J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: Analysis of the study of unfolding (denaturation) and refolding (renaturation) processes of these molecular chaperones and the effect of ligands and solvent composition seems to be useful for understanding the folding mechanism not only of the GroEL/GroES complex, but also of other oligomeric protein complexes.
Abstract: Molecular chaperones are a special class of heat shock proteins (Hsp) that assist the folding and formation of the quaternary structure of other proteins both in vivo and in vitro. However, some chaperones are complex oligomeric proteins, and one of the intriguing questions is how the chaperones fold. The representatives of the Escherichia coli chaperone system GroEL (Hsp60) and GroES (Hsp10) have been studied most intensively. GroEL consists of 14 identical subunits combined into two interacting ring-like structures of seven subunits each, while the co-chaperone GroES interacting with GroEL consists of seven identical subunits combined into a dome-like oligomeric structure. In spite of their complex quaternary structure, GroEL and GroES fold well both in vivo and in vitro. However, the specific oligomerization of GroEL subunits is dependent on ligands and external conditions. This review analyzes the literature and our own data on the study of unfolding (denaturation) and refolding (renaturation) processes of these molecular chaperones and the effect of ligands and solvent composition. Such analysis seems to be useful for understanding the folding mechanism not only of the GroEL/GroES complex, but also of other oligomeric protein complexes.
36 citations
TL;DR: Comparison of structures of 3-isopropylmalate dehydrogenase gives a detailed picture of the swelling of a cavity at the dimer interface and the generation of a new cleft on the molecular surface, which are accompanied by water penetration.
Abstract: Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 A resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.
36 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...The high-pressure environment used in this study was generated by a diamond anvil cell (DAC) of the pistoncylinder type (Chervin et al., 1995) with a culet diameter of 1 mm and a thickness of 1.49 mm (Boehler Almax type; Boehler & Hantsetters, 2004)....
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...(i) The pressure medium being liquid, crystals in the DAC were mobile and were moving during measurements of the X-ray diffraction....
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...…has been established and applied to structural studies of several macromolecules (Kundrot & Richards, 1986, 1987; Katrusiak & Dauter, 1996; Fourme et al., 2001, 2009; Urayama et al., 2002; Collins et al., 2005, 2011; Girard et al., 2007, 2010; Ascone et al., 2010; Kurpiewska & Kewiński, 2010)....
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...In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa....
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...Crystal movement in the DAC is significant at AR-NW12A because of the horizontal spindle axis of the goniometer....
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TL;DR: Iodine XANES and EXAFS data for eleven borosilicate glasses indicate iodide-like environments within the glass structure, where I � has Na or Li nearest-neighbors, and where the nearestneighbor cation type correlates to the most common network-modifying cation in the glass.
36 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...For most glasses, the portion of each fragment exposed to the X-ray beam turned dark (probably due to color centers) after several XAS scans; however, no changes in the data were observed from the first to last scan for each glass....
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TL;DR: An alternative approach to circumvent this problem is introduced by substituting the oxide ions in [IrO6]8− by isoelectronic fluorides to form the fluorido-iridate: [IrF6]2−, which emerges as an ideal model for iridates.
Abstract: New exotic phenomena have recently been discovered in oxides of paramagnetic Ir4+ ions, widely known as ‘iridates’. Their remarkable properties originate from concerted effects of the crystal field, magnetic interactions and strong spin-orbit coupling, characteristic of 5d metal ions. Despite numerous experimental reports, the electronic structure of these materials is still challenging to elucidate, and not attainable in the isolated, but chemically inaccessible, [IrO6]8– species (the simplest molecular analogue of the elementary {IrO6}8− fragment present in all iridates). Here, we introduce an alternative approach to circumvent this problem by substituting the oxide ions in [IrO6]8− by isoelectronic fluorides to form the fluorido-iridate: [IrF6]2−. This molecular species has the same electronic ground state as the {IrO6}8− fragment, and thus emerges as an ideal model for iridates. These results may open perspectives for using fluorido-iridates as building-blocks for electronic and magnetic quantum materials synthesized by soft chemistry routes. Iridates are known to exhibit a range of exotic electronic and magnetic behaviours but it is difficult to prepare isolated [IrO6]8− species via soft chemical routes. Here, the authors isolate the isoelectronic [IrF6]2−complex, and assess it as a model and for iridate analogues.
36 citations
01 Feb 2017
TL;DR: This article aims to guide efforts in protein–ligand complex crystal structure generation, with special consideration of protein construct design, and summarizes different approaches to co-crystallization and crystal soaking.
Abstract: With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein–ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting.
36 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...If the diffraction is poor despite optimizing the ligand concentration and stabilizing solution, cross-linking with glutaraldehyde prior to soaking might help to stabilize the crystals (Lusty, 1999)....
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References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
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TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
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TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
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TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations