Match!

Investigation of the Initial Crystallization Stage in Lysozyme Solutions by Small-Angle X-ray Scattering

Published on Apr 6, 2016in Crystal Growth & Design4.15
· DOI :10.1021/acs.cgd.5b01662
Mikhail Kovalchuk7
Estimated H-index: 7
,
A. E. Blagov7
Estimated H-index: 7
+ 6 AuthorsVladimir V. Volkov1
Estimated H-index: 1
Cite
Abstract
From the base structure of tetragonal lysozyme crystals, the octamer cluster was selected as the possible element of crystal growth. The proposed model was verified by small-angle X-ray scattering (SAXS) measurements of lysozyme solutions. The results showed a noticeable presence of lysozyme dimers and octamers under crystallization conditions and the total absence of oligomers under conditions where crystal growth was impossible.
  • References (30)
  • Citations (15)
Cite
References30
Newest
Published on Aug 31, 2015in Russian Chemical Reviews4.61
Konstantin M. Boyko8
Estimated H-index: 8
(RAS: Russian Academy of Sciences),
Vladimir O. Popov19
Estimated H-index: 19
(RAS: Russian Academy of Sciences),
M. V. Kovalchuk11
Estimated H-index: 11
(RAS: Russian Academy of Sciences)
Published on Jan 1, 2015in Faraday Discussions3.71
Maria A. Vorontsova8
Estimated H-index: 8
(UH: University of Houston),
Dominique Maes25
Estimated H-index: 25
(Vrije Universiteit Brussel),
Peter G. Vekilov47
Estimated H-index: 47
(UH: University of Houston)
The two-step mechanism of nucleation of crystals in solutions posits that the formation of crystal nuclei occurs within structures of extended lifetimes, in which the nucleating solute is at high concentration. The validity of this mechanism has been demonstrated for proteins, small-molecule organic and inorganic materials, colloids, and polymers. Due to large molecule sizes, proteins are an ideal system to study the details of this nucleation pathway, in particular the formation mechanisms of t...
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 ...
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...
Published on Sep 1, 2014in Crystallography Reports0.75
Mikhail Kovalchuk7
Estimated H-index: 7
(RAS: Russian Academy of Sciences),
P. A. Prosekov5
Estimated H-index: 5
(RAS: Russian Academy of Sciences)
+ 5 AuthorsO. A. Kondratev3
Estimated H-index: 3
(RAS: Russian Academy of Sciences)
The results of an in situ study of the growth of tetragonal lysozyme crystals by high-resolution X-ray diffractometry are considered. The crystals are grown by the sitting-drop method on crystalline silicon substrates of different types: both on smooth substrates and substrates with artificial surface-relief structures using graphoepitaxy. The crystals are grown in a special hermetically closed crystallization cell, which enables one to obtain images with an optical microscope and perform in sit...
V. N. Korneev6
Estimated H-index: 6
(RAS: Russian Academy of Sciences),
V. A. Shlektarev4
Estimated H-index: 4
(RAS: Russian Academy of Sciences)
+ 5 AuthorsA.A. Vazina10
Estimated H-index: 10
(RAS: Russian Academy of Sciences)
The main results of the development of X-ray stations are presented. These stations are intended to solve problems concerning the structural biology of tissues at a high time resolution with the help of synchrotron radiation (SR) generated by the VEPP-3 storage ring (Siberian center of SR, Novosibirsk) and the Siberia-2 storage ring (National Research Centre Kurchatov Institute and the centre of nano-, bio-, information, and cognitive sciences, Moscow). The issues of selecting the optical scheme...
Published on Aug 1, 2010in Biophysical Journal3.67
Eugenia Pechkova18
Estimated H-index: 18
(UniGe: University of Genoa),
Ronald Gebhardt14
Estimated H-index: 14
(European Synchrotron Radiation Facility)
+ 1 AuthorsClaudio Nicolini35
Estimated H-index: 35
(UniGe: University of Genoa)
In this study, we used microbeam grazing-incidence small-angle x-ray scattering (μGISAXS) to investigate in situ protein nucleation and crystal growth assisted by a protein nanotemplate, and introduced certain innovations to improve the method. Our aim was to understand the protein nanotemplate method in detail, as this method has been shown to be capable of accelerating and increasing crystal size and quality, as well as inducing crystallization of proteins that are not crystallizable by classi...
Paul Emsley20
Estimated H-index: 20
(University of Oxford),
Bernhard Lohkamp11
Estimated H-index: 11
(KI: Karolinska Institutet)
+ 1 AuthorsKevin Cowtan26
Estimated H-index: 26
(Ebor: University of York)
Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graph...
Published on Feb 4, 2009in Crystal Growth & Design4.15
P.W.G. Poodt5
Estimated H-index: 5
,
M.C.R. Heijna7
Estimated H-index: 7
+ 3 AuthorsE. Vlieg31
Estimated H-index: 31
A new upside-down geometry is proposed to achieve the beneficial effects of microgravity crystal growth by making use of buoyant forces instead of compensating for them. We show by growth experiments on sodium chlorate and lysozyme that crystal growth in an upside-down geometry leads to the formation of a buoyancy assisted depletion zone where convection is suppressed. The effects on growth rate and morphology that are observed are all indicative of diffusion limited growth, just as would happen...
Published on Feb 1, 2008in Nature Methods28.47
Naomi E. Chayen33
Estimated H-index: 33
(Imperial College London),
Emmanuel N. Saridakis50
Estimated H-index: 50
Abstract Determining the structure of biological macromolecules by X-ray crystallography involves a series of steps: selection of the target molecule; cloning, expression, purification and crystallization; collection of diffraction data and determination of atomic positions. However, even when pure soluble protein is available, producing high-quality crystals remains a major bottleneck in structure determination. Here we present a guide for the non-expert to screen for appropriate crystallizatio...
Cited By15
Newest
M. A. Marchenkova7
Estimated H-index: 7
(RAS: Russian Academy of Sciences),
Petr V. Konarev23
Estimated H-index: 23
(RAS: Russian Academy of Sciences)
+ -3 AuthorsYurii V. Pisarevsky1
Estimated H-index: 1
(RAS: Russian Academy of Sciences)
AbstractThe pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric compositio...
Published on May 1, 2019in Thin Solid Films1.89
Mikhail V. Kovalchuk2
Estimated H-index: 2
(SPbU: Saint Petersburg State University),
A. S. Boikova2
Estimated H-index: 2
(RAS: Russian Academy of Sciences)
+ 7 AuthorsAlexey Seregin2
Estimated H-index: 2
(RAS: Russian Academy of Sciences)
Abstract An approach for forming Langmuir monolayers of proteins is described, with lysozyme serving as an example. The essence of this approach is the deposition of a lysozyme solution containing a precipitant, KCl, onto the water surface in a Langmuir trough. The results of small-angle X-ray scattering indicate that the precipitant in the protein solution causes a significant fraction (>10%) of the protein molecules to assemble into dimers and octamers. Studying the formation of these monolaye...
Published on Jan 1, 2019in Crystallography Reports0.75
Yu. A. Dyakova3
Estimated H-index: 3
,
A. S. Boikova2
Estimated H-index: 2
+ 5 AuthorsMikhail V. Kovalchuk2
Estimated H-index: 2
(SPbU: Saint Petersburg State University)
Published on Jan 1, 2019in Chemical Engineering Research & Design3.07
Izabela Poplewska5
Estimated H-index: 5
(Rzeszów University of Technology),
Andrzej Łyskowski5
Estimated H-index: 5
(Rzeszów University of Technology)
+ 3 AuthorsDorota Antos16
Estimated H-index: 16
(Rzeszów University of Technology)
Abstract The kinetics of protein crystallization was analyzed using a modified Small-Angle X-ray Scattering (SAXS) setup that was operated in a flow-through mode. The model protein for the study was lysozyme, which was crystallized from supersaturated aqueous solutions of ammonium sulfate. A small amount of the protein solution was forced to recirculate within the SAXS setup. The SAXS intensity curves were measured at different time intervals and converted into kinetic profiles using a calibrati...
Published on Nov 1, 2018in 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)
+ 5 AuthorsM. V. Koval’chuk1
Estimated H-index: 1
(SPbU: Saint Petersburg State University)
Published on Nov 1, 2018in Crystallography Reports0.75
Yu. V. Kordonskaya1
Estimated H-index: 1
(RAS: Russian Academy of Sciences),
V. I. Timofeev7
Estimated H-index: 7
(RAS: Russian Academy of Sciences)
+ 4 AuthorsMikhail V. Kovalchuk2
Estimated H-index: 2
(SPbU: Saint Petersburg State University)
Published on Sep 1, 2018in Crystallography Reports0.75
A. M. Popov (Kurchatov Institute), A. S. Boikova2
Estimated H-index: 2
(RAS: Russian Academy of Sciences)
+ 7 AuthorsM. V. Koval’chuk1
Estimated H-index: 1
(SPbU: Saint Petersburg State University)
A microfluidic cell has been developed for studying the structure of protein solutions using small-angle X-ray scattering. The use of prefabricated elements, which provide a small sample volume, allows one to adjust the microfluidic cell parameters to specific problems. Tests of lysozyme solutions were performed on a laboratory diffractometer AMUR-K (Institute of Crystallography, Russian Academy of Sciences), BM29 beamline (ESRF, Grenoble), and “DICSY” beamline of the Kurchatov synchrotron radia...
Published on Sep 1, 2018in 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)
Multilayer structures, consisting of successive lysozyme layers and layers of iodide and potassium ions, have been formed on a silicon substrate by the modified Langmuir–Schaefer method; the use of this technique implies preliminary preparation of a crystallization protein solution containing an oligomeric phase. The multilayer structure has been characterized by methods of X-ray reflectivity and total external reflection X-ray standing waves (TER XSW). The data obtained indicate the formation o...
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 ...