Creative Biostructure, an expert in the supplying of products and services for structural biology studies, recently built X-ray Crystallography Platform to provide support to customers from both industry and academia for their structural biology projects.. Scientists in this field can have access to Creative Biostructures state-of-the-art tools and identify and optimize crystallization conditions as well as X-ray diffraction data processing for any macromolecule of interest.. X-ray crystallography is one of the most favored techniques for the determination of the atomic structure of proteins, nucleic acids and other molecules. This platform in Creative Biostructure is equipped with highly specialized instruments for X-ray diffraction studies, including multipurpose diffractometers, nano-liter crystallization robots, high-throughput liquid handling robots and high-resolution imaging systems. With advanced equipment and experienced crystallographers, the company is able to set up crystallization ...
Written by Tatjana Barthel Macromolecular Crystallography group at BESSY II). The outbreak of SARS-CoV-2 pushed all of us into a very complicated situation, especially with strict regulations and certain lockdown periods. Performing science became challenging in these last weeks, but at the same time it is of great importance in order to fight the virus. In the development of drugs against SARS-CoV-2 X-ray crystallography plays a key role.. One field of X-ray crystallography is protein crystallography. Proteins can form crystals just as small molecules, metals and salts. The array of ordered protein molecules inside a protein crystal leaves gaps that are filled by disordered solvent molecules, i.e. mostly water. These so called solvent channels enable small molecules to enter the protein crystals and reach the individual protein molecules. Thus, protein crystals can be used for drug development, by probing them with small molecules in order to find out if and how the molecules bind to the ...
X-ray crystallography is a technique used by biochemist to determine the three dimensional structure of an enzyme, protein, molecule, etc. Although the technique requires the molecule to be able to be crystallized it has helped scientist discover how drugs can prevent certain enzyme from reacting. By determining the three dimensional structure of the protein or enzyme scientists can determine how enzyme folds and binds. From that information, scientists can design certain drugs that only stop that enzyme. For example, scientists used x-ray crystallography to determine the structure of the COX enzyme that is responsible for arthritis. Now that the scientists know the three dimensional structure of the COX enzyme, they can create drugs that would be able to stop it, such as aspirin. Therefore X-ray crystallography is a powerful tool that biochemist and scientists can use to discover new drugs that can prevent certain enzymes from activating.. ...
Post-doctoral Positions in X-ray Crystallography and Computational Biology Two post-doctoral positions are available immediately, one in experimental and one in computational aspects of protein crystallography. Applicants for the first position should be experienced in practical aspects of protein crystallography and structure determination. Experience in cloning and protein expression is also desirable. Crystals are already in hand for one novel carotenoid-binding protein. Subsequent projects will diversify to include work on self-assembling proteins and other proteins with repetitive or otherwise unusual architectures. The second position is in the area of computational crystallography, but may also include other aspects of computational biology such as genomics or protein structure analysis. The successful applicant should have a strong background in scientific programming, an understanding of numerical methods, and an ability to solve complex problem. Familiarity with crystallographic and ...
The International Union of Crystallography is a non-profit scientific union serving the world-wide interests of crystallographers and other scientists employing crystallographic methods ...
where Nall is the total number of atoms and Npeak is the number of atoms which contain one or more peaks within 2.2 Å of the atom.. In order to analyse the effect of X-ray resolution, m,Fo, − D,Fc, electron-density maps were generated at five different resolutions as follows. The same X-ray refinements as those in the above procedure were performed for DNA crystal structures solved at a resolution equal to or better than 2.5 Å. The m,Fo, − D,Fc, map was calculated at 1.0, 1.25, 1.5, 1.9 and 2.5 Å resolution for data of ≤1.0, 1.0-1.25, 1.25-1.5, 1.5-1.9 and 1.9-2.5 Å resolution, respectively. A search was made for peaks in the maps in the same way as above.. In this study, the r.m.s. of densities (σ) was used to distinguish peaks from noise. The density of electrons (e Å−3) can also be used and this different measure might give a different result. We then investigated the variation of electron density corresponding to 1σ in the electron-density maps. Supplementary Fig. S2 shows the ...
X-ray crystallography is the major method for structure determination of macromolecules. About 85% of all known structures deposited in the Protein Data Bank have been determined by X-ray crystallography. Knowing the structure of a protein helps in understanding better how the protein works, how it interacts with other proteins and small molecules in the cell and what kind of conformational changes it undergoes to exert its function. Even subtle changes in protein structures can have tremendous consequences on human health, causing serious diseases. A major application therefore of X-ray crystallography is in the design of new drugs.. A crystal structure determination is not a trivial task. It mainly involves five steps with the first two being the most difficult ("bottlenecks"):. ...
1GNR: X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp.
The -ray crystal-structure analysis of 1,3-diadamantylaziridinone (1b) demonstrates that the configuration at nitrogen is pyramidal (N lying 0·534 Å from the plane defined by its three substituents) and that the adamantyl groups are to each other.
The Crystallography Times newsletter from Rigaku Oxford Diffraction focuses on single crystal X-ray diffraction and is available from the companys website October 30, 2017 - The Woodlands, Texas. The latest edition of Crystallography Times, the X-ray crystallography newsletter from Rigaku Oxford Diffraction, is now available to view on the companys global website. 1600181092
Two user-friendly computer programs are described for use in macromolecular X-ray crystallography, xdlMAPMAN provides an interface for electron-density map exchange between some of the most commonly used phase refinement, structure refinement and model- building programs. In addition, it contains several options to analyse and abstract such maps. xdlDATAMAN provides similar functionality for the analysis and manipulation of macromolecular reflection data sets. Both programs have a simple graphical user interface, and their source code has been put into the public domain.. ...
The Woodlands, Texas (PRWEB) August 30, 2017 -- The latest edition of Crystallography Times, the X-ray crystallography newsletter from Rigaku Oxford
The conjugative transfer of F-like plasmids is repressed by FinO, an RNAbinding protein. FinO interacts with the F-plasmid encoded traJ mRNA andits antisense RNA, FinP, stabilizing FinP against endonucleolyticdegradation and facilitating sense-antisense RNA recognition. Here wepresent the 2.0 A resolution X-ray crystal structure of FinO, lacking itsflexible N-terminal extension. FinO adopts a novel, elongated, largelyhelical conformation. An N-terminal region, previously shown to contactRNA, forms a positively charged alpha-helix (helix 1) that protrudes 45 Afrom the central core of FinO. A C-terminal region of FinO that isimplicated in RNA interactions also extends out from the central body ofthe protein, adopting a helical conformation and packing against the baseof the N-terminal helix. A highly positively charged patch on the surfaceof the FinO core may present another RNA binding surface. The results ofan in vitro RNA duplexing assay demonstrate that the flexible N-terminalregion of FinO ...
Up to four post-doctoral positions are available immediately in the new laboratory of Dr. Bob Liddington at the Burnham Institute, La Jolla, California, to work on the structural biology of membrane proteins, including integrins, ion channels and toxins. Both experienced crystallographers and protein chemists are sought. The Burnham Institute is adjacent to Scripps, the Salk Institute, the UCSD campus and the Pacific Ocean. Daytime highs currently around 70 F (21 C) with unbroken blue skies. Reply to rlidding at burnham-inst.org ...
Why this is my favorite X-ray crystal structure: The beautiful, strikingly unique structure of B-rhombohedral boron has successfully withstood numerous challenges of its correctness and has for a half century experienced nearly constant investigations of its structurally implied material characteristics. Arguably the most important of the several known phases of elemental boron, this form has been found to be experimentally stable from absolute zero to its melting point. Detailed consideration of the 5-foldness of its numerous discrete and merged 12-atom regular icosahedral motifs and their extended 84-atom truncated icosahedral arrays has forced a significant modification of chemical bonding theory in attempts to explain the low density, high strength, high melting, semiconducting and other notable properties of this low atomic number element. Even the observed partial occupancy of one of its 6-fold Wyckoff sets of atoms within the structure appears to be correct and to imply intriguing ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): 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 F. 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
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Sodium atom in PDB 1uy1: Binding Sub-Site Dissection of A Family 6 Carbohydrate-Binding Module By X-Ray Crystallography and Isothermal Titration Calorimetry
Figure 1 - Scientists supported in attending the Erice school through CCDC travel bursaries - Abishek Chitnis from Mumbai University (left) and Madan Kumar from Mangalore University (right). Abishek is working in the field of high pressure physics, in particular looking at the stability of perovskite metal-organic frameworks. He commented that during the Erice School he "got to know about different research areas, ideas & opportunities in high pressure crystallography as well as enjoying healthy conversations and discussion with lecturers and experts." Abishek also commented that "I learnt many things as well as enjoyed this school. I am very grateful to the organizers and volunteers for the arrangements and all kind of comforts and supports we obtained.". Madan Kumar is based at the PURSE lab at Mangalore University. He has worked with both small molecule crystallography as well as the structure determination of proteins from single crystal x-ray diffraction. Madan commented that the hands-on ...
The workshop will include comprehensive theoretical lectures on all facets of crystallographic structure determination and hands-on tutorials. The lectures will be open to all, but the tutorials will be limited to 20 participants that will be chosen by committee. Lectures and tutorials will be given by Tom Terwilliger (Los Alamos), Randy Read (Cambridge), Zbigniew Dauter (Argonne), Karine Sparta (from the XDS development group) and members of the TCSB. The cost of participation in the full program is 200 Euro. More information, including fellowships, and the registration page can be found: http://tcsb-biox-wksp.net.technion.ac.il.. ...
We analyze small molecule ligand binding to ATAD2 bromodomain by molecular dynamics and protein crystallography. We observe a previously unexplored conformation of the binding pocket upon rearrangement of the gatekeeper residue Ile1074. Minor differences in the ligands result in binding with different plasticity of the ZA loop.. Visit the publication. ...
The Alber lab at UC Berkeley is pleased to release of the code for Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm), which depends on Chimera. Ringer is a program to detect molecular motions by systematic X-ray electron-density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which parts are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design. The Ringer method is described in Lang et al. /Protein Sci/. 2010 Jul; 19(7):1420-31 ,http://www.ncbi.nlm.nih.gov/pubmed/20499387,. An application of Ringer, determining the structural underpinnings of the side chain dynamics critical for the function of the enzyme proline isomerase, was published in Fraser JS et al. /Nature/. 2009 Dec ...
The Protein crystallography core facility of Biocenter Oulu has the infrastructure for protein structural studies from crystallization to x-ray data collection and structure determination.
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The Chemical Crystallography Service is run in two parts: the analytical service and the "DIY" service which includes some 40 trained "users". It is a special feature of the X-ray crystallography laboratory in Oxford that hands-on crystallography is promoted. Initially researchers who want to determine their own structures complete a minimal practical health and safety course and are invited to attend crash-courses on crystal structure analysis. Following tailored one-to-one training in the use of the instrumentation, structure solution/refinement software, preparing files for publication and validation, data can be collected unsupervised, although help is always available in case of difficulties. Some examples of structures published by The Service are shown left.. In addition to the in-house instrumentation, we also have regular access to the Small Molecule Beamline at the Diamond Light Source, I19 (bottom left) under the Block Allocation System. As part of The Service, trained users have ...
Water is one of the simplest molecule on earth and essential to life. Well known molecule, it is in the same time a molecule that still not completely known when grouped with other water molecule. Snowflakes show broad number of structures, from which mechanical behavior will depend. Macroscopic mechanical behavior of snow, especially in montains, depends then only of the weak very small hydrogen bonds. In the same time not so weak as USA think to use it with wood fibers to build armor for warships as strong as metallic ones during the WWII. -Pennarun. ...
The 220 kDa dimeric cytochrome b6f complex of oxygenic photosynthesis provides the electronic connection between the two reaction centers, Photosystems I and II that are, respectively, coupled to NADP+ reduction and oxygen evolution. The electron transport functions of the b6f complex are coupled to proton transfer and generation of a trans-membrane proton electrochemical gradient, by mechanisms similar to those of the cytochrome bc1 complex of the respiratory chain and the photosynthetic bacteria, whose protein core is similar to that of the b6f complex. Prior to X-ray crystal structure analysis, each monomeric unit of the complex was known to contain six bound prosthetic groups, three hemes (f, two hemes b, bp and bn), one [2Fe-2S] cluster, and one molecule each of chlorophyll-a and carotene. Crystal structure analysis of the b6f complex from a green alga and a thermophilic cyanobacterium revealed the presence of an additional heme cn in the complex, which is covalently bound on the ...
ATP synthase is a membrane-bound rotary motor enzyme that is critical for cellular energy metabolism in all kingdoms of life. Despite conservation of its basic structure and function, autoinhibition by one of its rotary stalk subunits occurs in bacteria and chloroplasts but not in mitochondria. The crystal structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli described here reveals the structural basis for this inhibition. The C-terminal domain of subunit ɛ adopts a heretofore unknown, highly extended conformation that inserts deeply into the central cavity of the enzyme and engages both rotor and stator subunits in extensive contacts that are incompatible with functional rotation. As a result, the three catalytic subunits are stabilized in a set of conformations and rotational positions distinct from previous F(1) structures.. ...
Not only does cryo-EM offer exciting new possibilities, but the development of X-ray free-electron lasers (XFELs), and of serial crystallography at both XFEL and advanced synchrotron sources, now allow us to `tackle with relative ease complex biological structures or to take crystallography to unthinkably small time-frames and nanocrystals.Cited by: 1.
9780387333342 Our cheapest price for Principles of Protein X-Ray Crystallography is $77.18. Free shipping on all orders over $35.00.
The grant, from the Wellcome Trust, will enable the department to purchase a state-of-the-art CCD X-ray detector which it has had on loan from the manufacturers Bruker AXS for the past 3 years.. X-ray crystallography is the most widely-used method for solving the 3D structure of proteins. During the procedure, the X-rays are scattered by crystals of the protein and their pattern provides information about the shape of the molecule. The X-rays are detected using a highly efficient CCD detector.. The detector which has been on loan to the department is fast, efficient and easy to use. It has already enabled researchers to solve the structures of many important biomedical proteins including those involved in pathogen virulence, antibiotic biosynthesis, the cell division cycle and oxygen sensing.. In addition to high quality equipment, the X-ray facility relies on the support of the Facilities Manager, Dr Ed Lowe. Dr Lowe provides high level training and assistance to all users and maintains the ...
An entry from the Cambridge Structural Database, the worlds repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures ...
An entry from the Cambridge Structural Database, the worlds repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures ...
a) Single-crystal X-ray structure of 17 f. Ellipsoids are depicted at 30 % probability. b) Part of the crystal lattice packing diagram of 17 f to illustrate the
We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal. ...
Scientists have solved 1,000 protein structures using data collected at CLSs CMCF beamlines. These have been added to the Protein Data Bank - a collection of structures solved by researchers globally.
The malfunction of the transcriptional regulator RUNX1 is the major cause of several variants of acute human leukemias and its normal function is to regulate the development of the blood system in concert with other transcriptional co-regulators. RUNX1 belongs to a conserved family of heterodimeric transcription factors that share a conserved DNA binding domain, the Runt domain (RD), named after the first member of this group - Runt - found in Drosophila melanogaster. The binding partner CBFβ serves as a regulator of RUNX by enhancing its DNA binding affinity through an allosteric mechanism.. The main focus ofo my thesis work has been the crystallization and structural analysis of the RUNX1 RD and involved also more technical methodological aspects that can be applied to X-ray crystallography in general.. The high resolution crystal structure of the free RD shows that this immunoglobulin-like molecule undergoes significant structural changes upon binding to both CBFβ and DNA. This involves a ...
b) using the five-crystal substructure for each. The final electron-density map from the five-crystal data set itself was excellent, giving a MapCC of 85.3% and automated building of 1117 of the 1200 residues (93%) for the DnaK-ATP structure. Even the SAD-phased map without DM modification gave a MapCC of 46.6%. We also found that data sets that did not support substructure determination on their own could support overall structure determination when given the substructure of anomalous scatterers. Thus, single data set 1′ gave a MapCC of 73.0% and an 88% autobuilt atomic model. Only data from single-crystal set 5′, the worst crystal, and the single-wedge data sets other than wedge 1 did not support automated structure determination efficiently (40% autobuilt for crystal 5′, 39-47% for wedges 2 through 8). With the addition of data, either crystal by crystal or wedge by wedge, progressive improvements followed in the monitors of phasing effectiveness.. There are complications in measuring ...
Crystal Structure Analysis, Third Edition, explains how and why the detailed three-dimensional architecture of molecules can be determined by an analysis of the diffraction patterns obtained when X-rays or neutrons are scattered by the atoms in single crystals. Part 1 covers the nature of the crystalline state, diffraction in general, and diffraction by crystals, and also looks briefly at experimental procedures.
Caspases are important players in programmed cell death. Normal activities of caspases are critical for the cell life cycle and dysfunction of caspases may lead to the development of cancer and neurodegenerative diseases. They have become a popular target for drug design against abnormal cell death. In this study, the recognition of P5 position in substrates by caspase-3, -6 and -7 has been investigated by kinetics, modeling and crystallography. Crystal structures of caspase-3 and -7 in complexes with substrate analog inhibitor Ac-LDESD-CHO have been determined at resolutions of 1.61 and 2.45 Å, respectively, while a model of caspase-6/LDESD is constructed. Enzymatic study and structural analysis have revealed that Caspase-3 and -6 recognize P5 in pentapeptides, while caspase-7 lacks P5-binding residues. D-arginine dehydrogenase catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding imino acids and ammonia. The X-ray crystal structures of DADH and its complexes with
In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP + Pi. ATP + H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the gamma P-O-ADP bond-forming step via a double-proton transfer. At this step, the highly conserved alpha S344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar PO3- ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site
The Annual Meeting of the American Crystallographic Association (ACA) will be held July 28 - Aug. 1, 2012, at the Westin Waterfront Hotel in Boston, Mass. Crystallography is the science devoted to exploring the arrangement of atoms in regular crystalline solids and in complicated molecules. Scientists will present research spanning a diverse array of disciplines, including medicine, genomics, material science, and structural biology.. The following summaries link to full news releases and highlight a few of the meetings many noteworthy talks.. Speed and power of X-ray laser helps unlock molecular mysteries: New nanocrystallography technique shines light on biomolecules in action: By outrunning a lasers path of destruction, an international research team has created 3D images of fragile but biologically important molecules inside protein nanocrystals. Using the Linac Coherence Light Source (LCLS), a powerful X-ray laser at the SLAC National Accelerator Laboratory in Menlo Park, Calif., the ...
Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis.: The crystal str
Caspase-3 is a cysteine protease that hydrolyzes diverse intracellular proteins during programmed cell death (known as apoptosis). It has been a popular target for drug design against abnormal cell death for more than a decade. No approved caspase based drug, however, is available so far. Therefore, structural insights about the substrate recognition of caspase-3 are needed for the future development of caspase-3 based inhibitors and drugs. In this study, crystal structures of recombinant caspase-3 in complex with seven substrate analog inhibitors, including acetyl (Ac)-DEVD-aldehyde (Cho), Ac-DMQD-Cho, Ac-IEPD-Cho, Ac-YVAD-Cho, Ac-WEHD-Cho, Ac-VDVAD-Cho, and tert-butoxycarbonyl (Boc)-D-fluoromethylketone (Fmk), have been analyzed in combination with enzyme kinetic data and computational models. Seven crystal structures were determined at resolutions of 1.7-2.6Å. The binding conformation of each inhibitor residue at P1-P4 position was analyzed. The negative P1 aspartic acid side chain is exclusively
The productivity of the ESRFs Structural Biology facilities is currently unmatched within Europe. The basis of our success is the provision of many of the complementary techniques required to study complex problems. In this context, the ESRF Structural Biology Group provides tools, and crucially, access mechanisms, for experiments combining X-ray crystallography and bioSAXS (this may also be extended to bioSANS where appropriate); for experiments combining X-ray crystallography and spectroscopy; for experiments requiring the routine use of micro-focus X-ray beams in an automated fashion; for the collection of high quality diffraction data at both very high and very low resolutions. The provision of robust & reliable facilities for the experiments described above is coupled with the development of innovative methods. Most of the developments currently deployed result from the high quality in-house research carried out in the Group, examples of which are included in this chapter.. A brief perusal ...
All current inhibitors of HIV proteases that are used in clinical treatment of AIDS are targeted against dimeric form of protease. Retrovirus M-PMV infects rhesus monkeys and causes simian immunodeficiency syndrom (SAIDS). This virus is an excellent model for investigation of many processes in retroviruses and for development of new drugs against retroviruses. Our previous biochemical and NMR studies have indicated that in the absence of substrate or inhibitors M-PMV PR should fold into a stable monomer. For solution of crystal structure we prepared a protease mutant, which enabled to prepare a highly concentrated sample for crystallography. However, crystallographers in Poznan could not solve the structure by available molecular replacement and Rosetta programmes. A solution was finally obtained, after several years of experiments, by players of the online game FoldIt who were able to generate model of sufficient quality for successful molecular replacement and subsequent structure ...
A post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of fungal membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques.. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage.. To apply for this role and for further details, including the ...
Overview. Research in my laboratory is focused on understanding fundamental biological processes in atomic detail. A multi-disciplinary strategy is employed using macromolecular X-ray crystallography to determine high resolution, three-dimensional images of proteins and appropriate complexes. The structural information is combined with biochemical, biophysical, genetic, and computational analyses to address questions central to cancer biology. In addition to generating basic biological insights, this approach may facilitate the development new therapeutic agents for the treatment cancer and other diseases.. DNA Replication. My laboratory has contributed to understanding the molecular mechanisms that underlie accurate and mutagenic DNA replication. By integrating high-resolution X-ray structures with functional studies and computational analyses we have been able to elucidate key features that determine high-fidelity DNA replication. This work included exploitation of the properties of a DNA ...
The results are reported here of a XAS study of the O K-edge in oxide minerals, focused on triangular (C2ν site symmetry) and tetrahedral (Td, C2ν and C1) environments involving diverse coordinating cations within four crystal structure types: rutile-type (rutile, pyrolusite and cassiterite), fluorite-type (thorianite), spinel-type (spinel s.s.) and garnet-type (andradite). Full multiple-scattering calculations are compared to actual spectra with the aim of interpreting pre-edge peaks and post-edge features. Comments are presented on the role of combinations between O 2p and metal valence bands. It is concluded that the details and the energy of the O K-edge are influenced by the electronic state and coordination geometry of the surrounding cations in connection with the site symmetry constraints of the coordinated oxygen atoms within the host crystal structure. ...
Aronov A.M., Baker C., Bemis G.W., Cao J., Chen G., Ford P.J., Germann U.A., Green J., Hale M.R., Jacobs M., Janetka J.W., Maltais F., Martinez-Botella G., Namchuk M.N., Straub J., Tang Q., Xie X.. The Ras/Raf/MEK/ERK signal transduction is a key oncogenic pathway implicated in a variety of human cancers. We have identified a novel series of pyrazolylpyrroles as inhibitors of ERK. Aided by the discovery of two distinct binding modes for the pyrazolylpyrrole scaffold, structure-guided optimization culminated in the discovery of 6p, a potent and selective inhibitor of ERK.. J. Med. Chem. 50:1280-1287(2007) [PubMed] [Europe PMC] ...
The new crystal structure shows the location of σ70 for the first time. Its a medium-sized protein (M.W. = 70,000) with five domains. The σ2, σ3, σ4 and σNCR domains form a tight interaction with core RNA polymerase but the flexible end of σ70 is the N-terminal domain (σ1.1) that binds weakly to the main groove where DNA interacts with the holoenzyme. This covers the active site of the enzyme where the first few nucleotides will be polymerized. That σ1.1 domain is shown as a yellow outline in the figure from the paper (below right). The structure of σ1.1 was difficult to resolve in the electron density map, indicating that it is not tightly bound ...
Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and promote apoptosis. Nek2 inhibition with small molecules, therefore, offers the prospect of a new therapy for cancer. To achieve this goal, a better understanding of the requirements for selective-inhibition of Nek2 is required. 6-Alkoxypurines were identified as ATP-competitive inhibitors of Nek2 and CDK2. Comparison with CDK2-inhibitor structures indicated that judicious modification of the 6-alkoxy and 2-arylamino substituents could achieve discrimination between Nek2 and CDK2. In this study, a library of 6-cyclohexylmethoxy-2-arylaminopurines bearing carboxamide, sulfonamide and urea substituents on the 2-arylamino ring was synthesized. Few of these compounds were selective for Nek2 over CDK2, with the best result being obtained for ...
The 3-D structures of CpSGL (5GZH and 5GZK) and BDI_3064 (5Z06) were determined by X-ray crystallography and showed an (α/α)6-fold of this family [1]. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 endo-β-1,2-glucanase (TfSGL) despite their low sequence similarity [3]. The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of endo-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite ...
從圖書館擷取資料! Advancing methods for biomolecular crystallography. [Randy J Read; Alexandre G Urzhumtsev; Vladimir Y Lunin;] -- This work presents a snapshot of the state of the art of modern biomolecular crystallography, from crystallisation through structure determination and even interactive presentation on the web. ...
GM2-activator protein (GM2-AP) is a lipid transfer protein that has the ability to stimulate the enzymatic processing of gangliosides as well as T-cell activation through lipid presentation. Our previous X-ray crystallographic studies of GM2-AP have revealed a large lipid binding pocket as the central overall feature of the structure with non-protein electron density within this pocket suggesting bound lipid. To extend these studies, we present here the 2A crystal structure of GM2-AP complexed with platelet activating factor (PAF). PAF is a potent phosphoacylglycerol whose toxic patho-physiological effects can be inhibited by GM2-AP. The structure shows an ordered arrangement of two bound lipids and a fatty acid molecule. One PAF molecule binds in an extended conformation within the hydrophobic channel that has an open and closed conformation, and was seen to contain bound phospholipid in the low pH apo structure. The second molecule is submerged inside the pocket in a U-shaped conformation with ...
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NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Crystals of the intermetallic compound, MgZn2, were prepared and the crystal structure was determined from x-ray data furnished by Laue and rotation photographs. The crystal was found to have hexagonal axes with a. = 5.15A and c. = 8.48A. The unit cell contains four molecules. The effect of absorption in the crystal in determining the wave-length giving a maximum intensity of reflection in Laue photographs was used to confirm the dimensions of the unit cell. The atoms have the positions: [...] where u = .830 and v = 0.62. The least distance between two magnesium atoms is 3.16A, between two zinc atoms, 2.52A, and between a magnesium and a zinc atom, 3.02A. The constitution diagram for the binary system, magnesium-zinc, has a pronounced maximum corresponding to the formation of an intermetallic compound, MgZn2, which forms eutectics with both constituents. Since both magnesium and ...
A display system includes a relatively higher resolution display for presenting visual information, and a relatively lower resolution display for presenting visual information, the displays being positioned to present the visual information images therefrom in substantially side-by-side relation, the lower resolution image being provided by the cooperation of focusing optics which form a real image at a retro-reflector, which reflects light along an optical path conjugate with light incident thereon to provide an image for viewing, and the higher resolution image being provided without passing through the focusing optics. A method of display includes forming a relatively lower resolution real image, reflecting the image to the eye of an observer, forming a relatively higher resolution image, and directing the relatively higher resolution image to the eye of the observer such that at least a portion of the relatively lower resolution image circumscribes at least a portion of the relatively higher
The structure of a large molecular fragment of factor Xa that lacks only a Gla (gamma-carboxyglutamic acid) domain (N-terminal 45 residues) has been solved by X-ray crystallography and refined at 2.2 A resolution to a crystallographic R-value of 0.168. The fragment identity was clearly established by automated Edman degradation. X-ray structure analysis confirmed the biochemical characterization and also revealed that the N-terminal epidermal growth factor (EGF)-like domain is flexibly disordered in crystals. The second EGF module, however, is positionally ordered making contacts with the catalytic domain. The overall folding of the catalytic domain is similar to that of alpha-thrombin, excluding the insertion loops of the latter with respect to simpler serine proteinases. The C-terminal arginine of the A-chain interacts in a substrate-like manner with the S1 specificity site of the active site of a crystallographically neighboring molecule. Based on this interaction and the structure of ...
Researchers have used a combined powder XRD, solid-state NMR and computational approach to determine the structure of 3,5-bis-O-decanoyl-2-deoxyguanosine.
This force field is intended for crystallographic structure determination. It may be used in conjunction with the ``parhcxdx.pro and ``tophcsdx.pro files for proteins. The parameters originated from Ha et al. (1988) and were modified as described by Weis et al. (1990). ...
I found many weak points in the Ants critique, but Id like to focus on the following point. Scientist in general make dubious or weak assumptions on their results, even experimentalist. After every CD or fluorescence spectrum we read that the protein behaves this or that: the protein: just one, no ensemble, no averaging, all the molecules the same... The native structure of proteins is usually assumed to be a rock the shape you see from the crystal structure, disregarding packing artifacts or the fact that the structure is an averaging (some people have found alternative conformation from the data discarded by crystallographers), even disregarding dynamical evidence from NMR. How many dimers emerge irresponsible from crystal structures, without further tests? How many more emerge from throughput screening in vitro tests in uncontrolled conditions, disregarding the effects of fusion-proteins, tags, cysteine oxidation, aggregation an so on? Almost everybody fit their unfolding curves to ...
I found many weak points in the Ants critique, but Id like to focus on the following point. Scientist in general make dubious or weak assumptions on their results, even experimentalist. After every CD or fluorescence spectrum we read that the protein behaves this or that: the protein: just one, no ensemble, no averaging, all the molecules the same... The native structure of proteins is usually assumed to be a rock the shape you see from the crystal structure, disregarding packing artifacts or the fact that the structure is an averaging (some people have found alternative conformation from the data discarded by crystallographers), even disregarding dynamical evidence from NMR. How many dimers emerge irresponsible from crystal structures, without further tests? How many more emerge from throughput screening in vitro tests in uncontrolled conditions, disregarding the effects of fusion-proteins, tags, cysteine oxidation, aggregation an so on? Almost everybody fit their unfolding curves to ...
Title: Journal of Applied Crystallography, Description: Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographi, By: Feedage Forager, ID: 29619, Grade: 88, Type:
National Seminar on Crystallography The National Seminar on Crystallography 43A was held at Indian Institute of Science Education and Research, Mohali during 28th and 30th March, 2014 by the Department of Chemical Sciences. This conference was
Use [email protected] as the username and leeds8116 as the password If you have not been trained to use the X-ray machine then you need to arrange a training session with Chi (Facility Manager). He must be satisfied that you know how to use the X-ray machine properly and are aware of the health and safety procedures, before you will be allowed to work unsupervised.. ...
Compound. EXEL-2880 (Supplementary Fig. S1) was synthesized at Exelixis ( 41) and its synthesis will be reported separately. The compound was licensed to GSK in December 2007 and is now called GSK1363089.. Kinase inhibition assays. Kinase inhibition was investigated using one of three assay formats: [33P]phosphoryl transfer, luciferase-coupled chemiluminescence, or AlphaScreen tyrosine kinase technology (Perkin-Elmer). Further assay details are provided in Supplementary Section. IC50 values were calculated by nonlinear regression analysis using XLFit.. Expression and X-ray crystallography of Met receptor. The Met kinase domain (1051-1348) was expressed with a NH2-terminal histidine tag and Tobacco Etch Virus protease cleavage site (MLLGSHHHHHHGENLYFQGS) in Sf9 insect cells using a modified pAcGP67 baculovirus DNA transfer vector (BD Pharmingen). Further details of protein purification and X-ray crystallography are provided in Supplementary Section.. Cell lines, cell culture conditions, and ...
!%Bruker AXS%! has launched its Smart X2S crystal-to-structure benchtop x-ray crystallography system for automated 3-D chemical structure determinatio
Activities: Coherent X-ray diffractive imaging of biological samples; Simulation of dynamics within samples irradiated by FEL pulse; Phase retrieval algorithms ...
Well I was reading BKs excellent blog Life of a Lab Rat (an opinion piece from the Guardian "Only biology is safe and, as everybody knows, biology is science for girls." WTF?) When I came upon a link to this great entry on x-ray crystallography (here is some background on what the hell x-ray crystallography…. ...
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Daily News How Gaining and Losing Weight Affects the Body Millions of measurements from 23 people who consumed extra calories every day for a month reveal changes in proteins, metabolites, and gut microbiota that accompany shifts in body mass.. ...
Rigaku VariMax optics are Confocal Max-Flux (CMF) optics used to generate an intense, monochromatic X-ray beam suitable for single-crystal X-ray crystallography.
by volunteering, or simply sending us feedback on the site. Scientists, teachers, writers, illustrators, and translators are all important to the program. If you are interested in helping with the website we have a Volunteer page to get the process started.. ...
Date: Jun 1, 2014. The 1962 book, Fifty Years of X-Ray Diffraction, dedicated to the International Union of Crystallography on the occasion of the commemoration meeting in Munich, July 1962, by P.P. Ewald (editor), and numerous crystallographers has been digitized and put on the web as a free site by the ICU.. Read More ...
Crystal structure models are used by material science professors to help explain how structure influences properties of various materials. Some models come in self assembly kits like the molymod line [2] or molecular model company [3] that range 20-40 Euros, but more detailed models can run hundreds of Euros [4]. Some can even be thousands of euros - particularly for large scale or complex models. Ideally, anyone interested in material science could print these structures in any size or format for a few pennies. Your project: develop an OpenSCAD script to make a 3-D printable model of your randomly selected crystal structure: Due Date Oct 4, 2017 ...
Crystal structure models are used by material science professors to help explain how structure influences properties of various materials. Some models come in self assembly kits like the molymod line [2] or molecular model company [3] that range 20-40 Euros, but more detailed models can run hundreds of Euros [4]. Some can even be thousands of euros - particularly for large scale or complex models. Ideally, anyone interested in material science could print these structures in any size or format for a few pennies. Your project: develop an OpenSCAD script to make a 3-D printable model of your randomly selected crystal structure: Due Date Oct 4, 2017 ...
Science. 2016;352(6286):687-90. Design of structurally distinct proteins using strategies inspired by evolution.. Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B.. Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. We describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. This method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds.. ...
Four dicoumarols (DC, 2-PyDC, 3-PyDC and 4-PyDC) were synthesized and characterized via IR, H-1 NMR, HRMS, and single crystal X-ray crystallography. Two ...
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Zinc atom in PDB 2fpx: Crystal Structure Of the N-Terminal Domain of E.Coli Hisb- Sulfate Complex.
A radial press comprising a first and a second structure, each having a press yoke that form a receiving chamber for a press tool. Under the action of a drive unit, the second structure can be linearl
Pris: 945,-. E-bok, 2015. Leveres direkte via nedlastning . Kjøp boken Symmetry, Spectroscopy, and Crystallography av Robert Glaser (ISBN 9783527684205) hos Adlibris.com. Fri frakt.
Density functional theory with dispersion corrections (DFT-D) was used to study pressure-induced effects in a novel energetic CL-20:HMX cocrystal and to understand what role its constituents CL-20 and HMX have. The structural, electronic, absorption, and mechanical properties of the cocrystal and its constituents were compared and analyzed in detail. The results indicate that the two constituents produce different effects on the crystal structure of the cocrystal in different directions. This distinct energy distribution in the cocrystal suggests that electron transitions may take place between the HMX and CL-20 molecules. The CL-20 in the cocrystal plays a leading role in the electronic structure of the cocrystal. The cocrystal has quite similar absorption spectra to ε-CL-20 but very different ones from β-HMX. Compared with the pure crystals, the mechanical properties of the cocrystal present a great anisotropy, which not only greatly strengthens the stiffness but also affects the... Read more ...
Dallas, Texas (PRWEB) July 18, 2019 -- FabriTec Structures announced the company has partnered with Architectural Record and BNP Media to certify, host, and
The advantage of this system is that it is very intuitive to the crystallographer. In addition, with Eulerian χ values of 0, 90, 180 or 270 degrees the spindle and vertical axes are parallel to the x or y axes of the detector. The main disadvantage of this system is that it is dependent on knowing the geometry of the camera.. While the crystal and cassette orientations follow the spindle/beam convention for Denzo, the beam, box printout, spot, margin, film width and length in the Denzo log file follow the data convention. The X-beam and Y-beam values are the distance from the edge of the data to the beam spot, in mm.. Crossfire is a measure of the X-ray beam divergence and focusing as it leaves the collimator and illuminates the crystal. Crossfire, being a symmetric tensor, has x, y, and xy components. It affects the prediction of partial reflections and their positions, not their angular width. It is expressed as angular divergence of the beam. The default value is zero crossfire, i.e. a ...
Face to this problematic, we propose to design and synthesize a new and anoriginal category of InhA inhibitors targeting, as for the validated antituberculardrug INH, the NADH/NAD+ cofactor-binding site. The design of these newcompounds, analogues of the cofactor, will be assisted by a rational computedmethodology involving structure-based and ligand-based techniques for thedefinition of a pharmacophore. The proof of concept will be validated by acombination of approaches such as: enzymology tests of InhA inhibitory activity,X-ray crystallographic analysis and by biological tests of MTB growth inhibition ...
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On the streets, fans would be at him, demonstrating him a download and a Office. It was like I kept got into the door of a Enough vault seller, he s. Lee was doing download the crystal lattice; the consent constituted changed away Worth.
9780198717591 Our cheapest price for Crystallography: A Very Short Introduction is $8.68. Free shipping on all orders over $35.00.
Snyder DA, Chen Y, Denissova NG, Acton T, Aramini JM, Ciano M, Karlin R, Liu J, Manor P, Rajan PA, et al. Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc. 2005 ;127(47):16505-11. ...
Snyder DA, Chen Y, Denissova NG, Acton T, Aramini JM, Ciano M, Karlin R, Liu J, Manor P, Rajan PA, et al. Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc. 2005 ;127(47):16505-11. ...
Over 4,714 mineral species descriptions are included in this HTML-linked table of crystallography for all known valid mineral species.
Five monomeric complexes of Co(ii), Cu(ii), Ni(ii), Zn(ii) and Ag(i) with 6-methoxyquinoline (6-MeOQ) as ligand have been prepared, and their crystal structures have been determined by single X-ray diffractions. The Cu(ii), Ni(ii) and Zn(ii) complexes are formulated as M(6-MeOQ)2Cl2, completing MN2Cl2 coordi
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Potassium atom in PDB 1zz0: Crystal Structure of A Hdac-Like Protein With Acetate Bound
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Calcium atom in PDB 1egq: Enhancement Of Enzyme Activity Through Three-Phase Partitioning: Crystal Structure of A Modified Serine Proteinase At 1.5 A Resolution
A new type of isomerism has been detected in the cyclidene family of lacunar dioxygen carriers, providing an additional Structural variable for the central of their oxygen affinity. In those rare complexes that do not have methyl substituents on the primary macrocycle, NMR and X-ray crystallographic data indicate that, in addition to their usual cis orientation, the bridges can also adopt a trans orientation. In the crystal structure of [Co(C8MeHH[16]cyclidene)](PF6)(2) . 3CH(3)OH, the bridge has this trails orientation with one end in the lid-on configuration while the other end is lid-off. The trans orientation of the bridge is identified as the principal cause of the decreased dioxygen affinity of such unsubstituted cyclidenes.. ...
Researchers in the field of structural biology, especially X-ray crystallography and protein nuclear magnetic resonance, are interested in knowing as much as possible about the state of their target protein in solution. Not only is this knowledge relevant to studies of biological function, it also facilitates determination of a protein structure using homogeneous monodisperse protein samples. A researcher faced with a new protein to study will have many questions even after that protein has been purified. Analytical ultracentrifugation (AUC) can provide all of this information readily from a small sample in a non-destructive way, without the need for labeling, enabling structure determination experiments without any wasting time and material on uncharacterized samples ...
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Read "Synthesis, crystal structure and antitumor activity of a dinuclear calcium complex based on 1,5-naphthalenedisulfonate and 2,2′-bipyridine ligands, Research on Chemical Intermediates" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
2. I am a chemist who has himself been in a very mathematical part of science (crystal structure determination). In the neighbouring lab, there were two guys which most of us thought to be a little odd and cracked up. They were trying to predict the structures of short metal complexes that were designed to look like the active centers of enzymes and wanted to emulate those enzymes\ functionality. Weird with that PC power we had back then (486s) and often it took weeks just to do one calculation and just to find out something had gone \ploink\. Looks like these things are not so weird anymore, and maybe I\d like to work off a little of the time I\ll spend in purgatory by already now acknowledging that, maybe, those guys weren\t so weird at all ...
Crystal structure of LepB313-618 and comparison with the VirA/EspG-family bacterial RabGAP and the TBC domain of Gyp1p. (A) Overall structure of LepB313-618 in