bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural studies of surface adhesins expressed by oral bacteria
Authors: Hall Michael , Kloppsteck Patrik , Persson Karina
Published: November 2015

Dental plaque is one of the most complex biofilms known and consists of hundreds of bacterial species. Plaque development is initiated by the attachment of salivary proteins to the tooth surface, followed by adherence of early colonizers, such as the Gram-positive Actinomyces oris and oral streptococci. These bacteria form an initial biofilm that is used as attachment surface for late colonizers. The key factors for these microorganisms to network with other bacteria and cells are their surface adhesins and pili. These Gram-positive surface proteins are assembled by very different mechanisms. One form represents the pili, that consists of polymerized proteins linked by covalent bonds with a large adhesin located at the tip. A second form consists of large monomeric proteins with N-terminal adhesive domains presented on stalks formed by repetitive small domains. A third form is represented by the antigen I/II proteins, expressed by oral streptococci. Antigen I/II have a unique fold where a central domain is presented on a stalk formed by intertwining flanking regions bringing both the N- and C-termini close to the cell wall. We have solved structures representing all three aforementioned groups; the pilin protein FimP from A. oris, the surface adhesin sgo0707 from Streptococcus gordonii and antigen I/II proteins from S. gordonii, Streptococcus mutans as well as from Streptococcus pyogenes. The late colonizers are often Gram-negative and one of these bacteria is the periodontal pathogen Porphyromonas gingivalis. This bacteria causes tooth loss and chronic inflammation and increasing evidence points to that P. gingivalis also is involved in the onset of disease at non-oral sites, causing cancer, cardiovascular disease and diabetes. This bacteria expresses two forms of pili with hitherto unexplored structures. Since these pili are important virulence factors we are focusing on structure determination also of these.
Perturbation of host autophagy by the Irish potato famine pathogen
Authors: Maqbool Abbas , Richard Richard , Bozkurt Tolga , Dagdas Yasin , Belhai Khaoula , Kamoun Sophien , Banfield Mark
Published: November 2015

Autophagy is a catabolic process involving degradation of dysfunctional cytoplasmic components to ensure cellular survival under starvation conditions. The process involves formation of double-membrane vesicles called autophagosomes and delivery of the inner constituents to lytic compartments. It can also target invading pathogens, such as intracellular bacteria, for destruction and is thus implicated in innate immune pathways [1]. In response, certain mammalian pathogens deliver effector proteins into host cells that inhibit autophagy and contribute to enabling parasitic infection [2]. Pyhtophthora infestans, the Irish potato famine pathogen, is a causative agent of late blight disease in potato and tomato crops. It delivers a plethora of modular effector proteins into plant cells to promote infection. Once inside the cell, RXLR-type effector proteins engage with host cell proteins, to manipulate host cell physiology for the benefit of the pathogen. As plants lack an adaptive immune system, this provides a robust mechanism for pathogens to circumvent host defense. PexRD54 is an intracellular RXLR-type effector protein produced by P. infestans. PexRD54 interacts with potato homologues of autophagy protein ATG8 in plant cells. We have been investigating the structural and biochemical basis of the PexRD54/ATG8 interaction in vitro. We have purified PexRD54 and ATG8 independently and in complex from E. coli. Using protein/protein interaction studies we have shown that PexRD54 binds ATG8 with sub-micromolar affinity. We have also determined the structure of PexRD54 in the presence of ATG8. This crystal structure provides key insights into how the previously reported WY-fold of oomycete RXLR-type effectors [3] can be organized in multiple repeats. The structural data also provides insights into the interaction between PexRD54 and ATG8, suggesting further experiments to understand the impact of this interaction on host cell physiology and how this benefits the pathogen.
Crystal Structure of the Trypanosoma cruzi Protein Tyrosine Phosphatase TcPTP1
Authors: Lountos George , Tropea Joseph , Waugh David
Published: November 2015

Chagas' disease is a neglected tropical disease transmitted by the flagellated protozoan, Trypanosoma cruzi, which affects millions of people particularly in Latin America. Only two approved drugs are available to treat the disease but they can present several side effects and are not very effective during the chronic stage of the disease. Therefore, given the large population that is at risk, there is a need to discover new molecular targets for drug design efforts. Recently, the T. cruzi protein tyrosine phosphatase, TcPTP1, was shown to play a role in the cellular differentiation and infectivity of the parasite, and therefore, raises its profile as a potential new therapeutic target. Although drug development targeting protein tyrosine phosphatases is challenging and not as advanced as in other targets such as kinases, structure-based drug design methods have shown to be vital in aiding the discovery of novel phosphatase inhibitors with high potency and improved specificity. Here, we present the 2.1 Angstroms resolution X-ray crystal structure of the T. cruzi TcPTP1 that provides structural insights into the active site environment that may be exploited in order to initiate structure-based drug design efforts to develop novel TcPTP1 inhibitors. Potential strategies to develop such inhibitors are also presented that may make it feasible to develop compounds that are specific for TcPTP1.
Crystal structure of JHP933 from Helicobacter pylori J99
Authors: Lee Sang Jae , Yoon Ji Young , Lee Bong-Jin , Suh Se Won
Published: November 2015

Helicobacter pylori infection is the main cause of chronic gastritis, gastric mucosal atrophy, peptic ulcer, and some forms of gastric cancer. There has been considerable interest in strain-specific genes found outside of the cag pathogenicity island, especially genes in the plasticity regions of H. pylori. In H. pylori strain J99, the plasticity region contains 48 genes ranging from jhp0914 to jhp0961. Because little is known about many of these genes in the plasticity region, further studies are necessary to elucidate their roles in H. pylori-associated pathogenesis. The JHP933 protein, encoded by the jhp0933 gene in the plasticity region of H. pylori J99, is one of the prevalently expressed proteins in some gastritis and peptic ulcer patients. However, its structure and function remain unknown. Here, we have determined the crystal structure of JHP933, revealing the first two-domain architecture of DUF1814 family. The N-terminal domain has the nucleotidyltransferase fold and the C-terminal domain is a helix bundle. Structural similarity of JHP933 to known nucleotidyltransferases is very remote, suggesting that it may function as a novel nucleotidyltransferase. It is expected that this study will facilitate functional characterization of JHP933 to obtain an insight into its role in pathogenesis by the H. pylori plasticity region.
Characterization of proline utilization pathway in Mycobacterium tuberculosis
Authors: Lagautriere Thomas , Bashiri Ghader , Cook Gregory , Baker Edward
Published: November 2015

The proline utilization pathway in Mycobacterium tuberculosis (Mtb) has been recently identified as an important factor in Mtb persistence in vivo, suggesting that this pathway could be a valuable therapeutic target against tuberculosis (TB). In Mtb, two distinct enzymes perform the conversion of proline into glutamate; the first step is the oxidation of proline into Δ1-pyrroline-5-carboxylic acid (P5C) by the flavoenzyme proline dehydrogenase (PruB) and the second reaction involves converting the tautomeric form of P5C (glutamate-γ-semialdehyde) into glutamate using the NAD+-dependent Δ1-pyrroline-5-carboxylic dehydrogenase (PruA). Here we describe three-dimensional structures of Mtb-PruA, determined by X-ray crystallography both in its apo state and in complex with NAD+ at 2.5 and 2.1 Å resolution, respectively. The structure reveals a conserved NAD+ binding mode, common to other related enzymes. Conformational differences in the active site, however, linked to changes in the dimer interface, suggest possibilities for selective inhibition of Mtb-PruA despite reasonably high sequence identity with other PruA enzymes. Using recombinant PruA and PruB, the proline utilization pathway in Mtb has also been reconstituted in vitro. Functional validation using a novel NMR approach has demonstrated that the PruA and PruB enzymes are together sufficient to convert proline to glutamate, the first such demonstration for monofunctional proline utilization enzymes.
Rubrerythrin from Trichomonas vaginalis- structural insights into its mechanism of action
Authors: Opel-Reading Helen , Luckner Sylvia , Schaller Ruth , Kurtz Donald , Krause Kurt
Published: November 2015

Trichomoniasis is a common STD with an estimated prevalence of 4 million infections in the United States. The organism that causes trichomoniasis, Trichomonas vaginalis, is essentially anaerobic and contains proteins such as peroxidases that help detoxify reactive oxygen species in its environment. A unique non-heme peroxidase called rubrerythrin, found in this organism, is homologous to bacterial peroxidases, and is markedly upregulated during oxidative stress. It could represent a target for therapeutic intervention given the importance of an anaerobic environment for this organism's survival. Using protein crystallography, we have determined the three-dimensional structure of two forms of this enzyme, the wild-type rubrerythrin which is reddish in colour and a mutant protein, T48A, which is purple. The genes were cloned and expressed in E. coli and purified using liquid chromatography. Crystallization was carried out using vapor diffusion methods. Following optimization, data sets were collected to 2.2Å at the Australian Synchrotron in Melbourne. The phase problem was solved using molecular replacement. Subsequent refinement in Space Group P21212 has yielded a structure with an Rwork/Rfree of 20.6 and 27.3 respectively. The resulting rubrerythrin structure is a dimer of four-helix bundles each containing two metal centers in a geometry and fold very similar to bacterial orthologs. Kinetic studies indicate that it can function as an efficient peroxidase, but only if all sites are occupied by iron. The key to the purple color of the T48A mutant rubrerythrin appears to involve the serendipitous formation of a charge-transfer complex involving the diiron site and a tyrosine, which is facilitated by this mutation. This is the first structure reported of a eukaryotic non-haem iron peroxidase. It is a potentially important virulence factor in T. vaginalis and will serve as a basis for further work to characterize its function within the organism.
Carbapenemase NDM-1, Structural Analysis of the Catalytic Mechanism
Authors: Kim Youngchang , Cunningham Mark , Tesar Christine , Jedrzejczak Robert , Mire Joseph , Binkowski Andrew , Babnigg Gyorgy , Sacchettini James , Joachimiak Andrzej
Published: November 2015

The New Delhi Metallo β-lactamase (NDM-1), first identified in Klebsiella pneumoniae has been shown to hydrolyze nearly all clinical β-lactam antibiotics including carbapenems, considered "last resort" antibiotics. Its gene resides on mobile plasmids that move between different strains of bacteria posing a serious global threat to human health. There have also been reports of several variants, up to NDM-9, some with increased carbapenemase activity. As part of the NIGMS PSI:Biology effort, the Midwest Center for Structural Genomics (MCSG) together with the Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors partnership, made significant progress in investigating the enzyme atomic structure and catalytic mechanism. A large number of protein constructs as well as mutants were made and a number of high-resolution structures of NDM-1 (no Zn, one Zn, two Zn, two Mn or Cd, and complexed with antibiotics) and NDM-1 variants, NDM-2, NDM-3, NDM-4, NDM-5 and NDM-6 have been determined. We have determined the two structures of Michaelis complex: NDM-1 with two cadmium ions and a mixture of hydrolyzed and unhydrolyzed ampicillin (1.50 Å) and one with two cadmium ions and partly hydrolyzed faropenem (2.00 Å). The crystal structures revealed a ligand-binding pocket consisting of several flexible loops capable of accommodating many β-lactam substrates of different sizes and shapes. The structures with various metals suggest that the distance between the two metal atoms is closely correlated with substrate binding efficiency and hydrolysis and the pH-dependency of catalytic activity. For better understanding of catalytic mechanism of NDM-1, particularly the dynamics of substrate binding and the energy surfaces along the suggested reaction pathways, molecular dynamics calculations and hybrid classical/quantum (QM/MM) calculations were performed. This work was supported by NIH Grant GM094585 and by the U.S. DOE, OBER contract DE-AC02-06CH11357
Crystal structure of M. tuberculosis phosphopantetheinyl transferase PptT
Authors: Jung James , Bashiri Ghader , Johnston Jodie , Brown Alistair , Ackerley David , Baker Edward
Published: November 2015

Phosphopantetheinyl transferases (PPTases) are essential enzymes that catalyze covalent attachment of the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to a conserved serine residue on acyl (ACP) and peptidyl carrier proteins (PCP) [1]. This post-translational modification converts the inactive apo-carrier proteins to the functional form, shuttling the intermediates of biosynthetic reactions catalyzed by fatty acid synthases (FAS), polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPSs). In Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), two PPTases, AcpS (type-I) and PptT (type-II), are involved in the biosynthesis of essential lipids, virulence factors and siderophores, activating over 20 target proteins [2]. These two proteins have been shown to be independently essential, suggesting that PPTases could be targeted against tuberculosis [2, 3]. We have expressed the Mtb-PptT protein as a fusion protein with maltose binding protein (MBP). The use of the MBP-PptT fusion protein overcame stability and solubility problems and resulted in successful crystallization. The structure of Mtb-PptT in complex with CoA was determined from the crystal of the fusion protein, solved at 1.75 Å resolution. Excellent electron density is present for all parts of the CoA molecule, revealing a conserved CoA-binding mode. Conformational and charge distribution differences in the putative ACP binding cleft, however, suggest a different mode of ACP binding compared to other homologues. This is the first and only three-dimensional structure of a type-II PPTase from pathogenic bacteria, providing structural features that can be exploited in drug development when compared with its human counterpart.
Structural characterisation of a Fic protein from Clostridium difficile
Authors: Welner Ditte , Dedic Emil , van Leeuwen Hans , Kuijper Ed , Jorgensen Rene , Jorgensen  , Jorgensen Rene
Published: November 2015

Fic domains in proteins are found in abundance in nature from the simplest prokaryotes to animals. Interestingly, Fic domains found in two virulence factors of gram-negative bacteria have recently been demonstrated to catalyse the transfer of an AMP moiety from ATP to small host GTPases (1,2). This post-translational modification has received considerable interest and a role for adenylylation in pathology and physiology is emerging. We have structurally characterised a newly identified Fic protein of the pathogenic gram-positive bacterium Clostridium difficile. A constitutively active inhibitory helix mutant of C. difficile Fic was purified, crystallised and data collected to 1.7 Å resolution. The structure confirms C. difficult Fic protein as an ATP binding protein and reveal a binding site similar to other confirmed virulent Fic proteins. Surprisingly, this gram-positive Fic protein does not seem to target GTPases in humans and currently target identification is being chased. The current status of the project will be presented.
SOD5 is the Prototype of a New Class of Cu-only Superoxide Dismutases
Authors: Galaleldeen Ahmad , Gleason Julie , Cabelli Diane , Hart John , Culotta Valeria
Published: November 2015

Superoxide dismutases (SODs) are antioxidant enzymes that catalyze the dismutation of superoxide into molecular oxygen and hydrogen peroxide. Candida albicans is a polymorphic fungus that causes the majority of fungal infections in humans. In the immunocompetent population, colonization of C. albicans can result in acute infections of the mucosal surfaces both in the oral and genital cavities, however, immunocompromised individuals encounter life-threatening systemic infections. Several factors contribute to the pathogenesis of C. albicans including the expression of SOD5; a postulated copper-zinc SOD. SOD5 enables C. albicans to evade the immune response of the host, namely the oxidative burst. In the absence of SOD5, reactive oxygen species (ROS) accumulate and C. albicans exhibit a severe loss in viability. Our studies sought to examine the crystal structure of SOD5. The protein was overexpressed in E. coli and due to its insolubility; it was denatured, refolded, and further purified. Following protein purification, a sedimentation velocity experiment was performed and the data revealed that SOD5 is a monomeric protein in solution. The structure was then determined using single crystal X-ray diffraction. The structure of SOD5 confirms that it is a prototype of monomeric SODs possessing a copper-only active site and lacking a zinc binding site. In addition, this protein was devoid of the electrostatic loop that typically characterizes all SOD1s. The SOD5 copper site is solvent accessible, cupped in an electrostatic architecture that could serve in superoxide guidance. SOD5-like proteins are widespread among fungal pathogens and appear adapted for the metal and oxidative challenges at the host-pathogen interface.
Insights into Activity Enhancement of H64A Carbonic Anhydrase by Imidazoles
Authors: Aggarwal Mayank , Tu Chingkuang , Silverman David , McKenna Robert
Published: November 2015

Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3-, respectively. The reaction follows a ping-pong mechanism, where the rate limiting step is the transfer of a proton from the zinc-bound solvent out of the active site, via His64 which is widely believed to be the proton shuttling residue. Being involved in a number of physiological processes such as respiration, pH regulation, ureagenesis etc., CAs are therapeutic targets for inhibition to treat various diseases. However, the physiologically dominant isoform is CA II, which is catalytically highly efficient and is easily crystallizable. Thus, most of our knowledge in the design of CA inhibitors with pharmacological applications is based on detailed CA II crystallographic studies. The catalytic activity of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines. This article examines the mechanism through which this activity enhancement might occur. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives have been determined and reveal multiple binding sites. We have identified two molecules of imidazoles that bind in region that is otherwise occupied by the "in" and "out" dual conformation of the side chain of His64 in wild-type CA II. The data presented here not only corroborates the importance of imidazole side chain of His64 in proton transfer during CA catalysis, but also provides a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used in higher concentrations) the activity of H64A CA II. In addition to inhibition of CA by these imidazoles, the presence of a large number of binding sites also gives insights and preliminary data required to fragment addition approach of drug design against CA.
The Ryanodine Receptor: Arrhythmias and Muscle Disorders at High Resolution
Authors: Van Petegem Filip
Published: November 2015

Calcium ions play crucial roles in our bodies, acting as second messengers in multiple signaling pathways. The resting calcium levels in the cytosol are very low, but can increase rapidly and transiently by influx from the extracellular space, or by release from intracellular stores. The Endoplasmic and Sarcoplasmic Reticulum (ER/SR) form major intracellular calcium stores. The `Ryanodine Receptor' (RyR) is a protein that dictates calcium release from the ER/SR. It forms a huge ion channel with a molecular weight exceeding 2 MegaDalton. RyRs are expressed in multiple cell types, but are particularly abundant in cardiac and skeletal muscle, where they are directly involved in excitation-contraction coupling. Three RyR isoforms exist in mammalian species (RyR1, RyR2, RyR3). Mutations in RyR1 and RyR2 have been linked to a number of devastating genetic disorders, including stress-induced cardiac arrhythmias (CPVT), malignant hyperthermia, and central core disease. In the past 5 years we have been solving crystal structures of several RyR domains. Cryo-electron microscopy structures have helped us to build pseudo-atomic models, allowing us to locate these domains in full-length RyRs. Over 80 disease mutations are scattered throughout the structures. The bulk of these affect domain-domain interactions. By comparing the RyR in the open and closed state, we find that some of these interactions are labile: they are disrupted during channel opening. Many disease mutations weaken these interactions, leading to facilitated channel opening, resulting in premature or prolonged release of calcium. In addition, many other disease mutations affect the same labile interactions allosterically. Stabilizing the closed-state domain-domain interactions may therefore be of therapeutic value.
Remote Access of the beamline BL17U at Shanghai Synchrotron Radiation Facility
Authors: Wang Qisheng , Sun Bo , Huang Sheng , Wang Zhijun , He Jianhua
Published: November 2015

BL17U at Shanghai Synchrotron Radiation Facility (SSRF) is a PX beamline designed to high resolution and high throughput structural determination of macromolecules and their complexes. Since it opened to user community at 2009, more than 800 structures are publicly deposited to PDB up to date by using the beamline. The beamline offer more than 160 research group beamtime, the beamtime is over subscribed seriously. Full automation is requested and the staffs keep improving the automation and convenience. Sample changer is critical for the remote operation, it let the users do not need to enter the hutch in their experiment. Several facilities have developed their own robot to achieve this purpose since ten years ago. While for a very shortly period to put the beamline in operation, we adopt the commercial robotics, ACTOR from RIGAKU company, as the sample changer. Users can put 5 uni-type pucks into the dewar one time, totally 80 cryocooled samples. The low level control software is offered by the vendor, although it is not open source, the software provide the API to further development, which can be used to integrate the robot to our software system. Under the help from SSRL, we implement the Blu-Ice/DCS system to our beamline for control and data acquisition [1]. Based on the Blu-Ice/DCS protocol [2], a new DHS is developed to integrate the ACTOR robot to Blu-Ice/DCS. All the function, such as the mount, exchange, dismount and anneal, are implemented as operations. Thus we can program the proper operation by the script engineer to meet the requirements. The intuitive GUI is in the same order as the PUCK in the dewar, the user just click the sample to mount and exchange their samples. Except the laser sensor used to make sure the sample mounted to goniohead successfully, at the same time the user can observe the mount process by the live video server which also integrated into the software. Thanks to the Blu-Ice, the multi GUI clients are supported. The authorized remote users connect to the facility intranet by VPN, by means of the NX client they can connect to the GUI computer on site, as shown in Figure 1. Then they can only run the GUI program for data collection, so the intranet network environment and the equipment are protected maximum.
MxDC & MxLIVE:Software for Macromolecular Crystallography Experiments at the CLS
Authors: Janzen Kathryn , Fodje Michel , Labiuk Shaun , Gorin James , Grochulski Pawel
Published: November 2015

The Canadian Macromolecular Crystallography Facility (CMCF) is a suite of two beamlines 08ID-1 and 08B1-1. Beamline 08B1-1 is a bending-magnet beamline for high-throughput macromolecular crystallography enabling Multiple-Wavelength Anomalous Dispersion (MAD) and Single-Wavelength Anomalous Dispersion (SAD) experiments with a high level of automation. We have developed an integrated software system with modules for beamline control, experiment management, and automated data processing for both on-side and remote users. The experiment management module, also known as MxLIVE (Macromolecular Crystallography Laboratory Information Virtual Environment) is responsible for managing the storage of information about samples, sample shipments, experiment requests, experiment results and data sets. It provides a web-based interface for users to submit sample information and experiment requests, track shipments en route to the CLS and review experiment results and data sets as they are completed on site, and for beamline staff to manage Mail-In data acquisition sessions, reducing the need for user travel to the synchrotron. The beamline control module includes a user-friendly interface for data collection, MxDC (Macromolecular Crystallography Data Collector). MxDC is fully integrated with beamline hardware as well as software applications such as MxLIVE and AutoProcess, an innovative data processing pipeline. This makes MxDC a hub for all experiment-focused activities at CMCF beamlines, including sample auto-mounting, centering and screening crystals, diffraction experiments, and automated data reduction.
I04-1, a future 'fragment screening' beamline facility at Diamond Light Source
Authors: Douangamath Alice , Brandao-Neto Jose , Williams Mark , Fearn Richard , Krojer Tobias , Aller Pierre , Henderson Keith , Longhi Emily , Allianelli Lucia , Von Delft Frank
Published: November 2015

I04-1 is one of the six macromolecular crystallography (MX) beamlines at Diamond Light Source (DLS), the third generation synchrotron light source in the UK. It was built and delivered in 2010 as a stable and reliable fixed-wavelength MX station. It is currently preparing to release its user programme for exploiting fragment screening using X-ray crystallography in structural medicinal chemistry projects. For this purpose, the beamline has been going through several upgrades in order to achieve unattended high-throughput ligand crystallography. The new developments are aiming at improving the flux, stability and reliability of the beamline and its auto-alignment. In parallel, a peripheral laboratory is being set up to provide a facility for medium throughput compound soaking. Jointly with the Structural Genomics Consortium (SGC), a semi-automatic crystal soaking and harvesting scheme, which will provide hundreds of MX samples per day, is being tested at DLS. The beamline can currently process 400 crystals per day. However, the recent upgrades and automation should further improve that throughput. In this presentation, we will summarise the current specifications of the beamline and its new features, the development of a peripheral laboratory for compounds soaking and underline the remaining work.
MacCHESS: Structural Biology at Cornell's High-Energy Synchrotron Source
Authors: Szebenyi Doletha , Cerione Richard , Cook Michael , Gillilan Richard , Huang Qingqiu , Kriksunov Irina , Lukk Tiit , Miller William , Schuller David , Smith Scott
Published: November 2015

"MacCHESS (""Macromolecular diffraction at CHESS"") is an NIH funded facility at the Cornell High Energy Synchrotron Source; we provide a user facility with an exceptional level of support, as well as pursuing research to benefit the entire structural biology community. CRYSTALLOGRAPHY: High-flux monochromatic beamlines outfitted with state-of-the-art equipment are available. BSL-2 biohazards can be handled. Research activities include on-line confocal microscopy, working with multiple small crystals, use of graphene to reduce background, etc. BIOSAXS: A dedicated beamline features: a dual SAXS/WAXS setup using 2 Pilatus detectors; an integrated computer-controlled flow system including robotic sample loading from 96-well trays, custom-made disposable, transparent sample cells, and a convenient graphical interface; a well-equipped wet lab for sample monitoring and final preparation; an in-line SEC-MALS/DLS-SAXS option. Microfluidic "lab-on-a-chip" units are under development. Periodic workshops are held to educate users in the intricacies of BioSAXS. PRESSURE CRYOCOOLING: Cryocooling crystals under pressure reduces both cooling-induced degradation and the need for penetrating cryoprotectants, and can stabilize mobile ligands and possibly reaction intermediates. We offer pressure-cryocooling as a service to CHESS users, while continuing to develop the method. Several sample mounting techniques are now available, and the technique has promise for use with biological samples other than crystals. FMI: To request beamtime, fill out a simple on-line proposal form at http://www.chess.cornell.edu. Mail-in service is available, and remote data collection is supported for experienced crystallography users. We welcome a chance to collaborate on "non-standard" experiments. For more information, contact User Administrator Kathy Dedrick (kd73@cornell.edu)."
The MxCuBE2/ISPyB environment for remote data collection at the ESRF
Authors: de Sanctis Daniele , Monaco Stephanie
Published: November 2015

MxCuBE, is a beamline control graphical user interface (GUI) for macromolecular crystallography (MX) experiments that was developed by the ESRF and has been in use since 2005. The GUI provides the user with a friendly interface to electronic devices, permitting to carry out experiments in a intuitive environment while benefiting from the increasing automation. Since its release, MxCuBE has become the preferred MX data acquisition software, also installed at other European synchrotron sites [SOLEIL, EMBL@PETRAIII, BESSY and MAXLAB].In September 2013, after intense recoding, experiment design and testing, the ESRF has deployed MxCuBE2 on all the ESRF's MX beamlines. This new generation of GUI is capable of interfacing with a variety of low level control systems. MxCuBE2, written in the Python programming language, has a radical new appearance and provides an updated environment for performing complicated multi-crystal/multi-position MX experiments in a modular, logical and automatic fashion. ISPyB is a Laboratory Information Management System (LIMS) conceived to record experimental parameters and basic reporting of the data obtained. Since 2009 ISPyB has been a collaboration between ESRF and Diamond Light Source (DLS) and the LIMS is now a multi-site, generic system for synchrotron-based (MX) experiments. The current version allows users to track their sample location (to/from & at the synchrotron), facilitates transmission of information from and to other LIMS, records experiment details, and provides the results - including reflection files - of automatic data processing protocols. Indeed as experiments have become more complex and automated ISPyB has become more than just a repository for project histories - it has become a support for rapid decision making during experiments. The combination of these two indispensable tools in every day users life at the European Synchrotron Radiation Facility will be presented and discussed.
Remote Access to Diamond Light Source – Adding Flexibility to MX Experiments
Authors: Hall David , Aller Pierre , Ashton Alun , Axford Danny , Douangamath Alice , Fearn Richard , Hathaway Paul , Levik Karl , McAuley Katherine , Williams Mark
Published: November 2015

Diamond Light Source (DLS) provides a suite of world-leading beamlines for macromolecular crystallography (MX) experiments which are used by scientists from all over the world. Key to their success is an integrated approach to automating the hardware and software environments such that it is only necessary to enter the beamline hutch to change large batches of samples for the robotic sample changers. Alongside investing in automation, all beamlines are also equipped with Pilatus 6M-F detectors (25 – 100 Hz) resulting in fast data collections and high turnover of samples. Rapid downstream processing of the resulting data has been developed since this is essential to drive experimental decisions. The feedback from these pipelines needs to be made readily available to users in a timely manner and a number of tools are available for both local and remote visualization of results. Remote access to these facilities was a design requirement from the outset. Several tools have been integrated and developed to streamline the process of remote access yet give the same software environment remotely as would be experienced if the experimenter was present at the beamline. The advent of remote access for cryogenically frozen samples has led to the implementation of new shift patterns for the user programme, enabling frequent short shifts for the many groups who use DLS. Remote access to MX beamlines is also a prerequisite of many industrial clients of DLS. For the future we are moving forward with the development of remote access for in-situ data collection from crystallization plates following on from the success of this method for screening and collecting data by users at the beamlines. The implementation and impact of remote access at DLS will be presented here.
Modulated protein crystal structure with 28 molecules in the asymmetric unit
Authors: Jaskolski Mariusz , Sliwiak Joanna , Kowiel Marcin , McCoy Airlie , Read Randy , Dauter Zbigniew
Published: November 2015

In modulated crystals short-range translational order is lost and the atomic structure cannot be defined by the contents of a single small unit cell. The wave of disorder is described by a modulation function, which restores long-range periodicity. If the modulation period divided by the unit cell translation is a rational number, then the modulation is commensurate, and can be described in an expanded unit cell. Otherwise it is incommensurate. The diffraction pattern of a modulated structure contains strong main reflections from the basic unit cell, surrounded by weaker satellites from the modulation wave. Modulated structures are rare in protein crystallography. Stress factors induce in plants the expression of Pathogenesis-Related (PR) proteins, divided into 17 classes. PR proteins of class 10 (PR-10) are well studied structurally but their biological function is unclear with an implication in phytohormone binding. PR-10/hormone complexes are studied using fluorescent probes such as ANS (8-anilino-1-naphthalene sulfonate). We crystallized Hyp-1, a PR-10 protein from St John's wort, in complex with ANS. Solution of the apparent P4(1)22 crystal structure was impossible by standard molecular replacement because of evident tetartohedral twinning and a bizarre modulation of reflection intensities with l periodicity of 7. The structure was solved using Phaser and data expanded to P1 symmetry. Ultimately, the structure turned out to have C2 symmetry with 28 independent protein molecules, arranged in dimers around a non-crystallographic (NCS) screw along c with a pitch of ~1/7. The seven-fold repetition along c is indicative of a commensurate modulated structure: the NCS copies are similar but not identical. For instance, the consecutive Hyp-1 molecules bind a varying number (0-3) of the ligand molecules. The structure has been successfully refined to R=22.2% using conventional methods, i.e. with unit cell expanded to encompass the entire commensurate modulation period.
Selective time-dependent changes of Cu(DPPE)(DMP)·PF6on photoexcitation
Authors: Trzop Elzbieta , Fournier Bertrand , Jarzembska Katarzyna , Sokolow Jesse , Kaminski Radoslaw , Benedict Jason , Chen Yang , Henning Robert , Coppens Philip
Published: November 2015

Thanks to their potential applications as light-emitting devices, chemical sensors and dye-sensitized solar cells, heteroleptic copper (I) complexes have been extensively studied. Cu(DPPE)(DMP)·PF6(dppe= 1,2-bis(diphenylphosphino)ethane; dmp = 2,9-dimethyl-1,10-phenanthroline) crystallizes in the monoclinic system, P21/c, with two independent molecules in the asymmetric unit. Previous studies on this system [1,2] show strong temperature-dependent emission. The complex was studied at 90K under 355nm laser excitation. At this temperature, the luminescence decay for Cu(DPPE)(DMP)·PF6is biexponential with lifetimes of ~3μs and ~28μs. Two time-resolved X-ray diffraction techniques were applied for studies: (1) a Laue technique at BioCARS ID-14 beamline at the Advanced Photon Source, and (2) monochromatic diffraction at a newly constructed in-house pump-probe monochromatic facility at the University at Buffalo. Structural changes determined with the two methods are in qualitative agreement; discrepancies in position of the Cu and P atoms were observed. The molecular distortions were smaller than those determined at 16K in the earlier synchrotron study by Vorontsov et al. [2]. Photodeformation maps (see Figure below), in which the increase in temperature on photoexcitation has been eliminated, clearly illustrate the photoinduced atomic shifts for both data sets. Results will be compared with those obtained for other studied heteroleptic copper (I) complexes, for instance Cu[(1,10-phenanthroline-N,N′) bis(triphenylphosphine)]·BF4[3]. The in-house pump-probe facility is discussed by Radoslaw Kaminski at this meeting. Research funded by the National Science Foundation (CHE1213223). BioCARS Sector 14 at APS is supported by NIH (RR007707). The Advanced Photon Source is funded by the Office of Basic Energy Sciences, U.S. Department of Energy, (W-31-109-ENG-38). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.
Direct observation of the excited state structure of a Ag(I)-Cu(I) complex
Authors: Jarzembska Katarzyna , Kaminski Radoslaw , Fournier Bertrand , Trzop Elzbieta , Sokolow Jesse , Chen Yang , Henning Robert , Coppens Philip
Published: November 2015

Heterodentate coordination complexes have been extensively studied because of their rich electronic and luminescent properties, which are of importance in the design of molecular devices. The short metal-metal contacts found in such complexes determine the nature of the lowest lying emissive states, and must be explored in order to understand their physical properties. Recent advances in time-resolved (TR) synchrotron techniques supported by specific data collection strategies and data processing procedures [1] allow for elucidation of molecular excited state geometries in the solid state. The approach has been so far successfully applied to several high-quality Laue-data sets collected at the 14-ID BioCars beamline at the Advanced Photon Source.[2] In this contribution we present synchrotron TR experiment results obtained for a new solvent-free crystal form of a model complex containing Ag(I) and Cu(I) (Ag2Cu2L4, L = 2-diphenylphosphino-3-methylindole).[3] This system exhibits red solid-state luminescence with a lifetime of about 1 µs. This is one of the shortest-lived excited states we have studied so far with the Laue technique. The relatively short lifetime goes along with significant structural changes observed upon irradiation, such as, the Ag...Ag distance shortening of about 0.2 Å in the excited state. The results clearly show strengthening of the Ag...Ag interactions suggesting a bond formation upon excitation. The photocrystallographic findings are supported by spectroscopic measurements and quantum computations. The results confirm the triplet nature of the emissive state originating mainly from a ligand-to-metal charge transfer. Research funded by the NSF (CHE1213223). BioCARS Sector 14 is supported by NIH, National Center for Research Resources (RR007707). APS is funded by the U.S. DOE, Office of Basic Energy Sciences (W-31-109-ENG-38). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.
XRPD study of photo-induced HS→LS relaxation of hydrated [Fe(pyrazine)Pt(CN)4]
Authors: Delgado Teresa , Tissot Antoine , Besnard Céline , Guénée Laure , Pattison Philip , Hauser Andreas
Published: November 2015

The 2D layer compound [Fe(pyrazine)Pt(CN)4] has received a lot of attention because of its spin transition with a large hysteresis at room temperature, the possibility of bidirectional light-switching, and its potential as sensor for various gases [1], and in a recent study it served as test case for time-resolved electron diffraction on the nano-second time scale [2]. The present study focuses on the photo-induced HS → LS relaxation of the hydrated compound monitored by synchrotron XRPD measurements at 10 K (Figure 1). For the title compound, the time evolution of the XRD pattern shows a complex relaxation behaviour, which can be modelled with an initial random relaxation followed by a nucleation and growth process.
High-pressure Synthesis of New layered Oxyhalide Perovskites
Authors: Tsujimoto Yoshihiro , Matsushita Yoshitaka , Yamaura Kazunari , Uchikoshi Tetsuo
Published: November 2015

The development of transition metal oxides with perovskite-based structure has stimulated the search for mixed anion systems such as oxynitrides, oxyhalides and oxysulfides because incorporation of two different anions in one structure offers further opportunity to effectively induce chemical and physical properties that the pure oxides cannot possess. Such mixed anion phases, however, are difficult to be synthesized by a conventional high-temperature reaction. In this study, we have employed a high pressure technique to overcome this issue, and succeessfully synthesized a series of new layered oxhalide compounds. We present structural and magnetic properties of high-valent nickel oxyhalides Sr2NiO3X (X = F, Cl), and square-planar coordinated oxychlorides Sr2MO2Cl2 (Mn, Ni) and Ba2PdO2Cl2, isostructural with superconducting parent compund Ca2CuO2Cl2.
High-T, High-P Hydrothermal Synthesis of Uranium Silicates and Germanates
Authors: Lii Kwang-Hwa
Published: November 2015

Most uranium minerals can be classified as oxidized species in which U is fully oxidized to U(VI), and reduced species, in which U occurs primarily as U(IV). Uranyl silicates are an important group of uranium(VI) minerals in the altered zones of many uranium deposits [1]. Uranyl silicates have also received attention because they form when spent nuclear fuel interacts with water containing silicon under oxidizing conditions. One naturally occurring uranium(IV) silicate exists, namely coffinite (USiO4), which is the most important ore mineral for uranium after uraninite. Numerous synthetic uranium(VI) silicates and germanates containing organic amines or alkali metals as countercations have also been reported [2]. In contrast to the uranium(VI) compounds, the chemistry of materials containing uranium(V) is considerably less developed owing to the tendency of U(V) to either oxidize to U(VI) or disproportionate to U(IV) and U(VI). We have synthesized a pentavalent-uranium silicate and a germanate by a high-temperature, high-pressure hydrothermal method in gold ampoules contained in a high-pressure reaction vessel at ca. 600 °C and 170 MPa [3a,b]. Following the synthesis of the U(V) compounds, a number of mixed-valence uranium silicates and germanates have been synthesized, for example, a mixed-valence uranium(IV,V) silicate, Cs2K(UO)2Si4O12 [3c], a uranium(IV,VI) germanate, Cs8U(UO2)3(Ge3O9)3·3H2O [3d], uranium(V,VI) silicates and germanates, A3(U2O4)Ge2O7 (A = Rb, Cs) and [Na9F2][(UO2)3(Si2O7)2] [3e,f], and a uranium(IV,V,VI) silicate, Na7UO2(UO)2(UO2)2Si4O16 [3g] in which three oxidation states of uranium co-exist in one compound. In addition, tetravalent-uranium compounds, Cs2USi6O15 and Cs4UGe8O20 [3h,i], were also synthesized. All members in the family of uranium silicates and germanates with the oxidation states of uranium from +4 to +6 have been observed. In this presentation the high-temperature, high-pressure hydrothermal synthesis, crystal structures, and XPS spectroscopy of these interesting compounds will be reported.
Exploring Host-Guest Interactions: a Single Crystal High-Pressure study
Authors: Eikeland Espen , Madsen Solveig , Overgaard Jacob , Spackman Mark , Iversen Bo
Published: November 2015

Single crystal X-ray diffraction data from several Hydroquinone clathrate systems, with various small guest molecules (e.g. HCOOH, MeOH), have been obtained up to a pressure of 10 GPa, using a diamond anvil cell (DAC). Hydroquinone clathrates are key examples of supramolecular aggregates, having a diverse structural chemistry controlled, to a large extent, by the detailed intermolecular interactions between the host and the guest molecules. Although supramolecular chemistry is the foundation for the design and development of advanced materials (e.g. for catalysis, targeted drug delivery, chemical separation and nonlinear optics) the basic understanding leading to such complex systems are often lacking. High pressure (HP) crystallography is an excellent method of systematically increasing host-guest interactions by forcing the molecules closer together, often leading to interesting and unexpected results. At ambient pressure smaller guest molecules are often disordered inside the clathrate cavities. As the external pressure increases the cavities shrink, and it seems likely that guest molecules will order inside the cavity breaking the host symmetry. Guest ordering transitions are also found upon cooling. In this work, results from HP studies of the hydroquinone – formic acid system reveal that the structure is stable up to 10 GPa, at which pressure the guest cavity volume is reduced by more than 50 % without ordering of the guest atoms. Earlier studies have shown that the empty Hydroquinone clathrate undergoes a phase transition into a nonporous structure already at 0.4 GPa. [1] This indicates that formic acid stabilizes the host framework through strong intermolecular host-guest interactions, but without lowering the host symmetry.