodenheimer3
Estimated H-index: 3
(NCSU: North Carolina State University),
Flora Meilleur18
Estimated H-index: 18
(NCSU: North Carolina State University)
Neutron protein crystallography is a powerful tool for investigating protein chemistry because it directly locates hydrogen atom positions in a protein structure. The visibility of hydrogen and deuterium atoms arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction at resolutions typical of protein crystals. Neutrons have the additional benefit to structural biology of not inducing radiation damage in protein crys...
John Paul Bacik5
Estimated H-index: 5
(LANL: Los Alamos National Laboratory),
Sophanit Mekasha6
Estimated H-index: 6
(NMBU: Norwegian University of Life Sciences)
+ 8 AuthorsVincent G. H. Eijsink58
Estimated H-index: 58
(NMBU: Norwegian University of Life Sciences)
Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for t...