The application and use of chemical space mapping to interpret crystallization screening results.

PubMed

Snell, Edward H; Nagel, Ray M; Wojtaszcyk, Ann; O'Neill, Hugh; Wolfley, Jennifer L; Luft, Joseph R

2008-12-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually.

A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase.

PubMed

Kolek, Stefan Andrew; Bräuning, Bastian; Stewart, Patrick Douglas Shaw

2016-04-01

Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crystallization. Seed crystals are grown directly in LCP and, as with conventional rMMS, a seeding experiment is combined with an additive experiment. The new method was used with the bacterial integral membrane protein OmpF, and it was found that it increased the number of crystallization hits by almost an order of magnitude: without microseeding one new hit was found, whereas with LCP-rMMS eight new hits were found. It is anticipated that this new method will lead to better diffracting crystals of membrane proteins. A method of generating seed gradients, which allows the LCP seed stock to be diluted and the number of crystals in each LCP bolus to be reduced, if required for optimization, is also demonstrated.

Optimizing Associative Experimental Design for Protein Crystallization Screening

PubMed Central

Dinç, Imren; Pusey, Marc L.; Aygün, Ramazan S.

2016-01-01

The goal of protein crystallization screening is the determination of the main factors of importance to crystallizing the protein under investigation. One of the major issues about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for maximizing the chances of a successful (crystalline) outcome. In this paper, we propose an experimental design method called “Associative Experimental Design (AED)” and an optimization method includes eliminating prohibited combinations and prioritizing reagents based on AED analysis of results from protein crystallization experiments. AED generates candidate cocktails based on these initial screening results. These results are analyzed to determine those screening factors in chemical space that are most likely to lead to higher scoring outcomes, crystals. We have tested AED on three proteins derived from the hyperthermophile Thermococcus thioreducens, and we applied an optimization method to these proteins. Our AED method generated novel cocktails (count provided in parentheses) leading to crystals for three proteins as follows: Nucleoside diphosphate kinase (4), HAD superfamily hydrolase (2), Nucleoside kinase (1). After getting promising results, we have tested our optimization method on four different proteins. The AED method with optimization yielded 4, 3, and 20 crystalline conditions for holo Human Transferrin, archaeal exosome protein, and Nucleoside diphosphate kinase, respectively. PMID:26955046

Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins

PubMed Central

Li, Liang; Mustafi, Debarshi; Fu, Qiang; Tereshko, Valentina; Chen, Delai L.; Tice, Joshua D.; Ismagilov, Rustem F.

2006-01-01

High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a “hybrid” droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as ≈140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in ≈10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 μl of protein solution, ≈1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization. PMID:17159147

Screening and Characterization of Hydrate Forms of T-3256336, a Novel Inhibitor of Apoptosis (IAP) Protein Antagonist.

PubMed

Takeuchi, Shoko; Kojima, Takashi; Hashimoto, Kentaro; Saito, Bunnai; Sumi, Hiroyuki; Ishikawa, Tomoyasu; Ikeda, Yukihiro

2015-01-01

Different crystal packing of hydrates from anhydrate crystals leads to different physical properties, such as solubility and stability. Investigation of the potential of varied hydrate formation, and understanding the stability in an anhydrous/hydrate system, are crucial to prevent an undesired transition during the manufacturing process and storage. Only one anhydrous form of T-3256336, a novel inhibitor of apoptosis (IAP) protein antagonist, was discovered during synthesis, and no hydrate form has been identified. In this study, we conducted hydrate screening such as dynamic water vapor sorption/desorption (DVS), and the slurry experiment, and characterized the solid-state properties of anhydrous/hydrate forms to determine the most desirable crystalline form for development. New hydrate forms, both mono-hydrate and hemi-hydrate forms, were discovered as a result of this hydrate screening. The characterization of two new hydrate forms was conducted, and the anhydrous form was determined to be the most desirable development form of T-3256336 in terms of solid-state stability. In addition, the stability of the anhydrous form was investigated using the water content and temperature controlled slurry experiment to obtain the desirable crystal form in the crystallization process. The water content regions of the stable phase of the desired form, the anhydrous form, were identified for the cooling crystallization process.

Can the propensity of protein crystallization be increased by using systematic screening with metals?

PubMed

Hegde, Raghurama P; Pavithra, Gowribidanur C; Dey, Debayan; Almo, Steven C; Ramakumar, S; Ramagopal, Udupi A

2017-09-01

Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization. © 2017 The Protein Society.

Protein crystal screening and characterization for serial femtosecond nanocrystallography

PubMed Central

Darmanin, Connie; Strachan, Jamie; Adda, Christopher G.; Ve, Thomas; Kobe, Bostjan; Abbey, Brian

2016-01-01

The recent development of X-ray free electron lasers (XFELs) has spurred the development of serial femtosecond nanocrystallography (SFX) which, for the first time, is enabling structure retrieval from sub-micron protein crystals. Although there are already a growing number of structures published using SFX, the technology is still very new and presents a number of unique challenges as well as opportunities for structural biologists. One of the biggest barriers to the success of SFX experiments is the preparation and selection of suitable protein crystal samples. Here we outline a protocol for preparing and screening for suitable XFEL targets. PMID:27139248

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Trace fluorescent labeling for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pusey, Marc, E-mail: marc.pusey@ixpressgenes.com; Barcena, Jorge; Morris, Michelle

2015-06-27

The presence of a covalently bound fluorescent probe at a concentration of <0.5% does not affect the outcome of macromolecule crystallization screening experiments. Additionally, the fluorescence can be used to determine new, not immediately apparent, lead crystallization conditions. Fluorescence can be a powerful tool to aid in the crystallization of proteins. In the trace-labeling approach, the protein is covalently derivatized with a high-quantum-yield visible-wavelength fluorescent probe. The final probe concentration typically labels ≤0.20% of the protein molecules, which has been shown to not affect the crystal nucleation or diffraction quality. The labeled protein is then used in a plate-screening experimentmore » in the usual manner. As the most densely packed state of the protein is the crystalline form, then crystals show as the brightest objects in the well under fluorescent illumination. A study has been carried out on the effects of trace fluorescent labeling on the screening results obtained compared with nonlabeled protein, and it was found that considering the stochastic nature of the crystal nucleation process the presence of the probe did not affect the outcomes obtained. Other effects are realised when using fluorescence. Crystals are clearly seen even when buried in precipitate. This approach also finds ‘hidden’ leads, in the form of bright spots, with ∼30% of the leads found being optimized to crystals in a single-pass optimization trial. The use of visible fluorescence also enables the selection of colors that bypass interfering substances, and the screening materials do not have to be UV-transparent.« less

Computational crystallization

PubMed Central

Altan, Irem; Charbonneau, Patrick; Snell, Edward H.

2016-01-01

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. PMID:26792536

Automation in biological crystallization.

PubMed

Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

2014-06-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

Automation in biological crystallization

PubMed Central

Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

2014-01-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

Fragment-based screen against HIV protease.

PubMed

Perryman, Alexander L; Zhang, Qing; Soutter, Holly H; Rosenfeld, Robin; McRee, Duncan E; Olson, Arthur J; Elder, John E; Stout, C David

2010-03-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

Fragment-Based Screen against HIV Protease

PubMed Central

Perryman, A. L.; Zhang, Q.; Soutter, H. H.; Rosenfeld, R.; McRee, D. E.; Olson, A. J.; Elder, J. E.; Stout, C. D.

2009-01-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly16Gly17Gln18 loop where the amide of Gly17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14 and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target. PMID:20659109

Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments.

PubMed

Offermann, Lesa R; He, John Z; Mank, Nicholas J; Booth, William T; Chruszcz, Maksymilian

2014-03-01

The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes.

PubMed

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M; Polizzo, Gina M; Ericson, Daniel L; Roessler, Christian G; Campos, Olven; Ma, Millie Y; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M; Sweet, Robert M; Soares, Alexei S

2014-05-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

PubMed Central

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M.; Polizzo, Gina M.; Ericson, Daniel L.; Roessler, Christian G.; Campos, Olven; Ma, Millie Y.; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

2014-01-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component. PMID:24816088

Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

PubMed Central

Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

2015-01-01

Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

Maximizing Macromolecule Crystal Size for Neutron Diffraction Experiments

NASA Technical Reports Server (NTRS)

Judge, R. A.; Kephart, R.; Leardi, R.; Myles, D. A.; Snell, E. H.; vanderWoerd, M.; Curreri, Peter A. (Technical Monitor)

2002-01-01

A challenge in neutron diffraction experiments is growing large (greater than 1 cu mm) macromolecule crystals. In taking up this challenge we have used statistical experiment design techniques to quickly identify crystallization conditions under which the largest crystals grow. These techniques provide the maximum information for minimal experimental effort, allowing optimal screening of crystallization variables in a simple experimental matrix, using the minimum amount of sample. Analysis of the results quickly tells the investigator what conditions are the most important for the crystallization. These can then be used to maximize the crystallization results in terms of reducing crystal numbers and providing large crystals of suitable habit. We have used these techniques to grow large crystals of Glucose isomerase. Glucose isomerase is an industrial enzyme used extensively in the food industry for the conversion of glucose to fructose. The aim of this study is the elucidation of the enzymatic mechanism at the molecular level. The accurate determination of hydrogen positions, which is critical for this, is a requirement that neutron diffraction is uniquely suited for. Preliminary neutron diffraction experiments with these crystals conducted at the Institute Laue-Langevin (Grenoble, France) reveal diffraction to beyond 2.5 angstrom. Macromolecular crystal growth is a process involving many parameters, and statistical experimental design is naturally suited to this field. These techniques are sample independent and provide an experimental strategy to maximize crystal volume and habit for neutron diffraction studies.

Computational crystallization.

PubMed

Altan, Irem; Charbonneau, Patrick; Snell, Edward H

2016-07-15

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

DMA Modulus as a Screening Parameter for Compatibility of Polymeric Containment Materials with Various Solutions for use in Space Shuttle Microgravity Protein Crystal Growth (PCG) Experiments

NASA Technical Reports Server (NTRS)

Wingard, Charles Doug; Munafo, Paul M. (Technical Monitor)

2002-01-01

Protein crystals are grown in microgravity experiments inside the Space Shuttle during orbit. Such crystals are basically grown in a five-component system containing a salt, buffer, polymer, organic and water. During these experiments, a number of different polymeric containment materials must be compatible with up to hundreds of different PCG solutions in various concentrations for durations up to 180 days. When such compatibility experiments are performed at NASA/MSFC (Marshall Space Flight Center) simultaneously on containment material samples immersed in various solutions in vials, the samples are rather small out of necessity. DMA4 modulus was often used as the primary screening parameter for such small samples as a pass/fail criterion for incompatibility issues. In particular, the TA Instruments DMA 2980 film tension clamp was used to test rubber O-rings as small in I.D. as 0.091 in. by cutting through the cross-section at one place, then clamping the stretched linear cord stock at each end. The film tension clamp was also used to successfully test short length samples of medical/surgical grade tubing with an O.D. of 0.125 in.

Protein Crystallization Using Room Temperature Ionic Fluids

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Paley, Mark Steve; Turner, Megan B.; Rogers, Robin D.

2006-01-01

The ionic liquids (ILs) 1-butyl-3-methylimidizolium chloride (C4mim-C1), 1-butyl-3- methylimidizolium diethyleneglycol monomethylethersulfate ([C4mim]DEMGS), and 1-butyl-1 -methylpyrollidinium dihydrogenphosphate ([p1,4]dhp) were tested for their effects on the crystallization of the proteins canavalin, beta-lactoglobulin B, xylanase, and glucose isomerase, using a standard high throughput screen. The crystallization experiments were set up with the ILs added to the protein solutions at 0.2 and 0.4 M final concentrations. Crystallization droplets were set up at three proteixprecipitant ratios (1:1, 2:1, and 4:l), which served to progressively dilute the effects of the screen components while increasing the equilibrium protein and IL concentrations. Crystals were obtained for all four proteins at a number of conditions where they were not obtained from the IL-free control experiment. Over half of the protein-IL combinations tested had more successful outcomes than negative, where the IL-free crystallization was better than the corresponding IL-containing outcome, relative to the control. One of the most common causes of a negative outcome was solubilization of the protein by the IL, resulting in a clear drop. In one instance, we were able to use the IL-induced solubilizing to obtain beta-lactoglobulin B crystals from conditions that gave precipitated protein in the absence of IL. The results suggest that it may be feasible to develop ILs specifically for the task of macromolecule crystallization.

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.

PubMed

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M F; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A; Gotz, Andy

2012-08-01

The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

Can computed crystal energy landscapes help understand pharmaceutical solids?

PubMed Central

Price, Sarah L.; Braun, Doris E.; Reutzel-Edens, Susan M.

2017-01-01

Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape. PMID:27067116

Controlled In Meso Phase Crystallization – A Method for the Structural Investigation of Membrane Proteins

PubMed Central

Kubicek, Jan; Schlesinger, Ramona; Baeken, Christian; Büldt, Georg; Schäfer, Frank; Labahn, Jörg

2012-01-01

We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i) the stabilization of membrane proteins in the meso phase, (ii) the control of hydration level and additive concentration by vapor diffusion. The new technology (iii) significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv) direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR) crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII) from Halobacterium salinarum for the first time. PMID:22536388

The promise of macromolecular crystallization in microfluidic chips

NASA Technical Reports Server (NTRS)

van der Woerd, Mark; Ferree, Darren; Pusey, Marc

2003-01-01

Microfluidics, or lab-on-a-chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bioanalytical and microscale biopreparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require a macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a microfluidics platform. Optimization methods, in which crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a microfluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation and harvesting of crystals as they are grown.

Crystal Nucleation Using Surface-Energy-Modified Glass Substrates.

PubMed

Nordquist, Kyle A; Schaab, Kevin M; Sha, Jierui; Bond, Andrew H

2017-08-02

Systematic surface energy modifications to glass substrates can induce nucleation and improve crystallization outcomes for small molecule active pharmaceutical ingredients (APIs) and proteins. A comparatively broad probe for function is presented in which various APIs, proteins, organic solvents, aqueous media, surface energy motifs, crystallization methods, form factors, and flat and convex surface energy modifications were examined. Replicate studies ( n ≥ 6) have demonstrated an average reduction in crystallization onset times of 52(4)% (alternatively 52 ± 4%) for acetylsalicylic acid from 91% isopropyl alcohol using two very different techniques: bulk cooling to 0 °C using flat surface energy modifications or microdomain cooling to 4 °C from the interior of a glass capillary having convex surface energy modifications that were immersed in the solution. For thaumatin and bovine pancreatic trypsin, a 32(2)% reduction in crystallization onset times was demonstrated in vapor diffusion experiments ( n ≥ 15). Nucleation site arrays have been engineered onto form factors frequently used in crystallization screening, including microscope slides, vials, and 96- and 384-well high-throughput screening plates. Nucleation using surface energy modifications on the vessels that contain the solutes to be crystallized adds a layer of useful variables to crystallization studies without requiring significant changes to workflows or instrumentation.

Use of Linear and Circular Polarization: The Secret LCD Screen and 3D Cinema

ERIC Educational Resources Information Center

Richtberg, Stefan; Girwidz, Raimund

2017-01-01

References to everyday life are important for teaching physics. Discussing polarization phenomena, liquid crystal displays (LCDs) and 3D cinemas provide such references. In this paper we describe experiments to support students' understanding of linearly polarized light as well as the phenomenon of inverted colors using a secret LCD screen.…

The role of mass transport in protein crystallization.

PubMed

García-Ruiz, Juan Manuel; Otálora, Fermín; García-Caballero, Alfonso

2016-02-01

Mass transport takes place within the mesoscopic to macroscopic scale range and plays a key role in crystal growth that may affect the result of the crystallization experiment. The influence of mass transport is different depending on the crystallization technique employed, essentially because each technique reaches supersaturation in its own unique way. In the case of batch experiments, there are some complex phenomena that take place at the interface between solutions upon mixing. These transport instabilities may drastically affect the reproducibility of crystallization experiments, and different outcomes may be obtained depending on whether or not the drop is homogenized. In diffusion experiments with aqueous solutions, evaporation leads to fascinating transport phenomena. When a drop starts to evaporate, there is an increase in concentration near the interface between the drop and the air until a nucleation event eventually takes place. Upon growth, the weight of the floating crystal overcomes the surface tension and the crystal falls to the bottom of the drop. The very growth of the crystal then triggers convective flow and inhomogeneities in supersaturation values in the drop owing to buoyancy of the lighter concentration-depleted solution surrounding the crystal. Finally, the counter-diffusion technique works if, and only if, diffusive mass transport is assured. The technique relies on the propagation of a supersaturation wave that moves across the elongated protein chamber and is the result of the coupling of reaction (crystallization) and diffusion. The goal of this review is to convince protein crystal growers that in spite of the small volume of the typical protein crystallization setup, transport plays a key role in the crystal quality, size and phase in both screening and optimization experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Xingyu; Stony Brook University, NY 11794-5215; Nanjing University, Nanjing, Jiangsu

A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin. Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the lowmore » consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.« less

Peculiarities of Crystallization of the Restriction Endonuclease EcoRII

NASA Technical Reports Server (NTRS)

Karpove, Elizaveta; Pusey, M.arc L.

1998-01-01

Nucleases interfere with most standard molecular biology procedures. We have purified and crystallized the restriction endonuclease EcoRII, which belongs to the type II of restriction- modification enzyme, to study the protein crystallization process using a "non standard" macromolecule. A procedure for the purification of EcoRII was developed and 99% pure protein as determined by SDS PAGE electrophoresis obtained. Light scattering experiments were performed to assist in screening protein suitable crystallization conditions. The second virial coefficient was determined as a function of precipitating salt concentration, using sodium chloride, ammonium sulfate, and sodium sulfate. Small (maximum size approximately 0.2 mm) well shaped crystals have been obtained. Larger poorly formed crystals (ca 0.5 mm) have also been obtained, but we have been unable to mount them for diff-raction analysis due to their extreme fragility. Crystallization experiments with PEG have shown that using this precipitant, the best crystals are obtained from slightly over-saturated solutions. Use of higher precipitant concentration leads to dendritic crystal formation. EcoRII is difficult to solubilize and meticulous attention must be paid to the presence of reducing agents.

The Promise of Macromolecular Crystallization in Micro-fluidic Chips

NASA Technical Reports Server (NTRS)

vanderWoerd, Mark; Ferree, Darren; Pusey, Marc

2003-01-01

Micro-fluidics, or lab on a chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bio-analytical and microscale bio-preparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require equilibrating macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a micro-fluidics platform. More complex optimization methods, where crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a micro-fluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation of crystals as they are grown.

An Experiment on the Particle-Wave Nature of Electrons

ERIC Educational Resources Information Center

Matteucci, Giorgio; Migliori, Andrea; Medina, Francisco; Castaneda, Roman

2009-01-01

A primary electron beam of a transmission electron microscope is scattered into secondary beams by the planes of atoms of a single crystal. These secondary beams are focused to form a diffraction pattern on the final screen. This experiment is similar to the Thompson one which, independently by Davisson and Germer, demonstrated the de Broglie…

In-situ data collection at the photon factory macromolecular crystallography beamlines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Yusuke, E-mail: yusuke.yamada@kek.jp; Matsugaki, Naohiro; Kato, Ryuichi

Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography, and in-situ diffraction experiment has a capability to make researchers to proceed this step more efficiently. At the Photon Factory, a new tabletop diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, an on-axis viewing system and a plate rack with a capacity for ten crystallization plates. These components sit on a common plate and are able to be placed on the existing diffractometer table. The CCD detector with a large active area and a pixel arraymore » detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and a user interface have also been developed. The new diffractometer has been operational for users and used for evaluation of crystallization screening since 2014.« less

Unraveling Complexity in the Solid Form Screening of a Pharmaceutical Salt: Why so Many Forms? Why so Few?

PubMed Central

2017-01-01

The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms. Structural diversity in the solid form landscape of B5HCl was apparent in the layer structures for the anhydrate polymorphs (Forms I and II), dihydrate and a family of solvates with alcohols. The alcohol solvates, which provided a distinct packing from the neat forms and the dihydrate, form layers with conserved hydrogen bonding between B5HCl and the solvent, as well as stacking of the aromatic rings. The ability of the alcohol hydrocarbon moieties to efficiently pack between the layers accounted for the difficulty in growing some solvate crystals and the inability of other solvates to crystallize altogether. Through a combination of experiment and computation, the crystallization problems, form stability, and desolvation pathways of B5HCl have been rationalized at a molecular level. PMID:29018305

Promoting protein crystallization using a plate with simple geometry.

PubMed

Chen, Rui-Qing; Yin, Da-Chuan; Liu, Yong-Ming; Lu, Qin-Qin; He, Jin; Liu, Yue

2014-03-01

Increasing the probability of obtaining protein crystals in crystallization screening is always an important goal for protein crystallography. In this paper, a new method called the cross-diffusion microbatch (CDM) method is presented, which aims to efficiently promote protein crystallization and increase the chance of obtaining protein crystals. In this method, a very simple crystallization plate was designed in which all crystallization droplets are in one sealed space, so that a variety of volatile components from one droplet can diffuse into any other droplet via vapour diffusion. Crystallization screening and reproducibility tests indicate that this method could be a potentially powerful technique in practical protein crystallization screening. It can help to obtain crystals with higher probability and at a lower cost, while using a simple and easy procedure.

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

Crystallization screening: the influence of history on current practice.

PubMed

Luft, Joseph R; Newman, Janet; Snell, Edward H

2014-07-01

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.

High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density

DOE PAGES

Teplitsky, Ella; Joshi, Karan; Ericson, Daniel L.; ...

2015-07-01

We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5 nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5 nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using thismore » system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. Moreover, a fragment mini-library was screened to observe two known lysozyme We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5 nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5 nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using this system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. A fragment mini-library was screened to observe two known lysozyme ligands using both co-crystallization and soaking. A similar approach was used to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5 nL of each component.ds using both co-crystallization and soaking. We used a A similar approach to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5 nL of each component.« less

Crystallization screening: the influence of history on current practice

PubMed Central

Luft, Joseph R.; Newman, Janet; Snell, Edward H.

2014-01-01

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. PMID:25005076

Use of Linear and Circular Polarization: The Secret LCD Screen and 3D Cinema

NASA Astrophysics Data System (ADS)

Richtberg, Stefan; Girwidz, Raimund

2017-10-01

References to everyday life are important for teaching physics. Discussing polarization phenomena, liquid crystal displays (LCDs) and 3D cinemas provide such references. In this paper we describe experiments to support students' understanding of linearly polarized light as well as the phenomenon of inverted colors using a secret LCD screen. Moreover we explain how 3D glasses work (when using polarizers) and introduce some experiments to point out why 3D cinemas use circularly polarized light instead of linearly polarized light. When using linearly polarized light, viewers must keep their head level all the time. Using circularly polarized light, this is not necessary.

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaikuad, Apirat, E-mail: apirat.chaikuad@sgc.ox.ac.uk; Knapp, Stefan; Johann Wolfgang Goethe-University, Building N240 Room 3.03, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main

An alternative strategy for PEG sampling is suggested through the use of four newly defined PEG smears to enhance chemical space in reduced screens with a benefit towards protein crystallization. The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially availablemore » crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.« less

High-density grids for efficient data collection from multiple crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassettemore » or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into theBlu-Ice/DCSSexperimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. As a result, crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.« less

High-density grids for efficient data collection from multiple crystals

PubMed Central

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Bonagura, Christopher A.; Brehmer, Winnie; Brunger, Axel T.; Calero, Guillermo; Caradoc-Davies, Tom T.; Chatterjee, Ruchira; Degrado, William F.; Fraser, James S.; Ibrahim, Mohamed; Kern, Jan; Kobilka, Brian K.; Kruse, Andrew C.; Larsson, Karl M.; Lemke, Heinrik T.; Lyubimov, Artem Y.; Manglik, Aashish; McPhillips, Scott E.; Norgren, Erik; Pang, Siew S.; Soltis, S. M.; Song, Jinhu; Thomaston, Jessica; Tsai, Yingssu; Weis, William I.; Woldeyes, Rahel A.; Yachandra, Vittal; Yano, Junko; Zouni, Athina; Cohen, Aina E.

2016-01-01

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures. PMID:26894529

High-density grids for efficient data collection from multiple crystals

DOE PAGES

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto; ...

2015-11-03

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassettemore » or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into theBlu-Ice/DCSSexperimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. As a result, crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.« less

Developments in the Implementation of Acoustic Droplet Ejection for Protein Crystallography.

PubMed

Wu, Ping; Noland, Cameron; Ultsch, Mark; Edwards, Bonnie; Harris, David; Mayer, Robert; Harris, Seth F

2016-02-01

Acoustic droplet ejection (ADE) enables crystallization experiments at the low-nanoliter scale, resulting in rapid vapor diffusion equilibration dynamics and efficient reagent usage in the empirical discovery of structure-enabling protein crystallization conditions. We extend our validation of this technology applied to the diverse physicochemical property space of aqueous crystallization reagents where dynamic fluid analysis coupled to ADE aids in accurate and precise dispensations. Addition of crystallization seed stocks, chemical additives, or small-molecule ligands effectively modulates crystallization, and we here provide examples in optimization of crystal morphology and diffraction quality by the acoustic delivery of ultra-small volumes of these cofactors. Additional applications are discussed, including set up of in situ proteolysis and alternate geometries of crystallization that leverage the small scale afforded by acoustic delivery. Finally, we describe parameters of a system of automation in which the acoustic liquid handler is integrated with a robotic arm, plate centrifuge, peeler, sealer, and stacks, which allows unattended high-throughput crystallization experimentation. © 2015 Society for Laboratory Automation and Screening.

Compact, high-resolution, gamma ray imaging for scintimammography and other medical diagostic applications

DOEpatents

Majewski, Stanislaw; Weisenberger, Andrew G.; Wojcik, Randolph F.; Steinbach, Daniela

1999-01-01

A high resolution gamma ray imaging device includes an aluminum housing, a lead screen collimator at an opened end of the housing, a crystal scintillator array mounted behind the lead screen collimator, a foam layer between the lead screen collimator and the crystal scintillator array, a photomultiplier window coupled to the crystal with optical coupling grease, a photomultiplier having a dynode chain body and a base voltage divider with anodes, anode wire amplifiers each connected to four anodes and a multi pin connector having pin connections to each anode wire amplifier. In one embodiment the crystal scintillator array includes a yttrium aluminum perovskite (YAP) crystal array. In an alternate embodiment, the crystal scintillator array includes a gadolinium oxyorthosilicate (GSO) crystal array.

High-throughput method for optimum solubility screening for homogeneity and crystallization of proteins

DOEpatents

Kim, Sung-Hou [Moraga, CA; Kim, Rosalind [Moraga, CA; Jancarik, Jamila [Walnut Creek, CA

2012-01-31

An optimum solubility screen in which a panel of buffers and many additives are provided in order to obtain the most homogeneous and monodisperse protein condition for protein crystallization. The present methods are useful for proteins that aggregate and cannot be concentrated prior to setting up crystallization screens. A high-throughput method using the hanging-drop method and vapor diffusion equilibrium and a panel of twenty-four buffers is further provided. Using the present methods, 14 poorly behaving proteins have been screened, resulting in 11 of the proteins having highly improved dynamic light scattering results allowing concentration of the proteins, and 9 were crystallized.

Rapid screening of the antimicrobial efficacy of Ag zeolites.

PubMed

Tosheva, L; Belkhair, S; Gackowski, M; Malic, S; Al-Shanti, N; Verran, J

2017-09-01

A semi-quantitative screening method was used to compare the killing efficacy of Ag zeolites against bacteria and yeast as a function of the zeolite type, crystal size and concentration. The method, which substantially reduced labor, consumables and waste and provided an excellent preliminary screen, was further validated by quantitative plate count experiments. Two pairs of zeolite X and zeolite beta with different sizes (ca. 200nm and 2μm for zeolite X and ca. 250 and 500nm for zeolite beta) were tested against Escherichia coli (E. coli) and Candida albicans (C. albicans) at concentrations in the range 0.05-0.5mgml -1 . Reduction of the zeolite crystal size resulted in a decrease in the killing efficacy against both microorganisms. The semi-quantitative tests allowed convenient optimization of the zeolite concentrations to achieve targeted killing times. Zeolite beta samples showed higher activity compared to zeolite X despite their lower Ag content, which was attributed to the higher concentration of silver released from zeolite beta samples. Cytotoxicity measurements using peripheral blood mononuclear cells (PBMCs) indicated that Ag zeolite X was more toxic than Ag zeolite beta. However, the trends for the dependence of cytotoxicity on zeolite crystal size at different zeolite concentrations were different for the two zeolites and no general conclusions about zeolite cytotoxicity could be drawn from these experiments. This result indicates a complex relationship, requiring the necessity for individual cytotoxicity measurements for all antimicrobial applications based on the use of zeolites. Copyright © 2017 Elsevier B.V. All rights reserved.

A Linear Relationship between Crystal Size and Fragment Binding Time Observed Crystallographically: Implications for Fragment Library Screening Using Acoustic Droplet Ejection

PubMed Central

Birone, Claire; Brown, Maria; Hernandez, Jesus; Neff, Sherry; Williams, Daniel; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

2014-01-01

High throughput screening technologies such as acoustic droplet ejection (ADE) greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above), the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above), the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size. PMID:24988328

A linear relationship between crystal size and fragment binding time observed crystallographically: implications for fragment library screening using acoustic droplet ejection.

PubMed

Cole, Krystal; Roessler, Christian G; Mulé, Elizabeth A; Benson-Xu, Emma J; Mullen, Jeffrey D; Le, Benjamin A; Tieman, Alanna M; Birone, Claire; Brown, Maria; Hernandez, Jesus; Neff, Sherry; Williams, Daniel; Allaire, Marc; Orville, Allen M; Sweet, Robert M; Soares, Alexei S

2014-01-01

High throughput screening technologies such as acoustic droplet ejection (ADE) greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above), the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above), the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size.

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

PubMed Central

Lasala, R.; Coudray, N.; Abdine, A.; Zhang, Z.; Lopez-Redondo, M.; Kirshenbaum, R.; Alexopoulos, J.; Zolnai, Z.; Stokes, D.L.; Ubarretxena-Belandia, I.

2014-01-01

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1,300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

Towards Automated Screening of Two-dimensional Crystals

PubMed Central

Cheng, Anchi; Leung, Albert; Fellmann, Denis; Quispe, Joel; Suloway, Christian; Pulokas, James; Carragher, Bridget; Potter, Clinton S.

2007-01-01

Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron microscopic imaging and evaluation of the trial grids is also possible. We, and others, have developed working prototypes for several of these tools and tested and evaluated them in a simple screen of 24 crystallization conditions. While further development of these tools is certainly required for a turn-key system, the goal of fully automated screening appears to be within reach. PMID:17977016

Automated macromolecular crystallization screening

DOEpatents

Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

2005-03-01

An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teplitsky, Ella; Joshi, Karan; Ericson, Daniel L.

We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5 nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5 nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using thismore » system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. Moreover, a fragment mini-library was screened to observe two known lysozyme We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5 nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5 nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using this system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. A fragment mini-library was screened to observe two known lysozyme ligands using both co-crystallization and soaking. A similar approach was used to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5 nL of each component.ds using both co-crystallization and soaking. We used a A similar approach to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5 nL of each component.« less

Three-Dimensional Large Screen Display Using Polymer-Dispersed Liquid-Crystal Light Valves and a Schlieren Optical System: Proposal and Basic Experiments

NASA Astrophysics Data System (ADS)

Takizawa, Kuniharu

A novel three-dimensional (3-D) projection display used with polarized eyeglasses is proposed. It consists of polymer-dispersed liquid crystal-light valves that modulate the illuminated light based on light scattering, a polarization beam splitter, and a Schlieren projection system. The features of the proposed display include a 3-D image display with a single projector, half size and half power consumption compared with a conventional 3-D projector with polarized glasses. Measured electro-optic characteristics of a polymer-dispersed liquid-crystal cell inserted between crossed polarizers suggests that the proposed display achieves small cross talk and high-extinction ratio.

Microgravity

NASA Image and Video Library

2001-10-01

High school students screen crystals of various proteins that are part of the ground-based work that supports Alexander McPherson's protein crystal growth experiment. The students also prepared and stored samples in the Enhanced Gaseous Nitrogen Dewar, which was launched on the STS-98 mission for delivery to the ISS. The crystals grown on the ground will be compared with crystals grown in orbit. Participants include Joseph Negron, of Terry Parker High School, Jacksonville, Florida; Megan Miskowski, of Ridgeview High School, Orange Park, Florida; and Sam Swank (shown), of Fletcher High School, Neptune Beach, Florida. The proteins are placed in plastic tubing that is heat-sealed at the ends, then flash-frozen and preserved in a liquid nitrogen Dewar. Aboard the ISS, the nitrogen will be allowed to evaporated so the samples thaw and then slowly crystallize. They will be analyzed after return to Earth. Photo credit: NASA/Marshall Space Flight Center.

Microgravity

NASA Image and Video Library

2001-10-01

High school students screen crystals of various proteins that are part of the ground-based work that supports Alexander McPherson's protein crystal growth experiment. The students also prepared and stored samples in the Enhanced Gaseous Nitrogen Dewar, which was launched on the STS-98 mission for delivery to the ISS. The crystals grown on the ground will be compared with crystals grown in orbit. Participants include Joseph Negron, of Terry Parker High School, Jacksonville, Florida; Megan Miskowski (shown), of Ridgeview High School, Orange Park, Florida; and Sam Swank, of Fletcher High School, Neptune Beach, Florida. The proteins are placed in plastic tubing that is heat-sealed at the ends, then flash-frozen and preserved in a liquid nitrogen Dewar. Aboard the ISS, the nitrogen will be allowed to evaporated so the samples thaw and then slowly crystallize. They will be analyzed after return to Earth. Photo credit: NASA/Marshall Space Flight Center.

Microgravity

NASA Image and Video Library

2001-10-01

High school students screen crystals of various proteins that are part of the ground-based work that supports Alexander McPherson's protein crystal growth experiment. The students also prepared and stored samples in the Enhanced Gaseous Nitrogen Dewar, which was launched on the STS-98 mission for delivery to the ISS. The crystals grown on the ground will be compared with crystals grown in orbit. Participants include Joseph Negron (shown), of Terry Parker High School, Jacksonville, Florida; Megan Miskowski, of Ridgeview High School, Orange Park, Florida; and Sam Swank, of Fletcher High School, Neptune Beach, Florida. The proteins are placed in plastic tubing that is heat-sealed at the ends, then flash-frozen and preserved in a liquid nitrogen Dewar. Aboard the ISS, the nitrogen will be allowed to evaporated so the samples thaw and then slowly crystallize. They will be analyzed after return to Earth. Photo credit: NASA/Marshall Space Flight Center.

Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.

PubMed

Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony Jun

2015-06-01

Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of dye to distinguish salt and protein crystals under microcrystallization conditions

NASA Technical Reports Server (NTRS)

Cosenza, Larry (Inventor); Gester, Thomas E. (Inventor); Bray, Terry L. (Inventor); DeLucas, Lawrence J. (Inventor); Hamrick, David T. (Inventor)

2007-01-01

An improved method of screening crystal growth conditions is provided wherein molecules are crystallized from solutions containing dyes. These dyes are selectively incorporated or associated with crystals of particular character thereby rendering crystals of particular character colored and improving detection of the dyed crystals. A preferred method involves use of dyes in protein solutions overlayed by oil. Use of oil allows the use of small volumes of solution and facilitates the screening of large numbers of crystallization conditions in arrays using automated devices that dispense appropriate solutions to generate crystallization trials, overlay crystallization trials with an oil, provide appropriate conditions conducive to crystallization and enhance detection of dyed (colored) or undyed (uncolored) crystals that result.

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

PubMed Central

Chaikuad, Apirat; Knapp, Stefan; von Delft, Frank

2015-01-01

The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant. PMID:26249344

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens.

PubMed

Chaikuad, Apirat; Knapp, Stefan; von Delft, Frank

2015-08-01

The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.

Quantitatively and Kinetically Identifying Binding Motifs of Amelogenin Proteins to Mineral Crystals Through Biochemical and Spectroscopic Assays

PubMed Central

Zhu, Li; Hwang, Peter; Witkowska, H. Ewa; Liu, Haichuan; Li, Wu

2014-01-01

Tooth enamel is the hardest tissue in vertebrate animals. Consisting of millions of carbonated hydroxyapatite crystals, this highly mineralized tissue develops from a protein matrix in which amelogenin is the predominant component. The enamel matrix proteins are eventually and completely degraded and removed by proteinases to form mineral-enriched tooth enamel. Identification of the apatite-binding motifs in amelogenin is critical for understanding the amelogenin–crystal interactions and amelogenin–proteinases interactions during tooth enamel biomineralization. A stepwise strategy is introduced to kinetically and quantitatively identify the crystal-binding motifs in amelogenin, including a peptide screening assay, a competitive adsorption assay, and a kinetic-binding assay using amelogenin and gene-engineered amelogenin mutants. A modified enzyme-linked immunosorbent assay on crystal surfaces is also applied to compare binding amounts of amelogenin and its mutants on different planes of apatite crystals. We describe the detailed protocols for these assays and provide the considerations for these experiments in this chapter. PMID:24188774

Goniometer-based femtosecond crystallography with X-ray free electron lasers

DOE PAGES

Cohen, Aina E.; Soltis, S. Michael; González, Ana; ...

2014-10-31

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore » to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β 2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

Goniometer-based femtosecond crystallography with X-ray free electron lasers

PubMed Central

Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

2014-01-01

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources. PMID:25362050

Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol.

PubMed

Fili, S; Valmas, A; Norrman, M; Schluckebier, G; Beckers, D; Degen, T; Wright, J; Fitch, A; Gozzo, F; Giannopoulou, A E; Karavassili, F; Margiolaki, I

2015-09-01

This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50-8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.

Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol

PubMed Central

Fili, S.; Valmas, A.; Norrman, M.; Schluckebier, G.; Beckers, D.; Degen, T.; Wright, J.; Fitch, A.; Gozzo, F.; Giannopoulou, A. E.; Karavassili, F.; Margiolaki, I.

2015-01-01

This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs. PMID:26306195

The collection of MicroED data for macromolecular crystallography.

PubMed

Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

2016-05-01

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

[Preparation and Performance of Ultrafast γ-CuI Scintillation Conversion Screen].

PubMed

Xia, Ming; Gu, Mu; Liu, Xiao-lin; Liu, Bo; Huang, Shi-ming; Ni, Chen

2015-04-01

Micro-columnar structured γ-CuI scintillation conversion screen with columnar diameter in the micrometer and thickness about 17 µm were prepared by thermal evaporation method on quartz substrates with different temperatures. X-ray excited luminescence spectra of the screens show two peaks located at 430 nm and near 700 nm, which correspond to the fast and slow emission components, respectively. The fast one dominated. The intensity of 430 nm peak decreased as the substrate temperature rose from 170 °C to 210 °C. At the same time the intensity of 700 nm band increased. The changes may be attributed to the iodine loss from screen caused by the substrate temperature. The phenomenon of iodine loss was observed by the Rutherford backscattering experiment. The crystal structure of the screens presents (111) preferred orientation, which is independent of the substrate temperature. As the temperature rose to 210 °C, two weak additional peaks of (220) and (420) γ-CuI crystal planes in X-ray diffraction patterns appeared due to the increase in kinetic energy of CuI molecules. The scanning electron microscopy images of the screens showed that the columnar structure was improved when the substrate temperature increased from 170 °C to 190 °C, but it would be degenerated when the temperature continued to rise to 210 °C because of the surface and bulk diffusion effects of the depositing molecules. Finally, the spatial resolution of the γ-CuI scintillation screens was measured by knife-edge method, and they are 4.5, 7.2 and 5.6lp · mm(-1) for the screens prepared at the substrates temperatures of 170, 190 and 210 °C, respectively. The result shows that micro-column structure could improve the spatial resolution of γ-CuI scintillation screen.

Accurate quasiparticle calculation of x-ray photoelectron spectra of solids

NASA Astrophysics Data System (ADS)

Aoki, Tsubasa; Ohno, Kaoru

2018-05-01

It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

Accurate quasiparticle calculation of x-ray photoelectron spectra of solids.

PubMed

Aoki, Tsubasa; Ohno, Kaoru

2018-05-31

It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

High-throughput cocrystal slurry screening by use of in situ Raman microscopy and multi-well plate.

PubMed

Kojima, Takashi; Tsutsumi, Shunichirou; Yamamoto, Katsuhiko; Ikeda, Yukihiro; Moriwaki, Toshiya

2010-10-31

Cocrystal has attracted much attention in order to improve poor physicochemical properties, since cocrystal former crystallize with the ionic drugs as well as nonionic drugs. Cocrystal screening was usually conducted by crystallization, slurry and co-grinding techniques, however sensitivity, cost and time for screening were limited because of issues such as dissociation of cocrystal during crystallization and cost and time required for slurry and co-grinding methods. To overcome these issues, novel high-throughput cocrystal slurry screening was developed by using in situ Raman microscope and a multi-well plate. Cocrystal screening of indomethacin was conducted with 46 cocrystal formers and potential cocrystals were prepared on a large scale for the characterization with powder X-ray diffractometry, thermal analysis, and Raman microscopy and (1)H NMR spectroscopy. Compared with the characterization of scale-up cocrystals, the cocrystal screening indicated that indomethacin structured novel cocrystals with D/L-mandelic acid, nicotinamide, lactamide and benzamide which was not obtained in the screening with crystallization technique previously reported. In addition, the screening provided not only information of cocrystal formation within a day but also information of equilibrium of cocrystal formation and polymorphic transformation in one screening. Information obtained in this screening allows effective solid form selection by saving cost and time for the development. Copyright © 2010 Elsevier B.V. All rights reserved.

A low-cost method for visible fluorescence imaging.

PubMed

Tarver, Crissy L; Pusey, Marc

2017-12-01

A wide variety of crystallization solutions are screened to establish conditions that promote the growth of a diffraction-quality crystal. Screening these conditions requires the assessment of many crystallization plates for the presence of crystals. Automated systems for screening and imaging are very expensive. A simple approach to imaging trace fluorescently labeled protein crystals in crystallization plates has been devised, and can be implemented at a cost as low as $50. The proteins β-lactoglobulin B, trypsin and purified concanavalin A (ConA) were trace fluorescently labeled using three different fluorescent probes: Cascade Yellow (CY), Carboxyrhodamine 6G (CR) and Pacific Blue (PB). A crystallization screening plate was set up using β-lactoglobulin B labeled with CR, trypsin labeled with CY, ConA labeled with each probe, and a mixture consisting of 50% PB-labeled ConA and 50% CR-labeled ConA. The wells of these plates were imaged using a commercially available macro-imaging lens attachment for smart devices that have a camera. Several types of macro lens attachments were tested with smartphones and tablets. Images with the highest quality were obtained with an iPhone 6S and an AUKEY Ora 10× macro lens. Depending upon the fluorescent probe employed and its Stokes shift, a light-emitting diode or a laser diode was used for excitation. An emission filter was used for the imaging of protein crystals labeled with CR and crystals with two-color fluorescence. This approach can also be used with microscopy systems commonly used to observe crystallization plates.

High-throughput screening for thermoelectric sulphides by using crystal structure features as descriptors

NASA Astrophysics Data System (ADS)

Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team

With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.

Comparison of a rational vs. high throughput approach for rapid salt screening and selection.

PubMed

Collman, Benjamin M; Miller, Jonathan M; Seadeek, Christopher; Stambek, Julie A; Blackburn, Anthony C

2013-01-01

In recent years, high throughput (HT) screening has become the most widely used approach for early phase salt screening and selection in a drug discovery/development setting. The purpose of this study was to compare a rational approach for salt screening and selection to those results previously generated using a HT approach. The rational approach involved a much smaller number of initial trials (one salt synthesis attempt per counterion) that were selected based on a few strategic solubility determinations of the free form combined with a theoretical analysis of the ideal solvent solubility conditions for salt formation. Salt screening results for sertraline, tamoxifen, and trazodone using the rational approach were compared to those previously generated by HT screening. The rational approach produced similar results to HT screening, including identification of the commercially chosen salt forms, but with a fraction of the crystallization attempts. Moreover, the rational approach provided enough solid from the very initial crystallization of a salt for more thorough and reliable solid-state characterization and thus rapid decision-making. The crystallization techniques used in the rational approach mimic larger-scale process crystallization, allowing smoother technical transfer of the selected salt to the process chemist.

Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography

PubMed Central

Bruno, Andrew E.; Ruby, Amanda M.; Luft, Joseph R.; Grant, Thomas D.; Seetharaman, Jayaraman; Montelione, Gaetano T.; Hunt, John F.; Snell, Edward H.

2014-01-01

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields. PMID:24971458

E-beam-pumped semiconductor lasers

NASA Astrophysics Data System (ADS)

Rice, Robert R.; Shanley, James F.; Ruggieri, Neil F.

1995-04-01

The collapse of the Soviet Union opened many areas of laser technology to the West. E-beam- pumped semiconductor lasers (EBSL) were pursued for 25 years in several Soviet Institutes. Thin single crystal screens of II-VI alloys (ZnxCd1-xSe, CdSxSe1-x) were incorporated in laser CRTs to produce scanned visible laser beams at average powers greater than 10 W. Resolutions of 2500 lines were demonstrated. MDA-W is conducting a program for ARPA/ESTO to assess EBSL technology for high brightness, high resolution RGB laser projection application. Transfer of II-VI crystal growth and screen processing technology is underway, and initial results will be reported. Various techniques (cathodoluminescence, one- and two-photon laser pumping, etc.) have been used to assess material quality and screen processing damage. High voltage (75 kV) video electronics were procured in the U.S. to operate test EBSL tubes. Laser performance was documented as a function of screen temperature, beam voltage and current. The beam divergence, spectrum, efficiency and other characteristics of the laser output are being measured. An evaluation of the effect of laser operating conditions upon the degradation rate is being carried out by a design-of-experiments method. An initial assessment of the projected image quality will be performed.

UV LED lighting for automated crystal centring

PubMed Central

Chavas, Leonard M. G.; Yamada, Yusuke; Hiraki, Masahiko; Igarashi, Noriyuki; Matsugaki, Naohiro; Wakatsuki, Soichi

2011-01-01

A direct outcome of the exponential growth of macromolecular crystallography is the continuously increasing demand for synchrotron beam time, both from academic and industrial users. As more and more projects entail screening a profusion of sample crystals, fully automated procedures at every level of the experiments are being implemented at all synchrotron facilities. One of the major obstacles to achieving such automation lies in the sample recognition and centring in the X-ray beam. The capacity of UV light to specifically react with aromatic residues present in proteins or with DNA base pairs is at the basis of UV-assisted crystal centring. Although very efficient, a well known side effect of illuminating biological samples with strong UV sources is the damage induced on the irradiated samples. In the present study the effectiveness of a softer UV light for crystal centring by taking advantage of low-power light-emitting diode (LED) sources has been investigated. The use of UV LEDs represents a low-cost solution for crystal centring with high specificity. PMID:21169682

Optimization of protein buffer cocktails using Thermofluor.

PubMed

Reinhard, Linda; Mayerhofer, Hubert; Geerlof, Arie; Mueller-Dieckmann, Jochen; Weiss, Manfred S

2013-02-01

The stability and homogeneity of a protein sample is strongly influenced by the composition of the buffer that the protein is in. A quick and easy approach to identify a buffer composition which increases the stability and possibly the conformational homogeneity of a protein sample is the fluorescence-based thermal-shift assay (Thermofluor). Here, a novel 96-condition screen for Thermofluor experiments is presented which consists of buffer and additive parts. The buffer screen comprises 23 different buffers and the additive screen includes small-molecule additives such as salts and nucleotide analogues. The utilization of small-molecule components which increase the thermal stability of a protein sample frequently results in a protein preparation of higher quality and quantity and ultimately also increases the chances of the protein crystallizing.

Purification, Crystallization, and Preliminary X-ray Analysis of Native Canavalin

NASA Technical Reports Server (NTRS)

Pusey, Marc; Dowell, Jennifer; Ng, Joseph; Gavira, Jose A.

2003-01-01

The protein canavalin is a 7S vicilin, from the Jack Bean, Canavalis ensfomis. Canavalin is described as a seed storage protein, an energy source for a developing seed, as no other known activity or function has been found. The protein was first isolated and crystallized by Sumner and Howell (J. Biol. Chem. 113, 607-610, 1936). Canavalin spontaneously crystallizes after proteolytic cleavage at neutral pH, which removes residues 1-46, 224-245, and 325-330 and produces peptides of approximately 25, 13, and 12 kDa. Preliminary gel filtration experiments indicated the presence of nucleic acid with the uncleaved protein. We developed a dual column procedure, ion exchange followed by hydroxy apatite chromatography, that effectively removes the nucleic acid and yields an essentially pure uncut canavalin preparation with an OD 280/260 ratio of approximately 1.9-2.0. Standard crystallization screens using this material gave a number of positive results having a common requirement for alcohols and Mg(2+) ion, with crystals typically appearing within a day or less. Optimization experiments to date have shown that we can obtain crystals from pH 6.5 to pH 8.2, using MPD from 5 to 20% and 0.05 to 0.2M Mg(2+) (sulfate or acetate). The crystals are of space group P2(sub 1)2(sub 1)2(sub 1), unit cell dimensions, and a complete data set to 1.5 Angstroms, resolution has now been collected at a synchrotron source. Most importantly, the crystals are not twinned, a persistent problem with the most commonly obtained rhombohedral form of proteolytically cleaved canavalin.

Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization.

PubMed

Stieglitz, Benjamin; Rittinger, Katrin; Haire, Lesley F

2012-07-01

An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively.

The ESFRI Instruct Core Centre Frankfurt: automated high-throughput crystallization suited for membrane proteins and more.

PubMed

Thielmann, Yvonne; Koepke, Juergen; Michel, Hartmut

2012-06-01

Structure determination of membrane proteins and membrane protein complexes is still a very challenging field. To facilitate the work on membrane proteins the Core Centre follows a strategy that comprises four labs of protein analytics and crystal handling, covering mass spectrometry, calorimetry, crystallization and X-ray diffraction. This general workflow is presented and a capacity of 20% of the operating time of all systems is provided to the European structural biology community within the ESFRI Instruct program. A description of the crystallization service offered at the Core Centre is given with detailed information on screening strategy, screens used and changes to adapt high throughput for membrane proteins. Our aim is to constantly develop the Core Centre towards the usage of more efficient methods. This strategy might also include the ability to automate all steps from crystallization trials to crystal screening; here we look ahead how this aim might be realized at the Core Centre.

Crystallization screening test for the whole-cell project on Thermus thermophilus HB8

PubMed Central

Iino, Hitoshi; Naitow, Hisashi; Nakamura, Yuki; Nakagawa, Noriko; Agari, Yoshihiro; Kanagawa, Mayumi; Ebihara, Akio; Shinkai, Akeo; Sugahara, Mitsuaki; Miyano, Masashi; Kamiya, Nobuo; Yokoyama, Shigeyuki; Hirotsu, Ken; Kuramitsu, Seiki

2008-01-01

It was essential for the structural genomics of Thermus thermophilus HB8 to efficiently crystallize a number of proteins. To this end, three conventional robots, an HTS-80 (sitting-drop vapour diffusion), a Crystal Finder (hanging-drop vapour diffusion) and a TERA (modified microbatch) robot, were subjected to a crystallization condition screening test involving 18 proteins from T. thermophilus HB8. In addition, a TOPAZ (microfluidic free-interface diffusion) designed specifically for initial screening was also briefly examined. The number of diffraction-quality crystals and the time of appearance of crystals increased in the order HTS-80, Crystal Finder, TERA. With the HTS-80 and Crystal Finder, the time of appearance was short and the rate of salt crystallization was low. With the TERA, the number of diffraction-quality crystals was high, while the time of appearance was long and the rate of salt crystallization was relatively high. For the protein samples exhibiting low crystallization success rates, there were few crystallization conditions that were common to the robots used. In some cases, the success rate depended greatly on the robot used. The TOPAZ showed the shortest time of appearance and the highest success rate, although the crystals obtained were too small for diffraction studies. These results showed that the combined use of different robots significantly increases the chance of obtaining crystals, especially for proteins exhibiting low crystallization success rates. The structures of 360 of 944 purified proteins have been successfully determined through the combined use of an HTS-80 and a TERA. PMID:18540056

THF water hydrate crystallization: an experimental investigation

NASA Astrophysics Data System (ADS)

Devarakonda, Surya; Groysman, Alexander; Myerson, Allan S.

1999-08-01

Supersaturated solutions of THF-water hydrate system were experimentally studied before and during crystallization, to examine the system's behavior in the metastable zone and observe any anomalies suggesting cluster formation. Nucleation induction time measurements, with and without additives, were performed to screen potential growth inhibitors. Shifts in the onset points of crystallization for water and THF-water mixtures with additives were measured using differential scanning calorimetry (DSC). Aspartame was among one of the few successfully screened inhibitors. Preliminary on-line crystal size distribution (CSD) measurements were performed on this system to monitor the crystal size during crystallization. The CSD data was also used to compute the hydrate crystal growth rates, which were found to be in the order of 145 μm/h.

Fluorescent Approaches to High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

We have shown that by covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and the presence of the probe at low concentrations does not affect the X-ray data quality or the crystallization behavior. The presence of the trace fluorescent label gives a number of advantages when used with high throughput crystallizations. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a dark background. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Brightly fluorescent crystals are readily found against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. We are now testing the use of high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that kinetics leading to non-structured phases may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Preliminary experiments with test proteins have resulted in the extraction of a number of crystallization conditions from screening outcomes based solely on the presence of bright fluorescent regions. Subsequent experiments will test this approach using a wider range of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Screened dipolar interactions in some molecular crystals

NASA Astrophysics Data System (ADS)

Munn, R. W.; Hurst, M.

1990-10-01

Screened dipole energies and dipole electric fields are calculated for the crystals of HCN, meta- and para-nitroaniline, the nonlinear optical compounds POM, MAP and DAN, meta-dinitrobenzene, and acetanilide. Only para-nitroaniline is centrosymmetric, but all the crystals have significant negative dipole energies (of the order of -20 kJ mol -1) except for POM and metadinitrobenzene, where they are positive but small in magnitude. Local dipole fields are of the order of 10 GV m -1. The results assume that surface charge annuls any macroscopic dipole field. It is speculated that the observed preponderance of centrosymmetric crystals of polar molecules may reflect a favourable dipole energy in the initial crystal nucleus rather than the macroscopic crystal.

Membrane proteins, detergents and crystals: what is the state of the art?

PubMed Central

Loll, Patrick J.

2014-01-01

At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein–detergent complexes remains the dominant method­ology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein–detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors. PMID:25484203

Current trends in α-helical membrane protein crystallization: An update

PubMed Central

Parker, Joanne L; Newstead, Simon

2012-01-01

α-Helical membrane proteins (MPs) are the targets for many pharmaceutical drugs and play important roles in human physiology. In recent years, significant progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck in MP crystallography still remains, namely, the identification of conditions that give crystals that are suitable for structural determination. In 2008, we undertook an analysis of the crystallization conditions for 121 α-helical MPs to design a rationalized sparse matrix crystallization screen, MemGold. We now report an updated analysis that includes a further 133 conditions. The results reveal the current trends in α-helical MP crystallization with notable differences since 2008. The updated information has been used to design new crystallization and additive screens that should prove useful for both initial crystallization scouting and subsequent crystal optimization. PMID:22811290

Characterization of Phase Separation Propensity for Amorphous Spray Dried Dispersions.

PubMed

McNamara, Daniel; Yin, Shawn; Pan, Duohai; Crull, George; Timmins, Peter; Vig, Balvinder

2017-02-06

A generalized screening approach, applying isothermal calorimetry at 37 °C 100% RH, to formulations of spray dried dispersions (SDDs) for two active pharmaceutical ingredients (APIs) (BMS-903452 and BMS-986034) is demonstrated. APIs 452 and 034, with similar chemotypes, were synthesized and promoted during development for oral dosing. Both APIs were formulated as SDDs for animal exposure studies using the polymer hydroxypropylmethlycellulose acetyl succinate M grade (HPMCAS-M). 452 formulated at 30% (wt/wt %) was an extremely robust SDD that was able to withstand 40 °C 75% RH open storage conditions for 6 months with no physical evidence of crystallization or loss of dissolution performance. Though 034 was a chemical analogue with similar physical chemical properties to 452, a physically stable SDD of 034 could not be formulated in HPMCAS-M at any of the drug loads attempted. This study was used to develop experience with specific physical characterization laboratory techniques to evaluate the physical stability of SDDs and to characterize the propensity of SDDs to phase separate and possibly crystallize. The screening strategy adopted was to stress the formulated SDDs with a temperature humidity screen, within the calorimeter, and to apply orthogonal analytical techniques to gain a more informed understanding of why these SDDs formulated with HPMCAS-M demonstrated such different physical stability. Isothermal calorimetry (thermal activity monitor, TAM) was employed as a primary stress screen wherein the SDD formulations were monitored for 3 days at 37 °C 100% RH for signs of phase separation and possible crystallization of API. Powder X-ray diffraction (pXRD), modulated differential scanning calorimetry (mDSC), Fourier transform infrared spectroscopy (FTIR), and solid state nuclear magnetic resonance (ssNMR) were all used to examine formulated SDDs and neat amorphous drug. 452 SDDs formulated at 30% (wt/wt %) or less did not show phase separation behavior upon exposure to 37 °C 100% RH for 3 days. 034 SDD formulations from 10 through 50% (wt/wt %) all demonstrated thermal traces consistent with exothermic phase separation events over 3 days at 37 °C 100% RH in the TAM. However, only the 15, 30, and 50% containing 034 samples showed pXRD patterns consistent with crystalline material in post-TAM samples. Isothermal calorimetry is a useful screening tool to probe robust SDD physical performance and help investigate the level of drug polymer miscibility under a humid stress. Orthogonal analytical techniques such as pXRD, ssNMR, and FTIR were key in this SDD formulation screening to gain physical understanding and confirm or refute whether physical changes occur during the observed thermal events characterized by the calorimetric screening experiments.

Nonlinear AC susceptibility, surface and bulk shielding

NASA Astrophysics Data System (ADS)

van der Beek, C. J.; Indenbom, M. V.; D'Anna, G.; Benoit, W.

1996-02-01

We calculate the nonlinear AC response of a thin superconducting strip in perpendicular field, shielded by an edge current due to the geometrical barrier. A comparison with the results for infinite samples in parallel field, screened by a surface barrier, and with those for screening by a bulk current in the critical state, shows that the AC response due to a barrier has general features that are independent of geometry, and that are significantly different from those for screening by a bulk current in the critical state. By consequence, the nonlinear (global) AC susceptibility can be used to determine the origin of magnetic irreversibility. A comparison with experiments on a Bi 2Sr 2CaCu 2O 8+δ crystal shows that in this material, the low-frequency AC screening at high temperature is mainly due to the screening by an edge current, and that this is the unique source of the nonlinear magnetic response at temperatures above 40 K.

The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Colin J.; Carr, Paul D.; Kim, Hye-Kyung

2006-07-01

The metallo-glycerophosphodiesterase from E. aerogenes (GpdQ) has been cloned, expressed in E. coli and purified. Initial screening of crystallization conditions for this enzyme resulted in the identification of needles from one condition in a sodium malonate grid screen. Removal of the metals from the enzyme and subsequent optimization of these conditions led to crystals. The metallo-glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) has been cloned, expressed in Escherichia coli and purified. Initial screening of crystallization conditions for this enzyme resulted in the identification of needles from one condition in a sodium malonate grid screen. Removal of the metals from the enzyme andmore » subsequent optimization of these conditions led to crystals that diffracted to 2.9 Å and belonged to space group P2{sub 1}3, with unit-cell parameter a = 164.1 Å. Self-rotation function analysis and V{sub M} calculations indicated that the asymmetric unit contains two copies of the monomeric enzyme, corresponding to a solvent content of 79%. It is intended to determine the structure of this protein utilizing SAD phasing from transition metals or molecular replacement.« less

Recent Progress in the Structure Determination of GPCRs, a Membrane Protein Family with High Potential as Pharmaceutical Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherezov, Vadim; Abola, Enrique; Stevens, Raymond C.

2015-11-30

G protein-coupled receptors (GPCRs) constitute a highly diverse and ubiquitous family of integral membrane proteins, transmitting signals inside the cells in response to an assortment of disparate extra-cellular stimuli. Their strategic location on the cell surface and their involvement in crucial cellular and physiological processes turn these receptors into highly important pharmaceutical targets. Recent technological developments aimed at stabilization and crystallization of these receptors have led to significant breakthroughs in GPCR structure determination efforts. One of the successful approaches involved receptor stabilization with the help of a fusion partner combined with crystallization in lipidic cubic phase (LCP). The success ofmore » using an LCP matrix for crystallization is generally attributed to the creation of a more native, membrane-like stabilizing environment for GPCRs just prior to nucleation and to the formation of type I crystal lattices, thus generating highly ordered and strongly diffracting crystals. Here they describe protocols for reconstituting purified GPCRs in LCP, performing pre-crystallization assays, setting up crystallization trials in manual mode, detecting crystallization hits, optimizing crystallization conditions, harvesting, and collecting crystallographic data. The protocols provide a sensible framework for approaching crystallization of stabilized GPCRs in LCP, however, as in any crystallization experiment, extensive screening and optimization of crystallization conditions as well as optimization of protein construct and purification steps are required. The process remains risky and these protocols do not necessarily guarantee success.« less

Selecting Temperature for Protein Crystallization Screens Using the Temperature Dependence of the Second Virial Coefficient

PubMed Central

Liu, Jun; Yin, Da-Chuan; Guo, Yun-Zhu; Wang, Xi-Kai; Xie, Si-Xiao; Lu, Qin-Qin; Liu, Yong-Ming

2011-01-01

Protein crystals usually grow at a preferable temperature which is however not known for a new protein. This paper reports a new approach for determination of favorable crystallization temperature, which can be adopted to facilitate the crystallization screening process. By taking advantage of the correlation between the temperature dependence of the second virial coefficient (B 22) and the solubility of protein, we measured the temperature dependence of B 22 to predict the temperature dependence of the solubility. Using information about solubility versus temperature, a preferred crystallization temperature can be proposed. If B 22 is a positive function of the temperature, a lower crystallization temperature is recommended; if B 22 shows opposite behavior with respect to the temperature, a higher crystallization temperature is preferred. Otherwise, any temperature in the tested range can be used. PMID:21479212

Screening and Crystallization Plates for Manual and High-throughput Protein Crystal Growth

NASA Technical Reports Server (NTRS)

Thorne, Robert E. (Inventor); Berejnov, Viatcheslav (Inventor); Kalinin, Yevgeniy (Inventor)

2010-01-01

In one embodiment, a crystallization and screening plate comprises a plurality of cells open at a top and a bottom, a frame that defines the cells in the plate, and at least two films. The first film seals a top of the plate and the second film seals a bottom of the plate. At least one of the films is patterned to strongly pin the contact lines of drops dispensed onto it, fixing their position and shape. The present invention also includes methods and other devices for manual and high-throughput protein crystal growth.

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation

NASA Astrophysics Data System (ADS)

Theveneau, P.; Baker, R.; Barrett, R.; Beteva, A.; Bowler, M. W.; Carpentier, P.; Caserotto, H.; de Sanctis, D.; Dobias, F.; Flot, D.; Guijarro, M.; Giraud, T.; Lentini, M.; Leonard, G. A.; Mattenet, M.; McCarthy, A. A.; McSweeney, S. M.; Morawe, C.; Nanao, M.; Nurizzo, D.; Ohlsson, S.; Pernot, P.; Popov, A. N.; Round, A.; Royant, A.; Schmid, W.; Snigirev, A.; Surr, J.; Mueller-Dieckmann, C.

2013-03-01

Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This "first generation" of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

DOE PAGES

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.; ...

2016-11-11

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

Towards Protein Crystallization as a Process Step in Downstream Processing of Therapeutic Antibodies: Screening and Optimization at Microbatch Scale

PubMed Central

Zang, Yuguo; Kammerer, Bernd; Eisenkolb, Maike; Lohr, Katrin; Kiefer, Hans

2011-01-01

Crystallization conditions of an intact monoclonal IgG4 (immunoglobulin G, subclass 4) antibody were established in vapor diffusion mode by sparse matrix screening and subsequent optimization. The procedure was transferred to microbatch conditions and a phase diagram was built showing surprisingly low solubility of the antibody at equilibrium. With up-scaling to process scale in mind, purification efficiency of the crystallization step was investigated. Added model protein contaminants were excluded from the crystals to more than 95%. No measurable loss of Fc-binding activity was observed in the crystallized and redissolved antibody. Conditions could be adapted to crystallize the antibody directly from concentrated and diafiltrated cell culture supernatant, showing purification efficiency similar to that of Protein A chromatography. We conclude that crystallization has the potential to be included in downstream processing as a low-cost purification or formulation step. PMID:21966480

Screening of detergents for solubilization, purification and crystallization of membrane proteins: a case study on succinate:ubiquinone oxidoreductase from Escherichia coli

PubMed Central

Shimizu, Hironari; Nihei, Coh-ichi; Inaoka, Daniel Ken; Mogi, Tatushi; Kita, Kiyoshi; Harada, Shigeharu

2008-01-01

Succinate:ubiquinone oxidoreductase (SQR) was solubilized and purified from Escherichia coli inner membranes using several different detergents. The number of phospholipid molecules bound to the SQR molecule varied greatly depending on the detergent combination that was used for the solubilization and purification. Crystallization conditions were screened for SQR that had been solubilized and purified using 2.5%(w/v) sucrose monolaurate and 0.5%(w/v) Lubrol PX, respectively, and two different crystal forms were obtained in the presence of detergent mixtures composed of n-alkyl-oligoethylene glycol monoether and n-alkyl-maltoside. Crystallization took place before detergent phase separation occurred and the type of detergent mixture affected the crystal form. PMID:18765923

Screening of detergents for solubilization, purification and crystallization of membrane proteins: a case study on succinate:ubiquinone oxidoreductase from Escherichia coli.

PubMed

Shimizu, Hironari; Nihei, Coh-ichi; Inaoka, Daniel Ken; Mogi, Tatushi; Kita, Kiyoshi; Harada, Shigeharu

2008-09-01

Succinate:ubiquinone oxidoreductase (SQR) was solubilized and purified from Escherichia coli inner membranes using several different detergents. The number of phospholipid molecules bound to the SQR molecule varied greatly depending on the detergent combination that was used for the solubilization and purification. Crystallization conditions were screened for SQR that had been solubilized and purified using 2.5%(w/v) sucrose monolaurate and 0.5%(w/v) Lubrol PX, respectively, and two different crystal forms were obtained in the presence of detergent mixtures composed of n-alkyl-oligoethylene glycol monoether and n-alkyl-maltoside. Crystallization took place before detergent phase separation occurred and the type of detergent mixture affected the crystal form.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Liang; Nachtergaele, Sigrid; Seddon, Annela M.

This paper utilizes cyclodextrin-based host-guest chemistry in a microfluidic device to modulate the crystallization of membrane proteins and the process of concentration of membrane protein samples. Methyl-{beta}-cyclodextrin (MBCD) can efficiently capture a wide variety of detergents commonly used for the stabilization of membrane proteins by sequestering detergent monomers. Reaction Center (RC) from Blastochloris viridis was used here as a model system. In the process of concentrating membrane protein samples, MBCD was shown to break up free detergent micelles and prevent them from being concentrated. The addition of an optimal amount of MBCD to the RC sample captured loosely bound detergentmore » from the protein-detergent complex and improved sample homogeneity, as characterized by dynamic light scattering. Using plug-based microfluidics, RC crystals were grown in the presence of MBCD, giving a different morphology and space group than crystals grown without MBCD. The crystal structure of RC crystallized in the presence of MBCD was consistent with the changes in packing and crystal contacts hypothesized for removal of loosely bound detergent. The incorporation of MBCD into a plug-based microfluidic crystallization method allows efficient use of limited membrane protein sample by reducing the amount of protein required and combining sparse matrix screening and optimization in one experiment. The use of MBCD for detergent capture can be expanded to develop cyclodextrin-derived molecules for fine-tuned detergent capture and thus modulate membrane protein crystallization in an even more controllable way.« less

Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

PubMed Central

Abdallah, Bahige G.; Kupitz, Christopher; Fromme, Petra; Ros, Alexandra

2014-01-01

Traditional macroscale protein crystallization is accomplished non-trivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time consuming and resource intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large membrane protein complexes such as photosystem I (PSI) due to their large unit cells dominated by solvent and complex characteristics that call for even stricter buffer requirements. Structure determination techniques tailored for these ‘difficult to crystallize’ proteins such as femtosecond nanocrystallography are being developed, yet still need specific crystal characteristics. Here, we demonstrate a simple and robust method to screen protein crystallization conditions at low ionic strength in a microfluidic device. This is realized in one microfluidic experiment using low sample amounts, unlike traditional methods where each solution condition is set up separately. Second harmonic generation microscopy via Second Order Nonlinear Imaging of Chiral Crystals (SONICC) was applied for the detection of nanometer and micrometer sized PSI crystals within microchannels. To develop a crystallization phase diagram, crystals imaged with SONICC at specific channel locations were correlated to protein and salt concentrations determined by numerical simulations of the time-dependent diffusion process along the channel. Our method demonstrated that a portion of the PSI crystallization phase diagram could be reconstructed in excellent agreement with crystallization conditions determined by traditional methods. We postulate that this approach could be utilized to efficiently study and optimize crystallization conditions for a wide range of proteins that are poorly understood to date. PMID:24191698

3D mapping of turbulence: a laboratory experiment

NASA Astrophysics Data System (ADS)

Le Louarn, Miska; Dainty, Christopher; Paterson, Carl; Tallon, Michel

2000-07-01

In this paper, we present the first experimental results of the 3D mapping method. 3D mapping of turbulence is a method to remove the cone effect with multiple laser guide stars and multiple deformable mirrors. A laboratory experiment was realized to verify the theoretical predictions. The setup consisted of two turbulent phase screens (made with liquid crystal devices) and a Shack-Hartmann wavefront sensor. We describe the interaction matrix involved in reconstructing Zernike commands for multiple deformable mirror from the slope measurements made from laser guide stars. It is shown that mirror commands can indeed be reconstructed with the 3D mapping method. Limiting factors of the method, brought to light by this experiment are discussed.

Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segelke, B

2005-02-24

Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having anmore » increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.« less

Crystallizing Membrane Proteins in the Lipidic Mesophase. Experience with Human Prostaglandin E2 Synthase 1 and an Evolving Strategy.

PubMed

Li, Dianfan; Howe, Nicole; Dukkipati, Abhiram; Shah, Syed T A; Bax, Benjamin D; Edge, Colin; Bridges, Angela; Hardwicke, Phil; Singh, Onkar M P; Giblin, Ged; Pautsch, Alexander; Pfau, Roland; Schnapp, Gisela; Wang, Meitian; Olieric, Vincent; Caffrey, Martin

2014-04-02

The lipidic mesophase or in meso method for crystallizing membrane proteins has several high profile targets to its credit and is growing in popularity. Despite its success, the method is in its infancy as far as rational crystallogenesis is concerned. Consequently, significant time, effort, and resources are still required to generate structure-grade crystals, especially with a new target type. Therefore, a need exists for crystallogenesis protocols that are effective with a broad range of membrane protein types. Recently, a strategy for crystallizing a prokaryotic α-helical membrane protein, diacylglycerol kinase (DgkA), by the in meso method was reported (Cryst. Growth. Des.2013, 14, 2846-2857). Here, we describe its application to the human α-helical microsomal prostaglandin E2 synthase 1 (mPGES1). While the DgkA strategy proved useful, significant modifications were needed to generate structure-quality crystals of this important therapeutic target. These included protein engineering, using an additive phospholipid in the hosting mesophase, performing multiple rounds of salt screening, and carrying out trials at 4 °C in the presence of a tight binding ligand. The crystallization strategy detailed here should prove useful for generating structures of other integral membrane proteins by the in meso method.

Expanding pH screening space using multiple droplets with secondary buffers for protein crystallization

NASA Astrophysics Data System (ADS)

Zhang, Chen-Yan; Dong, Chen; Lu, Xiao-Li; Wang, Bei; He, Tian-Yuan; Yang, Rui-Zeng; Lin, Hua-Long; Yang, Xue-Zhou; Yin, Da-Chuan

2017-04-01

We have proposed a rational strategy for selecting a suitable pH of protein solution based on protein biochemical properties. However, it is difficult to use this strategy for biochemical properties unknown proteins. In this paper, a simpler and faster pH buffer strategy was proposed. An additional pH-controlling buffer was added to crystallization droplet mixed with protein solution and commercial crystallization reagents to adjust its pH. The results revealed that protein crystallization success rates were enhanced by this strategy due to expansion of the pH screening space, which was closely related with protein solubility. Thus, the possibility of reaching supersaturation was increased by using this strategy.

Lattice energy calculation - A quick tool for screening of cocrystals and estimation of relative solubility. Case of flavonoids

NASA Astrophysics Data System (ADS)

Kuleshova, L. N.; Hofmann, D. W. M.; Boese, R.

2013-03-01

Cocrystals (or multicomponent crystals) have physico-chemical properties that are different from crystals of pure components. This is significant in drug development, since the desired properties, e.g. solubility, stability and bioavailability, can be tailored by binding two substances into a single crystal without chemical modification of an active component. Here, the FLEXCRYST program suite, implemented with a data mining force field, was used to estimate the relative stability and, consequently, the relative solubility of cocrystals of flavonoids vs their pure crystals, stored in the Cambridge Structural Database. The considerable potency of this approach for in silico screening of cocrystals, as well as their relative solubility, was demonstrated.

Evolution of separate screening soliton pairs in a biased series photorefractive crystal circuit.

PubMed

Liu, Jinsong; Hao, Zhonghua

2002-06-01

This paper presents calculations for an idea in photorefractive spatial soliton, namely, screening solitons form in a biased series photorefractive crystal circuit consisting of two photorefractive crystals connected electronically by electrode leads in a chain with a voltage source. A system of two coupled equations is derived under appropriate conditions for two-beam propagation in the crystal circuit. The possibility of obtaining steady-state bright and dark screening soliton solutions is investigated in one dimension and, the existence of dark-dark, bright-dark, and bright-bright separate screening soliton pairs in such a circuit is proved. The numerical results show that the two solitons in a soliton pair can affect each other by the light-induced current and their coupling can affect their spatial profiles, dynamical evolutions, stabilities, and self-deflection. Under the limit in which the optical wave has a spatial extent much less than the width of the crystal, only the dark soliton can affect the other soliton by the light-induced current, but the bright soliton cannot. For a bright-dark or dark-dark soliton pair, the dark soliton in a weak input intensity can be obtained for a larger nonlinearity than for a stronger input intensity. For a bright-dark soliton pair, increasing the input intensity of the dark soliton can increase the bending angle of the bright soliton. Some potential applications are discussed.

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate

PubMed Central

2013-01-01

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at aw (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen. PMID:24027438

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate.

PubMed

Braun, Doris E; Bhardwaj, Rajni M; Arlin, Jean-Baptiste; Florence, Alastair J; Kahlenberg, Volker; Griesser, Ulrich J; Tocher, Derek A; Price, Sarah L

2013-09-04

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at a w (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen.

Cocrystal screening of hydroxybenzamides with benzoic acid derivatives: a comparative study of thermal and solution-based methods.

PubMed

Manin, Alex N; Voronin, Alexander P; Drozd, Ksenia V; Manin, Nikolay G; Bauer-Brandl, Annette; Perlovich, German L

2014-12-18

The main problem occurring at the early stages of cocrystal search is the choice of an effective screening technique. Among the most popular techniques of obtaining cocrystals are crystallization from solution, crystallization from melt and solvent-drop grinding. This paper represents a comparative analysis of the following screening techniques: DSC cocrystal screening method, thermal microscopy and saturation temperature method. The efficiency of different techniques of cocrystal screening was checked in 18 systems. Benzamide and benzoic acid derivatives were chosen as model systems due to their ability to form acid-amide supramolecular heterosynthon. The screening has confirmed the formation of 6 new cocrystals. The screening by the saturation temperature method has the highest screen-out rate but the smallest range of application. DSC screening has a satisfactory accuracy and allows screening over a short time. Thermal microscopy is most efficient as an additional technique used to interpret ambiguous DSC screening results. The study also included an analysis of the influence of solvent type and component solubility on cocrystal formation. Copyright © 2014 Elsevier B.V. All rights reserved.

Device and method for screening crystallization conditions in solution crystal growth

NASA Technical Reports Server (NTRS)

Carter, Daniel C. (Inventor)

1995-01-01

A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1g or microgravity environments comprising a housing, defining at least one pair of chambers for containing crystallization solutions is presented. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place, the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

Device and Method for Screening Crystallization Conditions in Solution Crystal Growth

NASA Technical Reports Server (NTRS)

Carter, Daniel C. (Inventor)

1997-01-01

A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1 g or microgravity environments comprising a housing defining at least one pair of chambers for containing crystallization solutions. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place. the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

Detergent-Specific Membrane Protein Crystallization Screens

NASA Technical Reports Server (NTRS)

Wiener, Michael

2007-01-01

A suite of reagents has been developed for three-dimensional crystallization of integral membranes present in solution as protein-detergent complexes (PDCs). The compositions of these reagents have been determined in part by proximity to the phase boundaries (lower consolute boundaries) of the detergents present in the PDCs. The acquisition of some of the requisite phase-boundary data and the preliminary design of several of the detergent- specific screens was supported by a NASA contract. At the time of expiration of the contract, a partial set of preliminary screens had been developed. This work has since been extended under non-NASA sponsorship, leading to near completion of a set of 20 to 30 different and unique detergent- specific 96-condition screens.

A calibration method for fringe reflection technique based on the analytical phase-slope description

NASA Astrophysics Data System (ADS)

Wu, Yuxiang; Yue, Huimin; Pan, Zhipeng; Liu, Yong

2018-05-01

The fringe reflection technique (FRT) has been one of the most popular methods to measure the shape of specular surface these years. The existing system calibration methods of FRT usually contain two parts, which are camera calibration and geometric calibration. In geometric calibration, the liquid crystal display (LCD) screen position calibration is one of the most difficult steps among all the calibration procedures, and its accuracy is affected by the factors such as the imaging aberration, the plane mirror flatness, and LCD screen pixel size accuracy. In this paper, based on the deduction of FRT analytical phase-slope description, we present a novel calibration method with no requirement to calibrate the position of LCD screen. On the other hand, the system can be arbitrarily arranged, and the imaging system can either be telecentric or non-telecentric. In our experiment of measuring the 5000mm radius sphere mirror, the proposed calibration method achieves 2.5 times smaller measurement error than the geometric calibration method. In the wafer surface measuring experiment, the measurement result with the proposed calibration method is closer to the interferometer result than the geometric calibration method.

Drug-drug cocrystals of antituberculous 4-aminosalicylic acid: Screening, crystal structures, thermochemical and solubility studies.

PubMed

Drozd, Ksenia V; Manin, Alex N; Churakov, Andrei V; Perlovich, German L

2017-03-01

Experimental multistage cocrystal screening of the antituberculous drug 4-aminosalicylic acid (PASA) has been conducted with a number of coformers (pyrazinamide (PYR), nicotinamide (NAM), isonicotinamide (iNAM), isoniazid (INH), caffeine (CAF) and theophylline (TPH)). The crystal structures of 4-aminosalicylic acid cocrystals with isonicotinamide ([PASA+iNAM] (2:1)) and methanol solvate with caffeine ([PASA+CAF+MeOH] (1:1:1)) have been determined by single X-ray diffraction experiments. For the first time for PASA cocrystals it has been found that the structural unit of the [PASA+iNAM] cocrystal (2:1) is formed by 2 types of heterosynthons: acid-pyridine and acid-amide. The desolvation study of the [PASA+CAF+MeOH] cocrystal solvate (1:1:1) has been conducted. The correlation models linking the melting points of the cocrystals with the melting points of the coformers used in this paper have been developed. The thermochemical and solubility properties for all the obtained cocrystals have been studied. Cocrystallization has been shown to lead not only to PASA solubility improving but also to its higher stability against the chemical decomposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

PubMed Central

Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; Roessler, Christian G.; Teplitsky, Ella; Joshi, Karan; Campos, Olven; Agarwal, Rakhi; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

2015-01-01

Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s−1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening. PMID:25615864

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

DOE PAGES

Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; ...

2014-06-01

Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s -1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away frommore » the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.« less

Propagation of biochirality: crossovers and nonclassical crystallization kinetics of aspartic acid in water.

PubMed

Lee, Tu; Lin, Yu Kun; Tsai, Ya Chung; Lee, Hung Lin

2013-11-01

All experimental procedures discussed could be treated as a screening tool for probing the existence of molecular association among the chiral molecules and the solvent system. The molecular association phases of a racemic conglomerate solution (CS) and a racemic compound solution (RCS), and the templating effect of aspartic acid solid surface were observed to minimize the chance of redissolving racemic conglomerate and racemic compound aspartic acid in water and reforming an RCS in crossovers experiments. Only 1 %wt% of l-aspartic acid was adequate enough to induce a transformation from a racemic compound aspartic acid to a racemic conglomerate aspartic acid. This would make the propagation of biochirality more feasible and sound. However, tetrapeptide, (l-aspartic acid)4 , failed to induce enantioseparation as templates purely by crystallization. Nonclassical crystallization theory was needed to take into account the existence of a CS. Fundamental parameters of the crystallization kinetics such as the induction time, interfacial energy, Gibbs energetic barrier, nucleation rate, and critical size of stable nuclei of: (i) racemic compound aspartic acid, (ii) racemic compound aspartic acid seeded with 1 %wt% l-aspartic acid, (iii) racemic conglomerate aspartic acid, and (iv) l-aspartic acid were evaluated and compared with different initial supersaturation ratios. Morphological studies of crystals grown from the crystallization kinetics were also carried out. © 2013 Wiley Periodicals, Inc.

LCDs are better: psychophysical and photometric estimates of the temporal characteristics of CRT and LCD monitors.

PubMed

Lagroix, Hayley E P; Yanko, Matthew R; Spalek, Thomas M

2012-07-01

Many cognitive and perceptual phenomena, such as iconic memory and temporal integration, require brief displays. A critical requirement is that the image not remain visible after its offset. It is commonly believed that liquid crystal displays (LCD) are unsuitable because of their poor temporal response characteristics relative to cathode-ray-tube (CRT) screens. Remarkably, no psychophysical estimates of visible persistence are available to verify this belief. A series of experiments in which white stimuli on a black background produced discernible persistence on CRT but not on LCD screens, during both dark- and light-adapted viewing, falsified this belief. Similar estimates using black stimuli on a white background produced no visible persistence on either screen. That said, photometric measurements are available that seem to confirm the poor temporal characteristics of LCD screens, but they were obtained before recent advances in LCD technology. Using current LCD screens, we obtained photometric estimates of rise time far shorter (1-6 ms) than earlier estimates (20-150 ms), and approaching those of CRTs (<1 ms). We conclude that LCDs are preferable to CRTs when visible persistence is a concern, except when black-on-white displays are used.

Aberration improvement of the floating 3D display system based on Tessar array and directional diffuser screen

NASA Astrophysics Data System (ADS)

Gao, Xin; Sang, Xinzhu; Yu, Xunbo; Zhang, Wanlu; Yan, Binbin; Yu, Chongxiu

2018-06-01

The floating 3D display system based on Tessar array and directional diffuser screen is proposed. The directional diffuser screen can smoothen the gap of lens array and make the 3D image's brightness continuous. The optical structure and aberration characteristics of the floating three-dimensional (3D) display system are analyzed. The simulation and experiment are carried out, which show that the 3D image quality becomes more and more deteriorative with the further distance of the image plane and the increasing viewing angle. To suppress the aberrations, the Tessar array is proposed according to the aberration characteristics of the floating 3D display system. A 3840 × 2160 liquid crystal display panel (LCD) with the size of 23.6 inches, a directional diffuser screen and a Tessar array are used to display the final 3D images. The aberrations are reduced and the definition is improved compared with that of the display with a single-lens array. The display depth of more than 20 cm and the viewing angle of more than 45° can be achieved.

Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method.

PubMed

Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Virtual screening is a computational technique for predicting a potent binding compound for a receptor protein from a ligand library. It has been a widely used in the drug discovery field to reduce the efforts of medicinal chemists to find hit compounds by experiments.Here, we introduce our novel structure-based virtual screening program, PL-PatchSurfer, which uses molecular surface representation with the three-dimensional Zernike descriptors, which is an effective mathematical representation for identifying physicochemical complementarities between local surfaces of a target protein and a ligand. The advantage of the surface-patch description is its tolerance on a receptor and compound structure variation. PL-PatchSurfer2 achieves higher accuracy on apo form and computationally modeled receptor structures than conventional structure-based virtual screening programs. Thus, PL-PatchSurfer2 opens up an opportunity for targets that do not have their crystal structures. The program is provided as a stand-alone program at http://kiharalab.org/plps2 . We also provide files for two ligand libraries, ChEMBL and ZINC Drug-like.

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

Large area projection liquid-crystal video display system with inherent grid pattern optically removed

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang (Inventor)

1992-01-01

A relatively small and low-cost system is provided for projecting a large and bright television image onto a screen. A miniature liquid crystal array is driven by video circuitry to produce a pattern of transparencies in the array corresponding to a television image. Light is directed against the rear surface of the array to illuminate it, while a projection lens lies in front of the array to project the image of the array onto a large screen. Grid lines in the liquid crystal array are eliminated by a spacial filter which comprises a negative of the Fourier transform of the grid.

Experimental cocrystal screening and solution based scale-up cocrystallization methods.

PubMed

Malamatari, Maria; Ross, Steven A; Douroumis, Dennis; Velaga, Sitaram P

2017-08-01

Cocrystals are crystalline single phase materials composed of two or more different molecular and/or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts. If one of the components is an active pharmaceutical ingredient (API), the term pharmaceutical cocrystal is often used. There is a growing interest among drug development scientists in exploring cocrystals, as means to address physicochemical, biopharmaceutical and mechanical properties and expand solid form diversity of the API. Conventionally, coformers are selected based on crystal engineering principles, and the equimolar mixtures of API and coformers are subjected to solution-based crystallization that are commonly employed in polymorph and salt screening. However, the availability of new knowledge on cocrystal phase behaviour in solid state and solutions has spurred the development and implementation of more rational experimental cocrystal screening as well as scale-up methods. This review aims to provide overview of commonly employed solid form screening techniques in drug development with an emphasis on cocrystal screening methodologies. The latest developments in understanding and the use of cocrystal phase diagrams in both screening and solution based scale-up methods are also presented. Final section is devoted to reviewing the state of the art research covering solution based scale-up cocrystallization process for different cocrystals besides more recent continuous crystallization methods. Copyright © 2017 Elsevier B.V. All rights reserved.

A rational approach to heavy-atom derivative screening

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joyce, M. Gordon; Radaev, Sergei; Sun, Peter D., E-mail: psun@nih.gov

2010-04-01

In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom-derivative screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasingmore » power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom derivative-screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. The method includes three basic steps: (i) the selection of likely reactive compounds for a given protein and specific crystallization conditions based on pre-defined heavy-atom compound reactivity profiles, (ii) screening of the chosen heavy-atom compounds for their ability to form protein adducts using mass spectrometry and (iii) derivatization of crystals with selected heavy-metal compounds using the quick-soak method to maximize diffraction quality and minimize non-isomorphism. Overall, this system streamlines the process of heavy-atom compound identification and minimizes the problem of non-isomorphism in phasing.« less

Direct Observation of Protein Microcrystals in Crystallization Buffer by Atmospheric Scanning Electron Microscopy

PubMed Central

Maruyama, Yuusuke; Ebihara, Tatsuhiko; Nishiyama, Hidetoshi; Konyuba, Yuji; Senda, Miki; Numaga-Tomita, Takuro; Senda, Toshiya; Suga, Mitsuo; Sato, Chikara

2012-01-01

X-ray crystallography requires high quality crystals above a given size. This requirement not only limits the proteins to be analyzed, but also reduces the speed of the structure determination. Indeed, the tertiary structures of many physiologically important proteins remain elusive because of the so-called “crystallization bottleneck”. Once microcrystals have been obtained, crystallization conditions can be optimized to produce bigger and better crystals. However, the identification of microcrystals can be difficult due to the resolution limit of optical microscopy. Electron microscopy has sometimes been utilized instead, with the disadvantage that the microcrystals usually must be observed in vacuum, which precludes the usage for crystal screening. The atmospheric scanning electron microscope (ASEM) allows samples to be observed in solution. Here, we report the use of this instrument in combination with a special thin-membrane dish with a crystallization well. It was possible to observe protein crystals of lysozyme, lipase B and a histone chaperone TAF-Iβ in crystallization buffers, without the use of staining procedures. The smallest crystals observed with ASEM were a few μm in width, and ASEM can be used with non-transparent solutions. Furthermore, the growth of salt crystals could be monitored in the ASEM, and the difference in contrast between salt and protein crystals made it easy to distinguish between these two types of microcrystals. These results indicate that the ASEM could be an important new tool for the screening of protein microcrystals. PMID:22949879

Direct observation of protein microcrystals in crystallization buffer by atmospheric scanning electron microscopy.

PubMed

Maruyama, Yuusuke; Ebihara, Tatsuhiko; Nishiyama, Hidetoshi; Konyuba, Yuji; Senda, Miki; Numaga-Tomita, Takuro; Senda, Toshiya; Suga, Mitsuo; Sato, Chikara

2012-01-01

X-ray crystallography requires high quality crystals above a given size. This requirement not only limits the proteins to be analyzed, but also reduces the speed of the structure determination. Indeed, the tertiary structures of many physiologically important proteins remain elusive because of the so-called "crystallization bottleneck". Once microcrystals have been obtained, crystallization conditions can be optimized to produce bigger and better crystals. However, the identification of microcrystals can be difficult due to the resolution limit of optical microscopy. Electron microscopy has sometimes been utilized instead, with the disadvantage that the microcrystals usually must be observed in vacuum, which precludes the usage for crystal screening. The atmospheric scanning electron microscope (ASEM) allows samples to be observed in solution. Here, we report the use of this instrument in combination with a special thin-membrane dish with a crystallization well. It was possible to observe protein crystals of lysozyme, lipase B and a histone chaperone TAF-Iβ in crystallization buffers, without the use of staining procedures. The smallest crystals observed with ASEM were a few μm in width, and ASEM can be used with non-transparent solutions. Furthermore, the growth of salt crystals could be monitored in the ASEM, and the difference in contrast between salt and protein crystals made it easy to distinguish between these two types of microcrystals. These results indicate that the ASEM could be an important new tool for the screening of protein microcrystals.

Attractive potential around a thermionically emitting microparticle.

PubMed

Delzanno, G L; Lapenta, G; Rosenberg, M

2004-01-23

We present a simulation study of the charging of a dust grain immersed in a plasma, considering the effect of thermionic electron emission from the grain. It is shown that the orbit motion limited theory is no longer reliable when electron emission becomes large: screening can no longer be treated within the Debye-Huckel approach and an attractive potential well can form, leading to the possibility of attractive forces on other grains with the same polarity. We suggest to perform laboratory experiments where emitting dust grains could be used to create nonconventional dust crystals or macromolecules.

A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yap, Thai Leong; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551; Chen, Yen Liang

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents anmore » interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.« less

A large area high resolution imaging detector for fast atom diffraction

NASA Astrophysics Data System (ADS)

Lupone, Sylvain; Soulisse, Pierre; Roncin, Philippe

2018-07-01

We describe a high resolution imaging detector based on a single 80 mm micro-channel-plate (MCP) and a phosphor screen mounted on a UHV flange of only 100 mm inner diameter. It relies on standard components and we describe its performance with one or two MCPs. A resolution of 80 μm rms is observed on the beam profile. At low count rate, individual impact can be pinpointed with few μm accuracy but the resolution is probably limited by the MCP channel diameter. The detector has been used to record the diffraction of fast atoms at grazing incidence on crystal surfaces (GIFAD), a technique probing the electronic density of the topmost layer only. The detector was also used to record the scattering profile during azimuthal scan of the crystal to produce triangulation curves revealing the surface crystallographic directions of molecular layers. It should also be compatible with reflection high energy electron (RHEED) experiment when fragile surfaces require a low exposure to the electron beam. The discussions on the mode of operation specific to diffraction experiments apply also to commercial detectors.

High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

PubMed Central

Hu, Ting-Chou; Korczyńska, Justyna; Smith, David K.; Brzozowski, Andrzej Marek

2008-01-01

Protein crystallization has been revolutionized by the intro­duction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-­glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here. PMID:18703844

Development of a New Class of Drugs To Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

ARdbd-DNA crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening operations with... Chiang , Y.T., Sharma, A., Peacock, J.W., Wang, W., Cherkasov, A., Rennie, P.S., Gleave, M.E., and Ong, C.J. (2016) Androgen Receptor transcriptionally

Phage display for the discovery of hydroxyapatite-associated peptides.

PubMed

Jin, Hyo-Eon; Chung, Woo-Jae; Lee, Seung-Wuk

2013-01-01

In nature, proteins play a critical role in the biomineralization process. Understanding how different peptide or protein sequences selectively interact with the target crystal is of great importance. Identifying such protein structures is one of the critical steps in verifying the molecular mechanisms of biomineralization. One of the promising ways to obtain such information for a particular crystal surface is to screen combinatorial peptide libraries in a high-throughput manner. Among the many combinatorial library screening procedures, phage display is a powerful method to isolate such proteins and peptides. In this chapter, we will describe our established methods to perform phage display with inorganic crystal surfaces. Specifically, we will use hydroxyapatite as a model system for discovery of apatite-associated proteins in bone or tooth biomineralization studies. This model approach can be generalized to other desired crystal surfaces using the same experimental design principles with a little modification of the procedures. © 2013 Elsevier Inc. All rights reserved.

Promoting crystallisation of the Salmonella enteritidis fimbriae 14 pilin SefD using deuterium oxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Bing; Garnett, James A.; Lee, Wei-chao

Highlights: Black-Right-Pointing-Pointer The benefits of D{sub 2}O in screening for crystallisation was explored. Black-Right-Pointing-Pointer The crystal structures of the SefD pilin in both H{sub 2}O and D{sub 2}O reveal differences. Black-Right-Pointing-Pointer Crystallisation improvements are explained by altered interactions in D{sub 2}O crystals. Black-Right-Pointing-Pointer D{sub 2}O is useful additive in sparse-matrix screening for crystallisation. -- Abstract: The use of heavy water (D{sub 2}O) as a solvent is commonplace in many spectroscopic techniques for the study of biological macromolecules. A significant deuterium isotope effect exists where hydrogen-bonding is important, such as in protein stability, dynamics and assembly. Here we illustrate the usemore » of D{sub 2}O in additive screening for the production of reproducible diffraction-quality crystals for the Salmonella enteritidis fimbriae 14 (SEF14) putative tip adhesin, SefD.« less

Serial Millisecond Crystallography of Membrane Proteins.

PubMed

Jaeger, Kathrin; Dworkowski, Florian; Nogly, Przemyslaw; Milne, Christopher; Wang, Meitian; Standfuss, Joerg

2016-01-01

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.

Optical fringe-reflection deflectometry with bundle adjustment

NASA Astrophysics Data System (ADS)

Xiao, Yong-Liang; Li, Sikun; Zhang, Qican; Zhong, Jianxin; Su, Xianyu; You, Zhisheng

2018-06-01

Liquid crystal display (LCD) screens are located outside of a camera's field of view in fringe-reflection deflectometry. Therefore, fringes that are displayed on LCD screens are obtained through specular reflection by a fixed camera. Thus, the pose calibration between the camera and LCD screen is one of the main challenges in fringe-reflection deflectometry. A markerless planar mirror is used to reflect the LCD screen more than three times, and the fringes are mapped into the fixed camera. The geometrical calibration can be accomplished by estimating the pose between the camera and the virtual image of fringes. Considering the relation between their pose, the incidence and reflection rays can be unified in the camera frame, and a forward triangulation intersection can be operated in the camera frame to measure three-dimensional (3D) coordinates of the specular surface. In the final optimization, constraint-bundle adjustment is operated to refine simultaneously the camera intrinsic parameters, including distortion coefficients, estimated geometrical pose between the LCD screen and camera, and 3D coordinates of the specular surface, with the help of the absolute phase collinear constraint. Simulation and experiment results demonstrate that the pose calibration with planar mirror reflection is simple and feasible, and the constraint-bundle adjustment can enhance the 3D coordinate measurement accuracy in fringe-reflection deflectometry.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

One Question, Multiple Answers: Biochemical and Biophysical Screening Methods Retrieve Deviating Fragment Hit Lists.

PubMed

Schiebel, Johannes; Radeva, Nedyalka; Köster, Helene; Metz, Alexander; Krotzky, Timo; Kuhnert, Maren; Diederich, Wibke E; Heine, Andreas; Neumann, Lars; Atmanene, Cedric; Roecklin, Dominique; Vivat-Hannah, Valérie; Renaud, Jean-Paul; Meinecke, Robert; Schlinck, Nina; Sitte, Astrid; Popp, Franziska; Zeeb, Markus; Klebe, Gerhard

2015-09-01

Fragment-based lead discovery is gaining momentum in drug development. Typically, a hierarchical cascade of several screening techniques is consulted to identify fragment hits which are then analyzed by crystallography. Because crystal structures with bound fragments are essential for the subsequent hit-to-lead-to-drug optimization, the screening process should distinguish reliably between binders and non-binders. We therefore investigated whether different screening methods would reveal similar collections of putative binders. First we used a biochemical assay to identify fragments that bind to endothiapepsin, a surrogate for disease-relevant aspartic proteases. In a comprehensive screening approach, we then evaluated our 361-entry library by using a reporter-displacement assay, saturation-transfer difference NMR, native mass spectrometry, thermophoresis, and a thermal shift assay. While the combined results of these screening methods retrieve 10 of the 11 crystal structures originally predicted by the biochemical assay, the mutual overlap of individual hit lists is surprisingly low, highlighting that each technique operates on different biophysical principles and conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Automating the application of smart materials for protein crystallization.

PubMed

Khurshid, Sahir; Govada, Lata; El-Sharif, Hazim F; Reddy, Subrayal M; Chayen, Naomi E

2015-03-01

The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as `smart materials') for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials.

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyburn, Tasia M.; Yankovskaya, Victoria; Bensing, Barbara A.

2012-07-11

The carbohydrate-binding region of the bacterial adhesin GspB from Streptococcus gordonii strain M99 (GspB{sub BR}) was expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. Separate sparse-matrix screening of GspB{sub BR} buffered in either 20 mM Tris pH 7.4 or 20 mM HEPES pH 7.5 resulted in different crystallographic behavior such that different precipitants, salts and additives supported crystallization of GspB{sub BR} in each buffer. While both sets of conditions supported crystal growth in space group P2{sub 1}2{sub 1}2{sub 1}, the crystals had distinct unit-cell parameters of a = 33.3, b = 86.7, c = 117.9 {angstrom} formore » crystal form 1 and a = 34.6, b = 98.3, c = 99.0 {angstrom} for crystal form 2. Additive screening improved the crystals grown in both conditions such that diffraction extended to beyond 2 {angstrom} resolution. A complete data set has been collected to 1.3 {angstrom} resolution with an overall R{sub merge} value of 0.04 and an R{sub merge} value of 0.33 in the highest resolution shell.« less

ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

PubMed Central

Hungler, Arnaud; Momin, Afaque; Diederichs, Kay; Arold, Stefan, T.

2016-01-01

Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for ‘crystallization and preliminary X-ray analysis’ publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. PMID:27980519

Structural and physicochemical characterization of pyridine derivative salts of anti-inflammatory drugs

NASA Astrophysics Data System (ADS)

Nechipadappu, Sunil Kumar; Trivedi, Darshak R.

2017-08-01

Salts of common anti-inflammatory drugs mefenamic acid (MFA), tolfenamic acid (TFA) and naproxen (NPX) with various pyridine derivatives (4-amino pyridine (4AP), 4-dimethylaminopyridine (DMAP) and 2-amino pyridine (2AP)) were synthesized by crystal engineering approach based on the pKa values of API's and the salt former. All the salts were characterized systematically by various spectroscopic methods including FT-IR and 1H NMR and the crystal structure was determined by single-crystal X-ray diffraction techniques (SCXRD). DMAP salt of NPX and 2AP salts of MFA and TFA were not obtained in the salt screening experiments. All the molecular salts exhibited 1:1 molecular stoichiometry in the asymmetric unit and except NPX-2AP salt, all the molecular salts included a water molecule in the crystal lattice. Physicochemical and structural properties between drug-drug molecular salts of MFA-4AP, TFA-4AP and NPX-4AP have been evaluated and it was found that these molecular salts were found to be stable for a time period of six months at ambient condition and further hydration of molecular salts were not observed even at accelerated humid conditions (∼75% RH). It was found that 4AP salts of MFA and TFA and DMAP salts of MFA and TFA are isostructural.

Development of a New Class of Drugs to Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

previous rat ARdbd-DNA crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening...to VPC-14449 as a model drug to assist on other related projects. 1. Tam, K., Dalal, K., Hsing, M., Cheng, C.W., Chiang , Y.T., Sharma, A., Peacock

Development of a New Class of Drugs To Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening operations with the ARdbd protein...related projects. 1. Tam, K., Dalal, K., Hsing, M., Cheng, C.W., Chiang , Y.T., Sharma, A., Peacock, J.W., Wang, W., Cherkasov, A., Rennie, P.S

New Large Diameter RF Complex Plasma Device

NASA Astrophysics Data System (ADS)

Meyer, John; Nosenko, Volodymyr; Thomas, Hubertus

2016-10-01

The Complex Plasma Research Group at the German Aerospace Center (DLR) in Oberpfaffenhofen has built a new large diameter rf plasma setup for dusty plasma experiments. The vacuum chamber is a stainless steel cylinder 0.90 m in diameter and 0.34 m in height with ports for viewing and measurement. A 0.85 m diameter plate in about the center serves as a powered electrode (13.56 MHz) with the chamber walls as the ground. It is pumped on by one of two Oerlikon turbo pumps with a pumping rate of 1100 l/s or 270 l/s. Argon gas is admitted into the chamber by an MKS mass flow meter and pumping is regulated by a butterfly valve to set pressure for experiments. A manual dropper is used to insert dust into the plasma. The dust is illuminated horizontally by a 660 nm 100 mW laser sheet and viewed from above by a Photron FASTCAM 1024 PCI camera. A vertical laser sheet of 635 nm will be used for side imaging. So far, single-layer plasma crystals of up to 15000 particles have been suspended. The particle velocity fluctuation spectra were measured and from these, the particle charge and screening length were calculated. Future experiments will explore the system-size dependence of the plasma crystal properties.

Recent results and new hardware developments for protein crystal growth in microactivity

NASA Technical Reports Server (NTRS)

Delucas, L. J.; Long, M. M.; Moore, K. M.; Smith, C.; Carson, M.; Narayana, S. V. L.; Carter, D.; Clark, A. D., Jr.; Nanni, R. G.; Ding, J.

1993-01-01

Protein crystal growth experiments have been performed on 16 space shuttle missions since April, 1985. The initial experiments utilized vapor diffusion crystallization techniques similar to those used in laboratories for earth-based experiments. More recent experiments have utilized temperature induced crystallization as an alternative method for growing high quality protein crystals in microgravity. Results from both vapor diffusion and temperature induced crystallization experiments indicate that proteins grown in microgravity may be larger, display more uniform morphologies, and yield diffraction data to significantly higher resolutions than the best crystals of these proteins grown on earth.

Method For Screening Microcrystallizations For Crystal Formation

DOEpatents

Santarsiero, Bernard D. , Stevens, Raymond C. , Schultz, Peter G. , Jaklevic, Joseph M. , Yegian, Derek T. , Cornell, Earl W. , Nordmeyer, Robert A.

2003-10-07

A method is provided for performing array microcrystallizations to determine suitable crystallization conditions for a molecule, the method comprising: forming an array of microcrystallizations, each microcrystallization comprising a drop comprising a mother liquor solution whose composition varies within the array and a molecule to be crystallized, the drop having a volume of less than 1 microliter; storing the array of microcrystallizations under conditions suitable for molecule crystals to form in the drops in the array; and detecting molecule crystal formation in the drops by taking images of the drops.

Real-time computer-generated hologram by means of liquid-crystal television spatial light modulator

NASA Technical Reports Server (NTRS)

Mok, Fai; Psaltis, Demetri; Diep, Joseph; Liu, Hua-Kuang

1986-01-01

The usefulness of an inexpensive liquid-crystal television) (LCTV) as a spatial light modulator for coherent-optical processing in the writing and reconstruction of a single computer-generated hologram has been demonstrated. The thickness nonuniformities of the LCTV screen were examined in a Mach-Zehnder interferometer, and the phase distortions were successfully removed using a technique in which the LCTV screen was submerged in a liquid gate filled with an index-matching nonconductive mineral oil with refractive index of about 1.45.

Four-Dimensional Screening Anti-Counterfeiting Pattern by Inkjet Printed Photonic Crystals.

PubMed

Hou, Jue; Zhang, Huacheng; Su, Bin; Li, Mingzhu; Yang, Qiang; Jiang, Lei; Song, Yanlin

2016-10-06

A four-dimensional screening anti-counterfeiting QR code composed of differently shaped photonic crystal (PC) dots has been fabricated that could display four images depending on different lighting conditions. By controlling the rheology of poly(dimethylsiloxane) (PDMS), three kinds of PC dots could be sequentially integrated into one pattern using the layer-by-layer printing strategy. The information can be encoded and stored in shapes and read out by the difference in optical properties. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

PubMed

Hu, Xiaohua; Chen, Nana; Li, Weichen

2016-07-01

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

Screens and Displays.

ERIC Educational Resources Information Center

Edstrom, Malin

1987-01-01

Discusses the characteristics of different computer screen technologies including the possible harmful effects on health of cathode ray tube (CRT) terminals. CRT's are compared to other technologies including liquid crystal displays, plasma displays, electroluminiscence displays, and light emitting diodes. A chart comparing the different…

What’s in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments

PubMed Central

Luft, Joseph R.; Wolfley, Jennifer R.; Snell, Edward H.

2011-01-01

Observations of crystallization experiments are classified as specific outcomes and integrated through a phase diagram to visualize solubility and thereby direct subsequent experiments. Specific examples are taken from our high-throughput crystallization laboratory which provided a broad scope of data from 20 million crystallization experiments on 12,500 different biological macromolecules. The methods and rationale are broadly and generally applicable in any crystallization laboratory. Through a combination of incomplete factorial sampling of crystallization cocktails, standard outcome classifications, visualization of outcomes as they relate chemically and application of a simple phase diagram approach we demonstrate how to logically design subsequent crystallization experiments. PMID:21643490

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

PubMed Central

Conrad, Chelsie E.; Nelson, Garrett; Stander, Natasha; Zatsepin, Nadia A.; Zook, James; Zhu, Lan; Geiger, James; Chun, Eugene; Kissick, David; Hilgart, Mark C.; Ogata, Craig; Ishchenko, Andrii; Nagaratnam, Nirupa; Roy-Chowdhury, Shatabdi; Coe, Jesse; Subramanian, Ganesh; Schaffer, Alexander; Ketwala, Gihan; Venugopalan, Nagarajan; Xu, Shenglan; Corcoran, Stephen; Ferguson, Dale; Weierstall, Uwe; Spence, John C. H.; Cherezov, Vadim; Fromme, Petra; Fischetti, Robert F.; Liu, Wei

2017-01-01

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals. PMID:28875031

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.

PubMed

Martin-Garcia, Jose M; Conrad, Chelsie E; Nelson, Garrett; Stander, Natasha; Zatsepin, Nadia A; Zook, James; Zhu, Lan; Geiger, James; Chun, Eugene; Kissick, David; Hilgart, Mark C; Ogata, Craig; Ishchenko, Andrii; Nagaratnam, Nirupa; Roy-Chowdhury, Shatabdi; Coe, Jesse; Subramanian, Ganesh; Schaffer, Alexander; James, Daniel; Ketwala, Gihan; Venugopalan, Nagarajan; Xu, Shenglan; Corcoran, Stephen; Ferguson, Dale; Weierstall, Uwe; Spence, John C H; Cherezov, Vadim; Fromme, Petra; Fischetti, Robert F; Liu, Wei

2017-07-01

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

DOE PAGES

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Nelson, Garrett; ...

2017-05-24

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advancedmore » Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. Furthermore, these developments will enable structure determination from smaller and/or weakly diffracting microcrystals.« less

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Nelson, Garrett

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advancedmore » Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. Furthermore, these developments will enable structure determination from smaller and/or weakly diffracting microcrystals.« less

The effective fine-structure constant of freestanding graphene measured in graphite.

PubMed

Reed, James P; Uchoa, Bruno; Joe, Young Il; Gan, Yu; Casa, Diego; Fradkin, Eduardo; Abbamonte, Peter

2010-11-05

Electrons in graphene behave like Dirac fermions, permitting phenomena from high-energy physics to be studied in a solid-state setting. A key question is whether or not these fermions are critically influenced by Coulomb correlations. We performed inelastic x-ray scattering experiments on crystals of graphite and applied reconstruction algorithms to image the dynamical screening of charge in a freestanding graphene sheet. We found that the polarizability of the Dirac fermions is amplified by excitonic effects, improving screening of interactions between quasiparticles. The strength of interactions is characterized by a scale-dependent, effective fine-structure constant, α(g)* (k,ω), the value of which approaches 0.14 ± 0.092 ~ 1/7 at low energy and large distances. This value is substantially smaller than the nominal α(g) = 2.2, suggesting that, on the whole, graphene is more weakly interacting than previously believed.

Life Prediction of Turbine Blade Nickel Base Superalloy Single Crystals.

DTIC Science & Technology

1986-08-01

mechanical properties between single crystals and the DS version of Mar-M200. Soon it was recognized again through the mechanical property - structure ... property achievements demonstrated by screening and simulated engine tests. 1 Single crystals are the results of extensive investigation on the mechanical ...behavior, (especially fatigue and creep) of, and the structure - property correlations in the equiaxed and directionally solidified (DS) nickel-base

Practical macromolecular cryocrystallography

PubMed Central

Pflugrath, J. W.

2015-01-01

Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented. PMID:26057787

SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands

PubMed Central

Huber, Sylwia; Casagrande, Fabio; Hug, Melanie N.; Wang, Lisha; Heine, Philipp; Kummer, Lutz; Plückthun, Andreas; Hennig, Michael

2017-01-01

The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands. In this report, surface plasmon resonance was used as primary method to screen 6369 compounds. Thereby 44 hits were identified and confirmed in competition as well as dose-response experiments. Furthermore, 4 out of 8 selected hits were validated using nuclear magnetic resonance spectroscopy as orthogonal biophysical method. Computational analysis of the compound structures, taking the known crystal structure of the endogenous peptide agonist into consideration, gave insight into the potential fragment-binding location and interactions and inspires chemistry efforts for further exploration of the fragments. PMID:28510609

Improving the dissolution and bioavailability of 6-mercaptopurine via co-crystallization with isonicotinamide.

PubMed

Wang, Jian-Rong; Yu, Xueping; Zhou, Chun; Lin, Yunfei; Chen, Chen; Pan, Guoyu; Mei, Xuefeng

2015-03-01

6-Mercaptopurine (6-MP) is a clinically important antitumor drug. The commercially available form was provided as monohydrate and belongs to BCS class II category. Co-crystallization screening by reaction crystallization method (RCM) and monitored by powder X-ray diffraction led to the discovery of a new co-crystal formed between 6-MP and isonicotinamide (co-crystal 1). Co-crystal 1 was thoroughly characterized by X-ray diffraction, FT-IR and Raman spectroscopy, and thermal analysis. Noticeably, the in vitro and in vivo studies revealed that co-crystal 1 possesses improved dissolution rate and superior bioavailability on animal model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure

PubMed Central

Jansen, Chimed; Wang, Huanchen; Kooistra, Albert J.; de Graaf, Chris; Orrling, Kristina; Tenor, Hermann; Seebeck, Thomas; Bailey, David; de Esch, Iwan J.P.; Ke, Hengming; Leurs, Rob

2013-01-01

Trypanosoma brucei cyclic nucleotide phosphodiesterase B1 (TbrPDEB1) and TbrPDEB2 have recently been validated as new therapeutic targets for human African Trypanosomiasis by both genetic and pharmacological means. In this study we report the crystal structure of the catalytic domain of the unliganded TbrPDEB1 and its use for the in silico screening for new TbrPDEB1 inhibitors with novel scaffolds. The TbrPDEB1 crystal structure shows the characteristic folds of human PDE enzymes, but also contains the parasite-specific P-pocket found in the structures of Leishmania major PDEB1 and Trypanosoma cruzi PDEC. The unliganded TbrPDEB1 X-ray structure was subjected to a structure-based in silico screening approach that combines molecular docking simulations with a protein-ligand interaction fingerprint (IFP) scoring method. This approach identified, six novel TbrPDEB1 inhibitors with IC50 values of 10–80 μM, which may be further optimized as potential selective TbrPDEB inhibitors. PMID:23409953

ICP-MS measurement of natural radioactivity at LNGS

NASA Astrophysics Data System (ADS)

Nisi, S.; Copia, L.; Dafinei, I.; di Vacri, M. L.

2017-10-01

Rare events search experiments, like those dedicated to the direct evidence of dark matter or neutrinoless double beta decay, are among the most exciting challenges of modern physics. The sensitivity of such experiments is driven by the background, which depends substantially on the radiopurity of the materials used for the experimental apparatus. Cutting edge measurement techniques are needed for a fast, sensitive and efficient screening of these materials and the certification of their production. Trace element measurements of high sensitivity and quick execution are mandatory also in other fields like tracing the geographical origin of food, temporal and geographical assignment of cultural heritage or monitoring environmental radioactivity. This work is an overview of the inorganic mass spectrometry facility available at Gran Sasso National Laboratory (LNGS) for radiopure material screening and is especially focused on its ICP-MS instrumentation. Analytical methods developed to achieve lowest detection limits in different types of matrix, like metals, polymers, crystals and composite materials, are also indicated. Detection limits of 10-18gg-1 for 226Ra, 10-14gg-1 for U and Th and 10-12gg-1 for K are attained through dedicated operation conditions of the instrumentation. Details are given on the results obtained for different experiments ongoing or under construction at LNGS.

Influence of pH, particle size and crystal form on dissolution behaviour of engineered nanomaterials.

PubMed

Avramescu, M-L; Rasmussen, P E; Chénier, M; Gardner, H D

2017-01-01

Solubility is a critical component of physicochemical characterisation of engineered nanomaterials (ENMs) and an important parameter in their risk assessments. Standard testing methodologies are needed to estimate the dissolution behaviour and biodurability (half-life) of ENMs in biological fluids. The effect of pH, particle size and crystal form on dissolution behaviour of zinc metal, ZnO and TiO 2 was investigated using a simple 2 h solubility assay at body temperature (37 °C) and two pH conditions (1.5 and 7) to approximately frame the pH range found in human body fluids. Time series dissolution experiments were then conducted to determine rate constants and half-lives. Dissolution characteristics of investigated ENMs were compared with those of their bulk analogues for both pH conditions. Two crystal forms of TiO 2 were considered: anatase and rutile. For all compounds studied, and at both pH conditions, the short solubility assays and the time series experiments consistently showed that biodurability of the bulk analogues was equal to or greater than biodurability of the corresponding nanomaterials. The results showed that particle size and crystal form of inorganic ENMs were important properties that influenced dissolution behaviour and biodurability. All ENMs and bulk analogues displayed significantly higher solubility at low pH than at neutral pH. In the context of classification and read-across approaches, the pH of the dissolution medium was the key parameter. The main implication is that pH and temperature should be specified in solubility testing when evaluating ENM dissolution in human body fluids, even for preliminary (tier 1) screening.

Dual centrifugation - A new technique for nanomilling of poorly soluble drugs and formulation screening by an DoE-approach.

PubMed

Hagedorn, Martin; Bögershausen, Ansgar; Rischer, Matthias; Schubert, Rolf; Massing, Ulrich

2017-09-15

The development of nanosuspensions of poorly soluble APIs takes a lot of time and high amount of active material is needed. In this publication the use of dual centrifugation (DC) for an effective and rapid API-nanomilling is described for the first time. DC differs from normal centrifugation by an additional rotation of the samples during centrifugation, resulting in a very fast and powerful movement of the samples inside the vials, which - in combination with milling beads - result in effective milling. DC-nanomilling was compared to conventional wet ball milling and results in same or even smaller particle sizes. Also drug concentrations up to 40% can be processed. The process is fast (typical 90min) and the temperature can be controlled. DC-nanomilling appears to be very gentle, experiments showed no change of the crystal structure during milling. Since batch sizes are very small (100-1000mg) and since 40 sample vials can be processed in parallel, DC is ideal for the screening of suitable polymer/surfactant combinations. Fenofibrate was used to investigate DC-nanomilling for formulation screening by applying a DoE-approach. The presented data also show that the results of DC-nanomilling experiments are highly comparable to the results obtained by common agitator mills. Copyright © 2017 Elsevier B.V. All rights reserved.

Microscopic origin of the charge transfer in single crystals based on thiophene derivatives: A combined NEXAFS and density functional theory approach

NASA Astrophysics Data System (ADS)

Chernenkaya, A.; Morherr, A.; Backes, S.; Popp, W.; Witt, S.; Kozina, X.; Nepijko, S. A.; Bolte, M.; Medjanik, K.; Öhrwall, G.; Krellner, C.; Baumgarten, M.; Elmers, H. J.; Schönhense, G.; Jeschke, H. O.; Valentí, R.

2016-07-01

We have investigated the charge transfer mechanism in single crystals of DTBDT-TCNQ and DTBDT-F4TCNQ (where DTBDT is dithieno[2,3-d;2',3'-d'] benzo[1,2-b;4,5-b']dithiophene) using a combination of near-edge X-ray absorption spectroscopy (NEXAFS) and density functional theory calculations (DFT) including final state effects beyond the sudden state approximation. In particular, we find that a description that considers the partial screening of the electron-hole Coulomb correlation on a static level as well as the rearrangement of electronic density shows excellent agreement with experiment and allows to uncover the details of the charge transfer mechanism in DTBDT-TCNQ and DTBDT-F4 TCNQ, as well as a reinterpretation of previous NEXAFS data on pure TCNQ. Finally, we further show that almost the same quality of agreement between theoretical results and experiment is obtained by the much faster Z+1/2 approximation, where the core hole effects are simulated by replacing N or F with atomic number Z with the neighboring atom with atomic number Z+1/2.

Automated macromolecular crystal detection system and method

DOEpatents

Christian, Allen T [Tracy, CA; Segelke, Brent [San Ramon, CA; Rupp, Bernard [Livermore, CA; Toppani, Dominique [Fontainebleau, FR

2007-06-05

An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

The Orthogonal In-Situ Machining of Single and Polycrystalline Aluminum and Copper, Volume 1. Ph.D. Thesis Final Report

NASA Technical Reports Server (NTRS)

Cohen, P. H.

1982-01-01

Metal cutting is a unique deformation process characterized by large strains, exceptionally high strain rates and few constraints to the deformation. These factors, along with the difficulty of directly measuring the shear angle, make chip formation difficult to model and understand. One technique for skirting the difficulty of post mortem chip measurement is to perform a cutting experiment dynamically in a scanning electron microscope. The performance of the in-situ experiment with full instrumentation allows for component force measurement, orientation measurement (on a round single crystal disk) and a timing device, all superimposed below the deformation on the TV monitor and recorded for future viewing. This allows the sher angle to be directly measured for the screen along with the other needed information.

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening.

PubMed

Ghattas, Mohammad A; Atatreh, Noor; Bichenkova, Elena V; Bryce, Richard A

2014-07-01

Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening. Copyright © 2014 Elsevier Inc. All rights reserved.

Purification, crystallization and preliminary X-ray characterization of prunin-1, a major component of the almond (Prunus dulcis) allergen amandin.

PubMed

Albillos, Silvia M; Jin, Tengchuan; Howard, Andrew; Zhang, Yuzhu; Kothary, Mahendra H; Fu, Tong-Jen

2008-07-09

The 11S globulins from plant seeds account for a number of major food allergens. Because of the interest in the structural basis underlying the allergenicity of food allergens, we sought to crystallize the main 11S seed storage protein from almond ( Prunus dulcis). Prunin-1 (Pru1) was purified from defatted almond flour by water extraction, cryoprecipitation, followed by sequential anion exchange, hydrophobic interaction, and size exclusion chromatography. Single crystals of Pru1 were obtained in a screening with a crystal screen kit, using the hanging-drop vapor diffusion method. Diffraction quality crystals were grown after optimization. The Pru1 crystals diffracted to at least 3.0 A and belong to the tetragonal space group P4(1)22, with unit cell parameters of a = b = 150.912 A, c = 165.248 A. Self-rotation functions and molecular replacement calculations showed that there are three molecules in the asymmetry unit with water content of 51.41%. The three Pru1 protomers are related by a noncrystallographic 3-fold axis and they form a doughnut-shaped trimer. Two prunin trimers form a homohexamer. Elucidation of prunin structure will allow further characterization of the allergenic features of the 11S protein allergens at the molecular level.

Purification of a Multidrug Resistance Transporter for Crystallization Studies

PubMed Central

Alegre, Kamela O.; Law, Christopher J.

2015-01-01

Crystallization of integral membrane proteins is a challenging field and much effort has been invested in optimizing the overexpression and purification steps needed to obtain milligram amounts of pure, stable, monodisperse protein sample for crystallography studies. Our current work involves the structural and functional characterization of the Escherichia coli multidrug resistance transporter MdtM, a member of the major facilitator superfamily (MFS). Here we present a protocol for isolation of MdtM to increase yields of recombinant protein to the milligram quantities necessary for pursuit of structural studies using X-ray crystallography. Purification of MdtM was enhanced by introduction of an elongated His-tag, followed by identification and subsequent removal of chaperonin contamination. For crystallization trials of MdtM, detergent screening using size exclusion chromatography determined that decylmaltoside (DM) was the shortest-chain detergent that maintained the protein in a stable, monodispersed state. Crystallization trials of MdtM performed using the hanging-drop diffusion method with commercially available crystallization screens yielded 3D protein crystals under several different conditions. We contend that the purification protocol described here may be employed for production of high-quality protein of other multidrug efflux members of the MFS, a ubiquitous, physiologically and clinically important class of membrane transporters. PMID:27025617

A new cadmium(II) complex with bridging dithiolate ligand: Synthesis, crystal structure and antifungal activity study

NASA Astrophysics Data System (ADS)

Singh, Mahesh Kumar; Sutradhar, Sanjit; Paul, Bijaya; Adhikari, Suman; Laskar, Folguni; Butcher, Raymond J.; Acharya, Sandeep; Das, Arijit

2017-07-01

A new polymeric complex of Cd(II) with 1,1-dicyanoethylene- 2,2-dithiolate [ i-MNT2- = {S2C:C(CN)2}2- ] as a bridging ligand has been synthesized and characterized on the basis of spectroscopy and single-crystal X-ray diffraction analysis. Single crystal X-ray diffraction analysis reveals that the Cadmium (II) complex is six coordinated 1D polymeric in nature. Biological screening effects in vitro of the synthesized polymeric complex has been tested against five fungi Synchitrium endobioticum, Pyricularia oryzae, Helminthosporium oryzae, Candida albicans(ATCC10231), Trichophyton mentagrophytes by the disc diffusion method. In vitro antifungal screening indicates that the complex exhibits fungistatic and fungicidal antifungal activity whereas K2i-MNT.H2O became silent on Synchitrium endobioticum, Pyricularia oryzae, Helminthosporium oryzae, Candida albicans (ATCC10231), Trichophyton mentagrophytes.

Shear-induced partial translational ordering of a colloidal solid

NASA Astrophysics Data System (ADS)

Ackerson, B. J.; Clark, N. A.

1984-08-01

Highly charged submicrometer plastic spheres suspended in water at low ionic strength will order spontaneously into bcc crystals or polycrystals. A simple linear shear orients and disorders these crystals by forcing (110) planes to stack normal to the shear gradient and to slide relative to each other with a <111> direction parallel to the solvent flow. In this paper we analyze in detail the disordering and flow processes occurring beyond the intrinsic elastic limit of the bcc crystal. We are led to a model in which the flow of a colloidal crystal is interpreted as a fundamentally different process from that found in atomic crystals. In the colloidal crystal the coupling of particle motion to the background fluid forces a homogeneous flow, where every layer is in motion relative to its neighboring layers. In contrast, the plastic flow in an atomic solid is defect mediated flow. At the lowest applied stress, the local bcc order in the colloidal crystal exhibits shear strains both parallel and perpendicular to the direction of the applied stress. The magnitude of these deformations is estimated using the configurational energy for bcc and distorted bcc crystals, assuming a screened Coulomb pair interaction between colloidal particles. As the applied stress is increased, the intrinsic elastic limit of the crystal is exceeded and the crystal begins to flow with adjacent layers executing an oscillatory path governed by the balance of viscous and screened Coulomb forces. The path takes the structure from the bcc1 and bcc2 twins observed at zero shear to a distorted two-dimensional hcp structure at moderate shear rates, with a loss of interlayer registration as the shear is increased. This theoretical model is consistent with other experimental observations, as well.

Mass spectrometric directed system for the continuous-flow synthesis and purification of diphenhydramine† †Electronic supplementary information (ESI) available: NMR spectra of selected product, mass spectra of selected products, crystallization information, and experimental procedures are supplied. See DOI: 10.1039/c7sc00905d Click here for additional data file.

PubMed Central

Loren, Bradley P.; Wleklinski, Michael; Koswara, Andy; Yammine, Kathryn; Hu, Yanyang

2017-01-01

A highly integrated approach to the development of a process for the continuous synthesis and purification of diphenhydramine is reported. Mass spectrometry (MS) is utilized throughout the system for on-line reaction monitoring, off-line yield quantitation, and as a reaction screening module that exploits reaction acceleration in charged microdroplets for high throughput route screening. This effort has enabled the discovery and optimization of multiple routes to diphenhydramine in glass microreactors using MS as a process analytical tool (PAT). The ability to rapidly screen conditions in charged microdroplets was used to guide optimization of the process in a microfluidic reactor. A quantitative MS method was developed and used to measure the reaction kinetics. Integration of the continuous-flow reactor/on-line MS methodology with a miniaturized crystallization platform for continuous reaction monitoring and controlled crystallization of diphenhydramine was also achieved. Our findings suggest a robust approach for the continuous manufacture of pharmaceutical drug products, exemplified in the particular case of diphenhydramine, and optimized for efficiency and crystal size, and guided by real-time analytics to produce the agent in a form that is readily adapted to continuous synthesis. PMID:28979759

21 CFR 884.2982 - Liquid crystal thermographic system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... breast cancer or other uses—(1) Identification. A nonelectrically powered or an AC-powered liquid crystal... for detection of breast cancer or other uses is a nonelectrically powered or an AC-powered device... screening for detection of breast cancer or other uses—(1) Identification. A nonelectrically powered or an...

21 CFR 884.2982 - Liquid crystal thermographic system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... breast cancer or other uses—(1) Identification. A nonelectrically powered or an AC-powered liquid crystal... for detection of breast cancer or other uses is a nonelectrically powered or an AC-powered device... screening for detection of breast cancer or other uses—(1) Identification. A nonelectrically powered or an...

21 CFR 884.2982 - Liquid crystal thermographic system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... breast cancer or other uses—(1) Identification. A nonelectrically powered or an AC-powered liquid crystal... for detection of breast cancer or other uses is a nonelectrically powered or an AC-powered device... screening for detection of breast cancer or other uses— (1) Identification. A nonelectrically powered or an...

21 CFR 884.2982 - Liquid crystal thermographic system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... breast cancer or other uses—(1) Identification. A nonelectrically powered or an AC-powered liquid crystal... for detection of breast cancer or other uses is a nonelectrically powered or an AC-powered device... screening for detection of breast cancer or other uses—(1) Identification. A nonelectrically powered or an...

21 CFR 884.2982 - Liquid crystal thermographic system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... breast cancer or other uses—(1) Identification. A nonelectrically powered or an AC-powered liquid crystal... for detection of breast cancer or other uses is a nonelectrically powered or an AC-powered device... screening for detection of breast cancer or other uses—(1) Identification. A nonelectrically powered or an...

JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals

PubMed Central

Takahashi, Sachiko; Ohta, Kazunori; Furubayashi, Naoki; Yan, Bin; Koga, Misako; Wada, Yoshio; Yamada, Mitsugu; Inaka, Koji; Tanaka, Hiroaki; Miyoshi, Hiroshi; Kobayashi, Tomoyuki; Kamigaichi, Shigeki

2013-01-01

The Japan Aerospace Exploration Agency (JAXA) started a high-quality protein crystal growth project, now called JAXA PCG, on the International Space Station (ISS) in 2002. Using the counter-diffusion technique, 14 sessions of experiments have been performed as of 2012 with 580 proteins crystallized in total. Over the course of these experiments, a user-friendly interface framework for high accessibility has been constructed and crystallization techniques improved; devices to maximize the use of the microgravity environment have been designed, resulting in some high-resolution crystal growth. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the ISS, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed. In this article, the current status of JAXA PCG is discussed, and a rational approach to high-quality protein crystal growth in microgravity based on numerical analyses is explained. PMID:24121350

An evaluation of adhesive sample holders for advanced crystallographic experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazzorana, Marco; Sanchez-Weatherby, Juan, E-mail: juan.sanchez-weatherby@diamond.ac.uk; Sandy, James

Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-controlled studies is investigated. The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposingmore » it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.« less

Evaluation and application of multiple scoring functions for a virtual screening experiment

NASA Astrophysics Data System (ADS)

Xing, Li; Hodgkin, Edward; Liu, Qian; Sedlock, David

2004-05-01

In order to identify novel chemical classes of factor Xa inhibitors, five scoring functions (FlexX, DOCK, GOLD, ChemScore and PMF) were engaged to evaluate the multiple docking poses generated by FlexX. The compound collection was composed of confirmed potent factor Xa inhibitors and a subset of the LeadQuest® screening compound library. Except for PMF the other four scoring functions succeeded in reproducing the crystal complex (PDB code: 1FAX). During virtual screening the highest hit rate (80%) was demonstrated by FlexX at an energy cutoff of -40 kJ/mol, which is about 40-fold over random screening (2.06%). Limited results suggest that presenting more poses of a single molecule to the scoring functions could deteriorate their enrichment factors. A series of promising scaffolds with favorable binding scores was retrieved from LeadQuest. Consensus scoring by pair-wise intersection failed to enrich the hit rate yielded by single scorings (i.e. FlexX). We note that reported successes of consensus scoring in hit rate enrichment could be artificial because their comparisons were based on a selected subset of single scoring and a markedly reduced subset of double or triple scoring. The findings presented in this report are based upon a single biological system and support further studies.

Crystal structure, phytochemical study and enzyme inhibition activity of Ajaconine and Delectinine

NASA Astrophysics Data System (ADS)

Ahmad, Shujaat; Ahmad, Hanif; Khan, Hidayat Ullah; Shahzad, Adnan; Khan, Ezzat; Ali Shah, Syed Adnan; Ali, Mumtaz; Wadud, Abdul; Ghufran, Mehreen; Naz, Humera; Ahmad, Manzoor

2016-11-01

The Crystal structure, comparative DFT study and phytochemical investigation of atisine type C-20 diterpenoid alkaloid ajaconine (1) and lycoctonine type C-19 diterpenoid alkaloid delectinine (2) is reported here. These compounds were isolated from Delphinium chitralense. Both the natural products 1 and 2 crystallize in orthorhombic crystal system with identical space group of P212121. The geometric parameters of both compounds were calculated with the help of DFT using B3LYP/6-31+G (p) basis set and HOMO-LUMO energies, optimized band gaps, global hardness, ionization potential, electron affinity and global electrophilicity are calculated. The compounds 1 and 2 were screened for acetyl cholinesterase and butyryl cholinesterase inhibition activities in a dose dependent manner followed by molecular docking to explore the possible inhibitory mechanism of ajaconine (1) and delectinine (2). The IC50 values of tested compounds against AChE were observed as 12.61 μM (compound 1) and 5.04 μM (compound 2). The same experiments were performed for inhibition of BChE and IC50 was observed to be 10.18 μM (1) and 9.21 μM (2). Promising inhibition activity was shown by both the compounds against AChE and BChE in comparison with standard drugs available in the market such as allanzanthane and galanthamine. The inhibition efficiency of both the natural products was determined in a dose dependent manner.

An evaluation of adhesive sample holders for advanced crystallographic experiments

PubMed Central

Mazzorana, Marco; Sanchez-Weatherby, Juan; Sandy, James; Lobley, Carina M. C.; Sorensen, Thomas

2014-01-01

The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed. PMID:25195752

Programmable diffractive lens for ophthalmic application

NASA Astrophysics Data System (ADS)

Millán, María S.; Pérez-Cabré, Elisabet; Romero, Lenny A.; Ramírez, Natalia

2014-06-01

Pixelated liquid crystal displays have been widely used as spatial light modulators to implement programmable diffractive optical elements, particularly diffractive lenses. Many different applications of such components have been developed in information optics and optical processors that take advantage of their properties of great flexibility, easy and fast refreshment, and multiplexing capability in comparison with equivalent conventional refractive lenses. We explore the application of programmable diffractive lenses displayed on the pixelated screen of a liquid crystal on silicon spatial light modulator to ophthalmic optics. In particular, we consider the use of programmable diffractive lenses for the visual compensation of refractive errors (myopia, hypermetropia, astigmatism) and presbyopia. The principles of compensation are described and sketched using geometrical optics and paraxial ray tracing. For the proof of concept, a series of experiments with artificial eye in optical bench are conducted. We analyze the compensation precision in terms of optical power and compare the results with those obtained by means of conventional ophthalmic lenses. Practical considerations oriented to feasible applications are provided.

Ophthalmic compensation of visual ametropia based on a programmable diffractive lens

NASA Astrophysics Data System (ADS)

Millán, Maria S.; Pérez-Cabré, Elisabet; Romero, Lenny A.; Ramírez, Natalia

2013-11-01

Pixelated liquid crystal displays have been widely used as spatial light modulators to implement programmable diffractive optical elements (DOEs), particularly diffractive lenses. Many different applications of such components have been developed in information optics and optical processors that take advantage of their properties of great flexibility, easy and fast refreshment, and multiplexing capability in comparison with equivalent conventional refractive lenses. In this paper, we explore the application of programmable diffractive lenses displayed on the pixelated screen of a liquid crystal on silicon spatial light modulator (LCoS-SLM) to ophthalmic optics. In particular, we consider the use of programmable diffractive lenses for the visual compensation of some refractive errors (myopia, hyperopia). The theoretical principles of compensation are described and sketched using geometrical optics and paraxial ray tracing. A series of experiments with artificial eye in optical bench are conducted to analyze the compensation accuracy in terms of optical power and to compare the results with those obtained by means of conventional ophthalmic lenses. Practical considerations oriented to feasible applications are provided.

[Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

PubMed

Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

2015-04-01

The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

Automating the application of smart materials for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khurshid, Sahir; Govada, Lata; EL-Sharif, Hazim F.

2015-03-01

The first semi-liquid, non-protein nucleating agent for automated protein crystallization trials is described. This ‘smart material’ is demonstrated to induce crystal growth and will provide a simple, cost-effective tool for scientists in academia and industry. The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as ‘smart materials’) for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of successmore » when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials.« less

A mobile phone-based Communication Support System for elderly persons.

PubMed

Ogawa, Hidekuni; Yonezawa, Yoshiharu; Maki, Hiromichi; Caldwell, W Morton

2007-01-01

A mobile phone-based communication support system has been developed for assisting elderly people to communicate by mobile phone. The system consists of a low power mobile phone (PHS phone) having a large liquid crystal screen. When an elderly person telephones, they then choose a communication person from registered support personnel pictures displayed on the liquid crystal screen. The PHS phone dials that person automatically. The elderly person can therefore easily recognize and verify the person. The newly-developed communication support system assists a significant percentage of elderly people with poor eyesight and memory, which frequently cause communication problems, such as dialing a wrong number.

A General Method for Discovering Inhibitors of Protein–DNA Interactions Using Photonic Crystal Biosensors

PubMed Central

Chan, Leo L.; Pineda, Maria; Heeres, James T.; Hergenrother, Paul J.; Cunningham, Brian T.

2009-01-01

Protein–DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis. As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great potential as therapeutics. Unfortunately, there are few methods available for the rapid identification of compounds that disrupt protein–DNA interactions. Here we show that photonic crystal (PC) technology can be utilized to detect protein–DNA interactions, and can be used in a high-throughput screening mode to identify compounds that prevent protein–DNA binding. The PC technology is used to detect binding between protein–DNA interactions that are DNA-sequence-dependent (the bacterial toxin–antitoxin system MazEF) and those that are DNA-sequence-independent (the human apoptosis inducing factor (AIF)). The PC technology was further utilized in a screen for inhibitors of the AIF–DNA interaction, and through this screen aurin tricarboxylic acid was identified as the first in vitro inhibitor of AIF. The generality and simplicity of the photonic crystal method should enable this technology to find broad utility for identification of compounds that inhibit protein–DNA binding. PMID:18582039

Mass spectrometric directed system for the continuous-flow synthesis and purification of diphenhydramine.

PubMed

Loren, Bradley P; Wleklinski, Michael; Koswara, Andy; Yammine, Kathryn; Hu, Yanyang; Nagy, Zoltan K; Thompson, David H; Cooks, R Graham

2017-06-01

A highly integrated approach to the development of a process for the continuous synthesis and purification of diphenhydramine is reported. Mass spectrometry (MS) is utilized throughout the system for on-line reaction monitoring, off-line yield quantitation, and as a reaction screening module that exploits reaction acceleration in charged microdroplets for high throughput route screening. This effort has enabled the discovery and optimization of multiple routes to diphenhydramine in glass microreactors using MS as a process analytical tool (PAT). The ability to rapidly screen conditions in charged microdroplets was used to guide optimization of the process in a microfluidic reactor. A quantitative MS method was developed and used to measure the reaction kinetics. Integration of the continuous-flow reactor/on-line MS methodology with a miniaturized crystallization platform for continuous reaction monitoring and controlled crystallization of diphenhydramine was also achieved. Our findings suggest a robust approach for the continuous manufacture of pharmaceutical drug products, exemplified in the particular case of diphenhydramine, and optimized for efficiency and crystal size, and guided by real-time analytics to produce the agent in a form that is readily adapted to continuous synthesis.

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

NASA Astrophysics Data System (ADS)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Broecker, Jana; Klingel, Viviane; Ou, Wei-Lin

In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometerbased X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble andmore » membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.« less

Electrical Characteristics CuFe2O4 Thick Film Ceramics Made with Different Screen Size Utiizing Fe2O3 Nanopowder Derived from Yarosite for NTC Thermistor

NASA Astrophysics Data System (ADS)

Wiendartun, Syarif, Dani Gustaman

2010-10-01

Fabrication of CuFe2O4 thick film ceramics utilizing Fe2O3 derived from yarosite using screen printing technique for NTC thermistor has been carried out. Effect of thickness variation due to different size of screen (screen 225; 300 and 375 mesh) has been studied. X-ray diffraction analyses (XRD) was done to know crystal structure and phases formation. SEM analyses was carried out to know microstructure of the films. Electrical properties characterization was done through measurement of electrical resistance at various temperatures (room temperature to 100° C). The XRD data showed that the films crystalize in tetragonal spinel. The SEM images showed that the screen with the smaller of the hole size, made the grain size was bigger. Electrical data showed that the larger the screen different size thickness variation (mesh), the larger the resistance, thermistor constant and sensitivity. From the electrical characteristics data, it was known that the electrical characteristics of the CuFe2O4 thick film ceramics followed the NTC characteristic. The value of B and RRT of the produced CuFe2O4 ceramics namely B = 3241-3484 K and RRT = 25.6-87.0 M Ohm, fitted market requirement.

Microscopic Mechanism of Doping-Induced Kinetically Constrained Crystallization in Phase-Change Materials.

PubMed

Lee, Tae Hoon; Loke, Desmond; Elliott, Stephen R

2015-10-07

A comprehensive microscopic mechanism of doping-induced kinetically constrained crystallization in phase-change materials is provided by investigating structural and dynamical dopant characteristics via ab initio molecular dynamics simulations. The information gained from this study may provide a basis for a fast screening of dopant species for electronic memory devices, or for understanding the general physics involved in the crystallization of doped glasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Experiment with Manifold Purposes: The Chemical Reactivity of Crystal Defects upon Crystal Dissolution.

ERIC Educational Resources Information Center

Lazzarini, Annaluisa Fantola; Lazzarini, Ennio

1983-01-01

Background information and procedures are provided for an experiment designed to introduce (1) crystal defects and their reactivity upon crystal dissolution; (2) hydrates electron and its reactivity; (3) application of radiochemical method of analysis; and (4) the technique of competitive kinetics. Suggested readings and additional experiments are…

Purification, Crystallization and Preliminary X-ray Characterization of Prunin-1, a Major Component of the Almond (Prunus dulcis) Allergen Amandin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albillos, Silvia M.; Jin, Tengchuan; Howard, Andrew

2008-08-04

The 11S globulins from plant seeds account for a number of major food allergens. Because of the interest in the structural basis underlying the allergenicity of food allergens, we sought to crystallize the main 11S seed storage protein from almond (Prunus dulcis). Prunin-1 (Pru1) was purified from defatted almond flour by water extraction, cryoprecipitation, followed by sequential anion exchange, hydrophobic interaction, and size exclusion chromatography. Single crystals of Pru1 were obtained in a screening with a crystal screen kit, using the hanging-drop vapor diffusion method. Diffraction quality crystals were grown after optimization. The Pru1 crystals diffracted to at least 3.0more » {angstrom} and belong to the tetragonal space group P4{sub 1}22, with unit cell parameters of a = b = 150.912 {angstrom}, c = 165.248 {angstrom}. Self-rotation functions and molecular replacement calculations showed that there are three molecules in the asymmetry unit with water content of 51.41%. The three Pru1 protomers are related by a noncrystallographic 3-fold axis and they form a doughnut-shaped trimer. Two prunin trimers form a homohexamer. Elucidation of prunin structure will allow further characterization of the allergenic features of the 11S protein allergens at the molecular level.« less

Crystallization of the Membrane-Associated Annexin B1: Roles of Additive Screen, Dynamic Light Scattering, and Bioactivity Assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, F.; Xu, Y; Azzi, A

2010-01-01

Annexin B1 (AnxB1) is a calcium-dependent phospholipid binding protein from Taenia solium cysticercus and has been reported to possess anticoagulant activity, to inhibit phospholipase A{sub 2}, and to regulate membrane transport. Native AnxB1 and its selenomethionyl derivative have been overproduced in Escherichia coli and purified. The results of dynamic light scattering analysis showed that Hepes buffer combined with low concentration salts (NaCl or CaCl{sub 2}) was beneficial for preventing aggregation and for AnxB1 stabilization in the storage. After the additive screen, crystals have been yielded in the presence of guanidine hydrochloride (Gn-HCl). We determined that a low concentration of Gn-HClmore » significantly delayed clotting time and increased anticoagulant activity. Analysis of the crystal showed that in the presence of Gn-HCl, AnxB1 crystallizes in orthorhombic space group, which is modified from the cubic space group for crystals grown in the absence of Gn-HCl. A high quality data set (at 1.9 {angstrom}) has been collected successfully for crystals of L-selenomethionine labeled protein in the presence of Gn-HCl, to solve the structure with the single anomalous dispersion method (SAD). The unit cell parameters are a = 102.35 {angstrom}, b = 103.59 {angstrom}, c = 114.60 {angstrom}, {alpha} = {beta} = {gamma} = 90.00{sup o}.« less

Orbitals for classical arbitrary anisotropic colloidal potentials

NASA Astrophysics Data System (ADS)

Girard, Martin; Nguyen, Trung Dac; de la Cruz, Monica Olvera

2017-11-01

Coarse-grained potentials are ubiquitous in mesoscale simulations. While various methods to compute effective interactions for spherically symmetric particles exist, anisotropic interactions are seldom used, due to their complexity. Here we describe a general formulation, based on a spatial decomposition of the density fields around the particles, akin to atomic orbitals. We show that anisotropic potentials can be efficiently computed in numerical simulations using Fourier-based methods. We validate the field formulation and characterize its computational efficiency with a system of colloids that have Gaussian surface charge distributions. We also investigate the phase behavior of charged Janus colloids immersed in screened media, with screening lengths comparable to the colloid size. The system shows rich behaviors, exhibiting vapor, liquid, gel, and crystalline morphologies, depending on temperature and screening length. The crystalline phase only appears for symmetric Janus particles. For very short screening lengths, the system undergoes a direct transition from a vapor to a crystal on cooling; while, for longer screening lengths, a vapor-liquid-crystal transition is observed. The proposed formulation can be extended to model force fields that are time or orientation dependent, such as those in systems of polymer-grafted particles and magnetic colloids.

Development of paracetamol-caffeine co-crystals to improve compressional, formulation and in vivo performance.

PubMed

Latif, Sumera; Abbas, Nasir; Hussain, Amjad; Arshad, Muhammad Sohail; Bukhari, Nadeem Irfan; Afzal, Hafsa; Riffat, Sualeha; Ahmad, Zeeshan

2018-07-01

Paracetamol, a frequently used antipyretic and analgesic drug, has poor compression moldability owing to its low plasticity. In this study, new co-crystals of paracetamol (PCM) with caffeine (as a co-former) were prepared and delineated. Co-crystals exhibited improved compaction and mechanical behavior. A screening study was performed by utilizing a number of methods namely dry grinding, liquid assisted grinding (LAG), solvent evaporation (SE), and anti-solvent addition using various weight ratios of starting materials. LAG and SE were found successful in the screening study. Powders at 1:1 and 2:1 weight ratio of PCM/CAF by LAG and SE, respectively, resulted in the formation of co-crystals. Samples were characterized by PXRD, DSC, and ATR-FTIR techniques. Compressional properties of PCM and developed co-crystals were analyzed by in-die heckle model. Mean yield pressure (Py), an inverse measure of plasticity, obtained from the heckle plots decreased significantly (p < .05) for co-crystals than pure drug. Intrinsic dissolution profile of co-crystals showed up to 2.84-fold faster dissolution than PCM and physical mixtures in phosphate buffer pH 6.8 at 37 °C. In addition, co-crystals formulated into tablets by direct compression method showed better mechanical properties like hardness and tensile strength. In vitro dissolution studies on tablets also showed enhanced dissolution profiles (∼90-97%) in comparison to the tablets of PCM prepared by direct compression (∼55%) and wet granulation (∼85%) methods. In a single dose sheep model study, co-crystals showed up to twofold increase in AUC and C max . A significant (p < .05) decrease in clearance as compared to pure drug was also recorded. In conclusion, new co-crystals of PCM were successfully prepared with improved tabletability in vitro and in vivo profile. Enhancement in AUC and C max of PCM by co-crystallization might suggest the dose reduction and avoidance of side effects.

Equilibrium Kinetics Studies and Crystallization Aboard the International Space Station (ISS) Using the Protein Crystallization Apparatus for Microgravity (PCAM)

NASA Technical Reports Server (NTRS)

Achari, Aniruddha; Roeber, Dana F.; Barnes, Cindy L.; Kundrot, Craig E.; Stinson, Thomas N. (Technical Monitor)

2002-01-01

Protein Crystallization Apparatus in Microgravity (PCAM) trays have been used in Shuttle missions to crystallize proteins in a microgravity environment. The crystallization experiments are 'sitting drops' similar to that in Cryschem trays, but the reservoir solution is soaked in a wick. From early 2001, crystallization experiments are conducted on the International Space Station using mission durations of months rather than two weeks on previous shuttle missions. Experiments were set up in April 2001 on Flight 6A to characterize the time crystallization experiments will take to reach equilibrium in a microgravity environment using salts, polyethylene glycols and an organic solvent as precipitants. The experiments were set up to gather data for a series of days of activation with different droplet volumes and precipitants. The experimental set up on ISS and results of this study will be presented. These results will help future users of PCAM to choose precipitants to optimize crystallization conditions for their target macromolecules for a particular mission with known mission duration. Changes in crystal morphology and size between the ground and space grown crystals of a protein and a protein -DNA complex flown on the same mission will also be presented.

Precision Crystal Calorimeters in High Energy Physics

ScienceCinema

Ren-Yuan Zhu

2017-12-09

Precision crystal calorimeters traditionally play an important role in high energy physics experiments. In the last two decades, it faces a challenge to maintain its precision in a hostile radiation environment. This paper reviews the performance of crystal calorimeters constructed for high energy physics experiments and the progress achieved in understanding crystal’s radiation damage as well as in developing high quality scintillating crystals for particle physics. Potential applications of new generation scintillating crystals of high density and high light yield, such as LSO and LYSO, in particle physics experiments is also discussed.

Protein crystal growth in a microgravity environment

NASA Technical Reports Server (NTRS)

Bugg, Charles E.

1988-01-01

Protein crystal growth is a major experimental problem and is the bottleneck in widespread applications of protein crystallography. Research efforts now being pursued and sponsored by NASA are making fundamental contributions to the understanding of the science of protein crystal growth. Microgravity environments offer the possibility of performing new types of experiments that may produce a better understanding of protein crystal growth processes and may permit growth environments that are more favorable for obtaining high quality protein crystals. A series of protein crystal growth experiments using the space shuttle was initiated. The first phase of these experiments was focused on the development of micro-methods for protein crystal growth by vapor diffusion techniques, using a space version of the hanging drop method. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth.

Improved crystallization of the coxsackievirus B3 RNA-dependent RNA polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jabafi, Ilham; Selisko, Barbara; Coutard, Bruno

2007-06-01

The first crystal of a coxsackievirus RNA-dependent RNA polymerase is reported. The Picornaviridae virus family contains a large number of human pathogens such as poliovirus, hepatitis A virus and rhinoviruses. Amongst the viruses belonging to the genus Enterovirus, several serotypes of coxsackievirus coexist for which neither vaccine nor therapy is available. Coxsackievirus B3 is involved in the development of acute myocarditis and dilated cardiomyopathy and is thought to be an important cause of sudden death in young adults. Here, the first crystal of a coxsackievirus RNA-dependent RNA polymerase is reported. Standard crystallization methods yielded crystals that were poorly suited tomore » X-ray diffraction studies, with one axis being completely disordered. Crystallization was improved by testing crystallization solutions from commercial screens as additives. This approach yielded crystals that diffracted to 2.1 Å resolution and that were suitable for structure determination.« less

Systematic Improvement of Protein Crystals by Determining the Supersolubility Curves of Phase Diagrams

PubMed Central

Saridakis, Emmanuel; Chayen, Naomi E.

2003-01-01

A systematic approach for improving protein crystals by growing them in the metastable zone using the vapor diffusion technique is described. This is a simple technique for optimization of crystallization conditions. Screening around known conditions is performed to establish a working phase diagram for the crystallization of the protein. Dilutions of the crystallization drops across the supersolubility curve into the metastable zone are then carried out as follows: the coverslips holding the hanging drops are transferred, after being incubated for some time at conditions normally giving many small crystals, over reservoirs at concentrations which normally yield clear drops. Fewer, much larger crystals are obtained when the incubation times are optimized, compared with conventional crystallization at similar conditions. This systematic approach has led to the structure determination of the light-harvesting protein C-phycocyanin to the highest-ever resolution of 1.45 Å. PMID:12547801

A drunken search in crystallization space.

PubMed

Fazio, Vincent J; Peat, Thomas S; Newman, Janet

2014-10-01

The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sauter, Nicholas K., E-mail: nksauter@lbl.gov; Hattne, Johan; Grosse-Kunstleve, Ralf W.

The Computational Crystallography Toolbox (cctbx) is a flexible software platform that has been used to develop high-throughput crystal-screening tools for both synchrotron sources and X-ray free-electron lasers. Plans for data-processing and visualization applications are discussed, and the benefits and limitations of using graphics-processing units are evaluated. Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h{sup −1}) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in realmore » time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units.« less

Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.

PubMed

Bowler, Michael G; Bowler, Matthew W

2014-01-01

The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

PubMed

Hiraki, Masahiko; Kato, Ryuichi; Nagai, Minoru; Satoh, Tadashi; Hirano, Satoshi; Ihara, Kentaro; Kudo, Norio; Nagae, Masamichi; Kobayashi, Masanori; Inoue, Michio; Uejima, Tamami; Oda, Shunichiro; Chavas, Leonard M G; Akutsu, Masato; Yamada, Yusuke; Kawasaki, Masato; Matsugaki, Naohiro; Igarashi, Noriyuki; Suzuki, Mamoru; Wakatsuki, Soichi

2006-09-01

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

78 FR 38452 - Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-26

... FURTHER INFORMATION CONTACT: Crystal Rennie, Enterprise Records Service (005R1B), Department of Veterans Affairs, 810 Vermont Avenue NW., Washington, DC 20420, (202) 632-7492, Fax (202) 632-7634 or email crystal... Response: One-time. Estimated Number of Respondents: 1,500. Dated: June 21, 2013. By direction of the...

Crystal packing modifies ligand binding affinity: the case of aldose reductase.

PubMed

Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X; Howard, Eduardo; Ginell, Stephan; Atmanene, Cédric; Van Dorsselaer, Alain; Sanglier-Cianférani, Sarah; Joachimiak, Andrzej; Podjarny, Alberto

2012-11-01

The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used. Copyright © 2012 Wiley Periodicals, Inc.

Chiral Crystallization of Ethylenediamine Sulfate

ERIC Educational Resources Information Center

Koby, Lawrence; Ningappa, Jyothi B.; Dakesssian, Maria; Cuccia, Louis A.

2005-01-01

The optimal conditions for the crystallization of achiral ethylenediamine sulfate into large chiral crystals that are ideal for polarimetry studies and observation using Polaroid sheets are presented. This experiment is an ideal undergraduate experiment, which clearly demonstrates the chiral crystallization of an achiral molecule.

Preliminary investigations of protein crystal growth using the Space Shuttle

NASA Technical Reports Server (NTRS)

Delucas, L. J.; Suddath, F. L.; Snyder, R.; Naumann, R.; Broom, M. B.; Pusey, M.; Yost, V.; Herren, B .; Carter, D.

1986-01-01

Four preliminary Shuttle experiments are described which have been used to develop prototype hardware for a more advanced system that will evaluate effects of gravity on protein crystal growth. The first phase of these experiments has centered on the development of micromethods for protein crystal growth by vapor-diffusion techniques (using a space version of the hanging-drop method) and on dialysis using microdialysis cells. Results suggest that the elimination of density-driven sedimentation can effect crystal morphology. In the dialysis experiment, space-grown crystals of concanavalin B were three times longer and 1/3 the thickness of earth-grown crystals.

Expression in Escherichia coli, refolding and crystallization of Aspergillus niger feruloyl esterase A using a serial factorial approach.

PubMed

Benoit, Isabelle; Coutard, Bruno; Oubelaid, Rachid; Asther, Marcel; Bignon, Christophe

2007-09-01

Hydrolysis of plant biomass is achieved by the combined action of enzymes secreted by microorganisms and directed against the backbone and the side chains of plant cell wall polysaccharides. Among side chains degrading enzymes, the feruloyl esterase A (FAEA) specifically removes feruloyl residues. Thus, FAEA has potential applications in a wide range of industrial processes such as paper bleaching or bio-ethanol production. To gain insight into FAEA hydrolysis activity, we solved its crystal structure. In this paper, we report how the use of four consecutive factorial approaches (two incomplete factorials, one sparse matrix, and one full factorial) allowed expressing in Escherichia coli, refolding and then crystallizing Aspergillus niger FAEA in 6 weeks. Culture conditions providing the highest expression level were determined using an incomplete factorial approach made of 12 combinations of four E. coli strains, three culture media and three temperatures (full factorial: 36 combinations). Aspergillus niger FAEA was expressed in the form of inclusion bodies. These were dissolved using a chaotropic agent, and the protein was purified by affinity chromatography on Ni column under denaturing conditions. A suitable buffer for refolding the protein eluted from the Ni column was found using a second incomplete factorial approach made of 96 buffers (full factorial: 3840 combinations). After refolding, the enzyme was further purified by gel filtration, and then crystallized following a standard protocol: initial crystallization conditions were found using commercial crystallization screens based on a sparse matrix. Crystals were then optimized using a full factorial screen.

Preferred viewing distance of liquid crystal high-definition television.

PubMed

Lee, Der-Song

2012-01-01

This study explored the effect of TV size, illumination, and viewing angle on preferred viewing distance in high-definition liquid crystal display televisions (HDTV). Results showed that the mean preferred viewing distance was 2856 mm. TV size and illumination significantly affected preferred viewing distance. The larger the screen size, the greater the preferred viewing distance, at around 3-4 times the width of the screen (W). The greater the illumination, the greater the preferred viewing distance. Viewing angle also correlated significantly with preferred viewing distance. The more deflected from direct frontal view, the shorter the preferred viewing distance seemed to be. Copyright © 2011 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors

NASA Astrophysics Data System (ADS)

Miguet, Laurence; Zhang, Ziding; Barbier, Maryse; Grigorov, Martin G.

2006-02-01

Human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) catalyzes the interconversion of cortisone into active cortisol. 11βHSD1 inhibition is a tempting target for the treatment of a host of human disorders that might benefit from blockade of glucocorticoid action, such as obesity, metabolic syndrome, and diabetes type 2. Here, we report an in silico screening study aimed at identifying new selective inhibitors of human 11βHSD1 enzyme. In the first step, homology modeling was employed to build the 3D structure of 11βHSD1. Further, molecular docking was used to validate the predicted model by showing that it was able to discriminate between known 11βHSD1 inhibitors or substrates and non-inhibitors. The homology model was found to reproduce closely the crystal structure that became publicly available in the final stages of this work. Finally, we carried out structure-based virtual screening experiments on both the homology model and the crystallographic structure with a database of 114'000 natural molecules. Among these, 15 molecules were consistently selected as inhibitors based on both the model and crystal structures of the enzyme, implying a good quality for the homology model. Among these putative 11βHSD1 inhibitors, two were flavonone derivatives that have already been shown to be potent inhibitors of the enzyme.

Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.

PubMed

Le Bihan, Yann-Vaï; Matot, Béatrice; Pietrement, Olivier; Giraud-Panis, Marie-Josèphe; Gasparini, Sylvaine; Le Cam, Eric; Gilson, Eric; Sclavi, Bianca; Miron, Simona; Le Du, Marie-Hélène

2013-03-01

Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local DNA melting and/or distortion. In this study, various Rap1-DNA crystal forms were obtained using specifically designed crystal screens. Analysis of the DNA conformation showed that its distortion was not sufficient to explain the permanganate reactivity. However, anomalous data collected at the Mn edge using a Rap1-DNA crystal soaked in potassium permanganate solution indicated that the DNA conformation in the crystal was compatible with interaction with permanganate ions. Sequence-conservation analysis revealed that double-Myb-containing Rap1 proteins all carry a fully conserved Arg580 at a position that may favour interaction with permanganate ions, although it is not involved in the hypersensitive cytosine distortion. Permanganate reactivity assays with wild-type Rap1 and the Rap1[R580A] mutant demonstrated that Arg580 is essential for hypersensitivity. AFM experiments showed that wild-type Rap1 and the Rap1[R580A] mutant interact with DNA over 16 successive binding sites, leading to local DNA stiffening but not to accumulation of the observed local distortion. Therefore, Rap1 may cause permanganate hypersensitivity of DNA by forming a pocket between the reactive cytosine and Arg580, driving the permanganate ion towards the C5-C6 bond of the cytosine.

Solution Growth and Characterization of Single Crystals on Earth and in Microgravity

NASA Technical Reports Server (NTRS)

Aggarwal, M. D.; Currie, J. R.; Penn, B. G.; Batra, A. K.; Lal, R. B.

2007-01-01

Crystal growth has been of interest to physicists and engineers for a long time because of their unique properties. Single crystals are utilized in such diverse applications as pharmaceuticals, computers, infrared detectors, frequency measurements, piezoelectric devices, a variety of high-technology devices, and sensors. Solution crystal growth is one of the important techniques to grow a variety of crystals when the material decomposes at the melting point and a suitable solvent is available to make a saturated solution at a desired temperature. In this Technical Memorandum (TM) an attempt is made to give the fundamentals of growing crystals from solution including improved designs of various crystallizers. Since the same solution crystal growth technique could not be used in microgravity, the authors proposed a new cooled-sting technique to grow crystals in space. The authors experience from conducting two Space Shuttle solution crystal growth experiments are also detailed in this TM and the complexity of solution growth experiments to grow crystals in space are also discussed. These happen to be some of the early experiments performed in space, and various lessons learned are described. A brief discussion of protein crystal growth that shares basic principles of the solution growth technique is given, along with some flight hardware information for growth in microgravity.

Growth and Characteristics of Bulk Single Crystals Grown from Solution on Earth and in Microgravity

NASA Technical Reports Server (NTRS)

Aggarwal, M. D.; Batra, A. K.; Lal, R. B.; Penn, Benjamin G.; Frazier, Donald O.

2011-01-01

The growth of crystals has been of interest to physicists and engineers for a long time because of their unique properties. Single crystals are utilized in such diverse applications as pharmaceuticals, computers, infrared detectors, frequency measurements, piezoelectric devices, a variety of high technology devices and sensors. Solution crystal growth is one of the important techniques to grow a variety of crystals when the material decomposes at the melting point and a suitable solvent is available to make a saturated solution at a desired temperature. In this chapter an attempt is made to give some fundamentals of growing crystals from solution including improved designs of various crystallizers. Since the same solution crystal growth technique could not be used in microgravity, authors had proposed a new cooled sting technique to grow crystals in space. Authors? experiences of conducting two space shuttle experiments relating to solution crystal growth are also detailed in this work. The complexity of these solution growth experiments to grow crystals in space are discussed. These happen to be some of the early experiments performed in space, and various lessons learned are described. A brief discussion of protein crystal growth that also shares basic principles of solution growth technique is given along with some flight hardware information for its growth in microgravity.

Follow up on the crystal growth experiments of the LDEF

NASA Technical Reports Server (NTRS)

Nielsen, K. F.; Lind, M. D.

1993-01-01

The results of the 4 solution growth experiments on the LDEF have been published elsewhere. Both the crystals of CaCO3, which were large and well shaped, and the much smaller TTF-TCNQ crystals showed unusual morphological behavior. The follow up on these experiments was begun in 1981, when ESA initiated a 'Concept Definition Study' on a large, 150 kg, Solution Growth Facility (SGF) to be included in the payload of EURECA-1, the European Retrievable Carrier. This carrier was a continuation of the European Spacelab and at that time planned for launch in 1987. The long delay of the LDEF retrieval and of subsequent missions brought about reflections both on the concept of crystal growth in space and on the choice of crystallization materials that had been made for the LDEF. Already before the LDEF retrieval, research on TTF-TCNQ had been stopped, and a planned growth experiment with TTF-TCNQ on the SGF/EURECA had been cancelled. The target of the SGF investigation is now more fundamental in nature. None of the crystals to be grown here are, like TTF-TCNQ, in particular demand by science or industry, and the crystals only serve the purpose of model crystals. The real purpose of the investigation is to study the growth behavior. One of the experiments, the Soret Coefficient Measurement experiment is not growing crystals at all, but has it as its sole purpose to obtain accurate information on thermal diffusion, a process of importance in crystal growth from solution.

Communications: Complete description of re-entrant phase behavior in a charge variable colloidal model system.

PubMed

Wette, Patrick; Klassen, Ina; Holland-Moritz, Dirk; Herlach, Dieter M; Schöpe, Hans Joachim; Lorenz, Nina; Reiber, Holger; Palberg, Thomas; Roth, Stephan V

2010-04-07

In titration experiments with NaOH, we have determined the full phase diagram of charged colloidal spheres in dependence on the particle density n, the particle effective charge Z(eff) and the concentration of screening electrolyte c using microscopy, light and ultrasmall angle x-ray scattering (USAXS). For sufficiently large n, the system crystallizes upon increasing Z(eff) at constant c and melts upon increasing c at only slightly altered Z(eff). In contrast to earlier work, equilibrium phase boundaries are consistent with a universal melting line prediction from computer simulation, if the elasticity effective charge is used. This charge accounts for both counterion condensation and many-body effects.

Thermal and convection analyses of the dendrite remelting rocket experiment; Experiment 74-21 in the space processing rocket program

NASA Technical Reports Server (NTRS)

Grodzka, P. G.; Pond, J. E.; Spradley, J. W.; Johnson, M. H.

1976-01-01

The Dendrite Remelting Rocket Experiment was performed aboard a Black Brant VC Sounding Rocket during a period which gravity levels of approximately 0.00001 g prevailed. The experiment consisted of cooling an aqueous ammonium chloride solution in a manner such that crystallization of ammonium chloride crystals proceeded throughout a three minute period of zero-g. The crystallization process during flight was recorded on 35 mm panatomic-x film. A number of ground crystallizations were similarly recorded for comparison purposes. The convective and thermal conditions in aqueous and metallic liquid systems were assessed under conditions of the flight experiment to help establish the relevance of the rocket experiment to metals casting phenomena. The results indicate that aqueous or metallic convective velocities in the Dendrite Remelting Rocket Experiment cell are of insignificant magnitudes at the 0.0001 to 0.00001 g levels of the experiment. The crystallization phenomena observed in the Rocket Experiment, therefore, may be indicative of how metals will solidify in low-g.

Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.

PubMed

Amano, Yasushi; Tanabe, Eiki; Yamaguchi, Tomohiko

2015-05-15

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800μM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51μM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging.

PubMed

Coughlan, H D; Darmanin, C; Phillips, N W; Hofmann, F; Clark, J N; Harder, R J; Vine, D J; Abbey, B

2015-07-01

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

PubMed Central

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.; Hofmann, F.; Clark, J. N.; Harder, R. J.; Vine, D. J.; Abbey, B.

2015-01-01

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources. PMID:26798804

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

DOE PAGES

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.; ...

2015-04-29

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Protein crystal growth results from the United States Microgravity Laboratory-1 mission

NASA Technical Reports Server (NTRS)

Delucas, Lawrence J.; Moore, K. M.; Vanderwoerd, M.; Bray, T. L.; Smith, C.; Carson, M.; Narayana, S. V. L.; Rosenblum, W. M.; Carter, D.; Clark, A. D, Jr.

1994-01-01

Protein crystal growth experiments have been performed by this laboratory on 18 Space Shuttle missions since April, 1985. In addition, a number of microgravity experiments also have been performed and reported by other investigators. These Space Shuttle missions have been used to grow crystals of a variety of proteins using vapor diffusion, liquid diffusion, and temperature-induced crystallization techniques. The United States Microgravity Laboratory - 1 mission (USML-1, June 25 - July 9, 1992) was a Spacelab mission dedicated to experiments involved in materials processing. New protein crystal growth hardware was developed to allow in orbit examination of initial crystal growth results, the knowledge from which was used on subsequent days to prepare new crystal growth experiments. In addition, new seeding hardware and techniques were tested as well as techniques that would prepare crystals for analysis by x-ray diffraction, a capability projected for the planned Space Station. Hardware that was specifically developed for the USML-1 mission will be discussed along with the experimental results from this mission.

Identifying, studying and making good use of macromolecular crystals

PubMed Central

Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

2014-01-01

Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed. PMID:25084371

Electrophoresis Gel Quantification with a Flatbed Scanner and Versatile Lighting from a Screen Scavenged from a Liquid Crystal Display (LCD) Monitor

ERIC Educational Resources Information Center

Yeung, Brendan; Ng, Tuck Wah; Tan, Han Yen; Liew, Oi Wah

2012-01-01

The use of different types of stains in the quantification of proteins separated on gels using electrophoresis offers the capability of deriving good outcomes in terms of linear dynamic range, sensitivity, and compatibility with specific proteins. An inexpensive, simple, and versatile lighting system based on liquid crystal display backlighting is…

Experimental Demonstration of Isomorphism.

ERIC Educational Resources Information Center

Kamenicek, J.; Melicharek, M.

2000-01-01

Describes some simple experiments related to the properties of crystals. Illustrates isomorphism using single crystals of alum. Presents experiments for determining how various mixture compositions affect the growth of salt crystals. (WRM)

Results of the TTF-TCNQ and the calcium carbonate crystallization on the Long Duration Exposure Facility

NASA Technical Reports Server (NTRS)

Nielsen, Kjeld Flemming; Lind, M. David

1992-01-01

Experiment A0139A on the Long Duration Exposure Facility (LDEF) carried four large containers into orbit five years with crystal growth solutions for lead sulfide, calcium carbonate, and TTF-TCNQ. Although temperature data was lost, the experimental program had been working since the valves in all containers had been opened. All four experiments produced crystals of varying quality. The calcium carbonate crystals had the best appearance. The TTF-TCNQ crystals were packed together near the valve openings of the container. When taken apart, the single crystals showed some unusual morphological properties. X ray investigations as well as conductivity measurements on long duration space grown TTF-TCNQ crystals will be presented. Comparisons will be made with our previous space solution growth experiments. The TTF-TCNQ crystals are no longer of the highest interest, so this activity has been terminated in favor of calcium carbonate and calcium phosphate crystallizations.

Protein crystal growth in microgravity

NASA Technical Reports Server (NTRS)

Rosenblum, William M.; Delucas, Lawrence J.; Wilson, William W.

1989-01-01

Major advances have been made in several of the experimental aspects of protein crystallography, leaving protein crystallization as one of the few remaining bottlenecks. As a result, it has become important that the science of protein crystal growth is better understood and that improved methods for protein crystallization are developed. Preliminary experiments with both small molecules and proteins indicate that microgravity may beneficially affect crystal growth. For this reason, a series of protein crystal growth experiments using the Space Shuttle was initiated. The preliminary space experiments were used to evolve prototype hardware that will form the basis for a more advanced system that can be used to evaluate effects of gravity on protein crystal growth. Various optical techniques are being utilized to monitor the crystal growth process from the incipient or nucleation stage and throughout the growth phase. The eventual goal of these studies is to develop a system which utilizes optical monitoring for dynamic control of the crystallization process.

Crystallization Experiments in the MgO-CO2-H2O system: Role of Amorphous Magnesium Carbonate Precursors in Magnesium Carbonate Hydrated Phases and Morphologies in Low Temperature Hydrothermal Fluids

NASA Astrophysics Data System (ADS)

Giampouras, Manolis; Garcia-Ruiz, Juan Manuel; Garrido, Carlos J.

2017-04-01

Numerous forms of hydrated or basic magnesium carbonates occur in the complex MgO-CO2-H2O system. Mineral saturation states from low temperature hydrothermal fluids in Semail Ophiolite (Oman), Prony Bay (New Caledonia) and Lost City hydrothermal field (mid-Atlantic ridge) strongly indicate the presence of magnesium hydroxy-carbonate hydrates (e.g. hydromagnesite) and magnesium hydroxides (brucite). Study of formation mechanisms and morphological features of minerals forming in the MgO-CO2-H2O system could give insights into serpentinization-driven, hydrothermal, alkaline environments, which are related to early Earth conditions. Temperature, hydration degree, pH and fluid composition are crucial factors regarding the formation, coexistence and transformation of such mineral phases. The rate of supersaturation, on the other hand, is a fundamental parameter to understand nucleation and crystal growth processes. All these parameters can be examined in a solution using different crystallization techniques. In the present study, we applied different crystallization techniques to synthesize and monitor the crystallization of Mg-bearing carbonates and hydroxides under abiotic conditions. Various crystallization techniques (counter-diffusion, vapor diffusion and unseeded solution mixing) were used to screen the formation conditions of each phase, transformation processes and structural development. Mineral and textural characterization of the different synthesized phases were carried out by X-ray diffraction (XRD), Raman spectroscopy and scanning electron microscopy coupled to dispersive energy spectroscopy (FE-SEM-EDS). Experimental investigation of the effect of pH level and silica content under variable reactant concentrations revealed the importance of Amorphous Magnesium Carbonate (AMC) in the formation of hydroxy-carbonate phases (hydromagnesite and dypingite). Micro-structural resemblance between AMC precursors and later stage crystalline phases highlights the critical role of internal molecule re-organization to form crystalline structures. Aggregation of AMC spherulites triggers biomimetic morphologies forming curling laminar structures and rings. The size and number of nesquehonite (MgCO3.3H2O) crystals are controlled by pH and Mg2+ ions at pH < 9. As pH increases, nesquehonite transforms to spherical, rosette-like dypingite and/or hydromagnesite. Crystallization experiments within silica gel impedes the normal growth of prismatic nesquehonite crystals and generates peculiar dendritic crystalline structures. Finally, vapor diffusion techniques resulted in synthesis of NH4+-bearing hydrated compounds after ammonium incorporation when [NH4+]/[Mg2+] ≥ 1 and ≥ 0.5M [NH4+]. Funding: We acknowledge funding from the People programme (Marie Curie Actions - ITN) of the European Union FP7 under REA Grant Agreement n˚ 608001.

Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase.

PubMed

Ericson, Daniel L; Yin, Xingyu; Scalia, Alexander; Samara, Yasmin N; Stearns, Richard; Vlahos, Harry; Ellson, Richard; Sweet, Robert M; Soares, Alexei S

2016-02-01

Improvements needed for automated crystallography include crystal detection and crystal harvesting. A technique that uses acoustic droplet ejection to harvest crystals was previously reported. Here a method is described for using the same acoustic instrument to detect protein crystals and to monitor crystal growth. Acoustic pulses were used to monitor the progress of crystallization trials and to detect the presence and location of protein crystals. Crystals were detected, and crystallization was monitored in aqueous solutions and in lipidic cubic phase. Using a commercially available acoustic instrument, crystals measuring ~150 µm or larger were readily detected. Simple laboratory techniques were used to increase the sensitivity to 50 µm by suspending the crystals away from the plastic surface of the crystallization plate. This increased the sensitivity by separating the strong signal generated by the plate bottom that can mask the signal from small protein crystals. It is possible to further boost the acoustic reflection from small crystals by reducing the wavelength of the incident sound pulse, but our current instrumentation does not allow this option. In the future, commercially available sound-emitting transducers with a characteristic frequency near 300 MHz should detect and monitor the growth of individual 3 µm crystals. © 2015 Society for Laboratory Automation and Screening.

Operation condition for continuous anti-solvent crystallization of CBZ-SAC cocrystal considering deposition risk of undesired crystals

NASA Astrophysics Data System (ADS)

Nishimaru, Momoko; Nakasa, Miku; Kudo, Shoji; Takiyama, Hiroshi

2017-07-01

Crystallization operation of cocrystal production has deposition risk of undesired crystals. Simultaneously, continuous manufacturing processes are focused on. In this study, conditions for continuous cocrystallization considering risk reduction of undesired crystals deposition were investigated on the view point of thermodynamics and kinetics. The anti-solvent cocrystallization was carried out in four-component system of carbamazepine, saccharin, methanol and water. From the preliminary batch experiment, the relationships among undesired crystal deposition, solution composition decided by mixing ratio of solutions, and residence time for the crystals were considered, and then the conditions of continuous experiment were decided. Under these conditions, the continuous experiment was carried out. The XRD patterns of obtained crystals in the continuous experiment showed that desired cocrystals were obtained without undesired crystals. This experimental result was evaluated by using multi-component phase diagrams from the view point of the operation point's movement. From the evaluation, it was found that there is a certain operation condition which the operation point is fixed with time in the specific domain without the deposition risk of undesired single component crystals. It means the possibility of continuous production of cocrystals without deposition risk of undesired crystals was confirmed by using multi-component phase diagrams.

Evaluation of parameters of color profile models of LCD and LED screens

NASA Astrophysics Data System (ADS)

Zharinov, I. O.; Zharinov, O. O.

2017-12-01

The purpose of the research relates to the problem of parametric identification of the color profile model of LCD (liquid crystal display) and LED (light emitting diode) screens. The color profile model of a screen is based on the Grassmann’s Law of additive color mixture. Mathematically the problem is to evaluate unknown parameters (numerical coefficients) of the matrix transformation between different color spaces. Several methods of evaluation of these screen profile coefficients were developed. These methods are based either on processing of some colorimetric measurements or on processing of technical documentation data.

The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

PubMed Central

Gilliland, Gary L.; Tung, Michael; Ladner, Jane

1996-01-01

The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

Use of the NP-40 detergent-mediated assay in discovery of inhibitors of beta-hematin crystallization.

PubMed

Sandlin, Rebecca D; Carter, Melissa D; Lee, Patricia J; Auschwitz, Jennifer M; Leed, Susan E; Johnson, Jacob D; Wright, David W

2011-07-01

The protozoan parasite responsible for malaria affects over 500 million people each year. Current antimalarials have experienced decreased efficacy due to the development of drug-resistant strains of Plasmodium spp., resulting in a critical need for the discovery of new antimalarials. Hemozoin, a crystalline by-product of heme detoxification that is necessary for parasite survival, serves as an important drug target. The quinoline antimalarials, including amodiaquine and chloroquine, act by inhibiting the formation of hemozoin. The formation of this crystal does not occur spontaneously, and recent evidence suggests crystallization occurs in the presence of neutral lipid particles located in the acidic digestive vacuole of the parasite. To mimic these conditions, the lipophilic detergent NP-40 has previously been shown to successfully mediate the formation of β-hematin, synthetic hemozoin. Here, an NP-40 detergent-based assay was successfully adapted for use as a high-throughput screen to identify inhibitors of β-hematin formation. The resulting assay exhibited a favorable Z' of 0.82 and maximal drift of less than 4%. The assay was used in a pilot screen of 38,400 diverse compounds at a screening concentration of 19.3 μM, resulting in the identification of 161 previously unreported β-hematin inhibitors. Of these, 48 also exhibited ≥ 90% inhibition of parasitemia in a Plasmodium falciparum whole-cell assay at a screening concentration of 23 μM. Eight of these compounds were identified to have nanomolar 50% inhibitory concentration values near that of chloroquine in this assay.

Babinet's principle in double-refraction systems

NASA Astrophysics Data System (ADS)

Ropars, Guy; Le Floch, Albert

2014-06-01

Babinet's principle applied to systems with double refraction is shown to involve spatial interchanges between the ordinary and extraordinary patterns observed through two complementary screens. As in the case of metamaterials, the extraordinary beam does not follow the Snell-Descartes refraction law, the superposition principle has to be applied simultaneously at two points. Surprisingly, by contrast to the intuitive impression, in the presence of the screen with an opaque region, we observe that the emerging extraordinary photon pattern, which however has undergone a deviation, remains fixed when a natural birefringent crystal is rotated while the ordinary one rotates with the crystal. The twofold application of Babinet's principle implies intensity and polarization interchanges but also spatial and dynamic interchanges which should occur in birefringent metamaterials.

A synergistic approach to protein crystallization: Combination of a fixed-arm carrier with surface entropy reduction

PubMed Central

Moon, Andrea F; Mueller, Geoffrey A; Zhong, Xuejun; Pedersen, Lars C

2010-01-01

Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail. PMID:20196072

Guidelines for the successful generation of protein–ligand complex crystals

PubMed Central

Müller, Ilka

2017-01-01

With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein–ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting. PMID:28177304

A drunken search in crystallization space

PubMed Central

Fazio, Vincent J.; Peat, Thomas S.; Newman, Janet

2014-01-01

The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition. PMID:25286930

Crystallization and preliminary crystallographic analysis of maganese(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from Bacillus sp. JF8

PubMed Central

Senda, Miki; Hatta, Takashi; Kimbara, Kazuhide; Senda, Toshiya

2010-01-01

A thermostable manganese(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase derived from Bacillus sp. JF8 was crystallized. The initial screening for crystallization was performed by the sitting-drop vapour-diffusion method using a crystallization robot, resulting in the growth of two crystal forms. The first crystal belonged to space group P1, with unit-cell parameters a = 62.7, b = 71.4, c = 93.6 Å, α = 71.2, β = 81.0, γ = 64.0°, and diffracted to 1.3 Å resolution. The second crystal belonged to space group I222, with unit-cell parameters a = 74.2, b = 90.8, c = 104.3 Å, and diffracted to 1.3 Å resolution. Molecular-replacement trials using homoprotocatechuate 2,3-dioxygenase from Arthrobacter globiformis (28% amino-acid sequence identity) as a search model provided a satisfactory solution for both crystal forms. PMID:20208161

The use of the liquid crystal display (LCD) panel as a teaching aid in medical lectures.

PubMed

Wong, K T

1992-01-01

The liquid crystal display (LCD) panel is designed to project on-screen information of a microcomputer onto a larger screen with the aid of a standard overhead projector, so that large audiences may view on-screen information without having to crowd around the TV monitor. As little has been written about its use as a visual aid in medical teaching, the present report documents its use in a series of pathology lectures delivered, over a 2-year period, to two classes of about 150 medical students each. Some advantages of the LCD panel over the 35mm slide include the flexibility of last-minute text changes and less lead time needed for text preparation. It eliminates the problems of messy last-minute changes in, and improves legibility of, handwritten overhead projector transparencies. The disadvantages of using an LCD panel include the relatively bulky equipment which may pose transport problems, image clarity that is inferior to the 35mm slide, and equipment costs.

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

DOE PAGES

Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

2015-01-01

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

Comparative Analysis of Thaumatin Crystals Grown on Earth and in Microgravity. Experiment 23

NASA Technical Reports Server (NTRS)

Ng, Joseph D.; Lorber, Bernard; Giege, Richard; Koszelak, Stanley; Day, John; Greenwood, Aaron; McPherson, Alexander

1998-01-01

The protein thaumatin was studied as a model macromolecule for crystallization in microgravity environment experiments conducted on two U.S. Space Shuttle missions (second United States Microgravity Laboratory (USML-2) and Life and Microgravity Spacelab (LMS)). In this investigation we evaluated and compared the quality of space- and Earth-grown thaumatin crystals using x-ray diffraction analysis and characterized them according to crystal size, diffraction resolution limit, and mosaicity. Two different approaches for growing thaumatin crystals in the microgravity environment, dialysis and liquid-liquid diffusion, were employed as a joint experiment by our two investigative teams. Thaumatin crystals grown under a microgravity environment were generally larger in volume with fewer total crystals. They diffracted to significantly higher resolution and with improved diffraction properties as judged by relative Wilson plots. The mosaicity for space-grown crystals was significantly less than for those grown on Earth. Increasing concentrations of protein in the crystallization chambers under microgravity lead to larger crystals. The data presented here lend further support to the idea that protein crystals of improved quality can be obtained in a microgravity environment.

Crystal Growth Furnace - An overview of the system configuration and planned experiments on the First United States Microgravity Laboratory mission

NASA Technical Reports Server (NTRS)

Srinivas, R.; Schaefer, D. A.

1992-01-01

The Crystal Growth Furnace (CGF) system configuration for the First United States Microgravity Laboratory (USML-1) mission is reviewed, and the planned on-orbit experiments are briefly described. The CGF is configured to accommodate four scientific experiments involving crystal growth which are based on the classical Bridgman method and CVT method, including vapor transport crystal growth of mercury cadmium telluride; crystal growth of mercury zinc telluride by directional solidification; seeded Bridgman growth of zinc-doped cadmium telluride; and Bridgman growth of selenium-doped gallium arsenide.

Model of melting (crystallization) process of the condensed disperse phase in the smoky plasmas

NASA Astrophysics Data System (ADS)

Dragan, G. S.; Kolesnikov, K. V.; Kutarov, V. V.

2018-01-01

The paper presents an analysis of the causes of a formation of spatial ordered grain structures in a smoky plasma. We are modeling the process of melting (crystallization) of a condensed phase in this environment taking into account the screened electrostatic interaction and the diffusion-drift force. We discuss an influence of the charge on the melting temperatures.

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

PubMed

Shaw, Neil; Cheng, Chongyun; Tempel, Wolfram; Chang, Jessie; Ng, Joseph; Wang, Xin-Yu; Perrett, Sarah; Rose, John; Rao, Zihe; Wang, Bi-Cheng; Liu, Zhi-Jie

2007-07-07

The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

Accommodative and convergence response to computer screen and printed text

NASA Astrophysics Data System (ADS)

Ferreira, Andreia; Lira, Madalena; Franco, Sandra

2011-05-01

The aim of this work was to find out if differences exist in accommodative and convergence response for different computer monitors' and a printed text. It was also tried to relate the horizontal heterophoria value and accommodative response with the symptoms associated with computer use. Two independents experiments were carried out in this study. The first experiment was measuring the accommodative response on 89 subjects using the Grand Seiko WAM-5500 (Grand Seiko Co., Ltd., Japan). The accommodative response was measured using three computer monitors: a 17-inch cathode ray tube (CRT), two liquid crystal displays LCDs, one 17-inch (LCD17) and one 15 inches (LCD15) and a printed text. The text displayed was always the same for all the subjects and tests. A second experiment aimed to measure the value of habitual horizontal heterophoria on 80 subjects using the Von Graefe technique. The measurements were obtained using the same target presented on two different computer monitors, one 19-inch cathode ray tube (CRT) and other 19 inches liquid crystal displays (LCD) and printed on paper. A small survey about the incidence and prevalence of symptoms was performed similarly in both experiments. In the first experiment, the accommodation response was higher in the CRT and LCD's than for paper. There were not found significantly different response for both LCD monitors'. The second experiment showed that, the heterophoria values were similar for all the stimuli. On average, participants presented a small exophoria. In both experiments, asthenopia was the symptom that presented higher incidence. There are different accommodative responses when reading on paper or on computer monitors. This difference is more significant for CRT monitors. On the other hand, there was no difference in the values of convergence for the computer monitors' and paper. The symptoms associated with the use of computers are not related with the increase in accommodation and with the horizontal heterophoria values.

Protein-crystal growth experiment (planned)

NASA Technical Reports Server (NTRS)

Fujita, S.; Asano, K.; Hashitani, T.; Kitakohji, T.; Nemoto, H.; Kitamura, S.

1988-01-01

To evaluate the effectiveness of a microgravity environment on protein crystal growth, a system was developed using 5 cubic feet Get Away Special payload canister. In the experiment, protein (myoglobin) will be simultaneously crystallized from an aqueous solution in 16 crystallization units using three types of crystallization methods, i.e., batch, vapor diffusion, and free interface diffusion. Each unit has two compartments: one for the protein solution and the other for the ammonium sulfate solution. Compartments are separated by thick acrylic or thin stainless steel plates. Crystallization will be started by sliding out the plates, then will be periodically recorded up to 120 hours by a still camera. The temperature will be passively controlled by a phase transition thermal storage component and recorded in IC memory throughout the experiment. Microgravity environment can then be evaluated for protein crystal growth by comparing crystallization in space with that on Earth.

Results of the TTF-TCNQ- and the calcium carbonate-crystallization on the Long Duration Exposure Facility

NASA Technical Reports Server (NTRS)

Nielsen, Kjeld Flemming; Lind, M. David

1991-01-01

Experiment AO139A on the Long Duration Exposure Facility (LDEF) carried four large containers into orbit for five years with crystal growth solutions for lead sulfide, calcium carbonate, and tetra thiafulvalene- tetra cyanoquino methane (TTF-TCNQ). The LDEF was in excellent condition after the long orbital stay, and although the temperature data was lost, the experiment program had been working since the valves in all containers were opened. All four experiments produced crystals; however, they were of varying quality. The calcium carbonate crystals had the best appearance. The TTF-TCNQ crystals were packed together near the valve openings of the container. When taken apart, the single crystals showed some unusual morphological properties. X-ray investigations as well as conductivity measurements on the long duration space grown TTF-TCNQ crystals are presented, and pictures of the calcium carbonate are shown. Comparisons are made with previous space solution growth experiments on the European Spacelab Mission and the Apollo-Soyuz Test Project.

Lead halide perovskites: Crystal-liquid duality, phonon glass electron crystals, and large polaron formation

PubMed Central

Miyata, Kiyoshi; Atallah, Timothy L.; Zhu, X.-Y.

2017-01-01

Lead halide perovskites have been demonstrated as high performance materials in solar cells and light-emitting devices. These materials are characterized by coherent band transport expected from crystalline semiconductors, but dielectric responses and phonon dynamics typical of liquids. This “crystal-liquid” duality implies that lead halide perovskites belong to phonon glass electron crystals, a class of materials believed to make the most efficient thermoelectrics. We show that the crystal-liquid duality and the resulting dielectric response are responsible for large polaron formation and screening of charge carriers, leading to defect tolerance, moderate charge carrier mobility, and radiative recombination properties. Large polaron formation, along with the phonon glass character, may also explain the marked reduction in hot carrier cooling rates in these materials. PMID:29043296

KENNEDY SPACE CENTER, FLA. - The crystals visible in this laboratory dish were part of an experiment carried on mission STS-107. Several experiments were found during the search for Columbia debris. Included in the Commercial ITA Biomedical Experiments payload on mission STS-107 are urokinase cancer research, microencapsulation of drugs, the Growth of Bacterial Biofilm on Surfaces during Spaceflight (GOBBSS), and tin crystal formation.

NASA Image and Video Library

2003-05-07

KENNEDY SPACE CENTER, FLA. - The crystals visible in this laboratory dish were part of an experiment carried on mission STS-107. Several experiments were found during the search for Columbia debris. Included in the Commercial ITA Biomedical Experiments payload on mission STS-107 are urokinase cancer research, microencapsulation of drugs, the Growth of Bacterial Biofilm on Surfaces during Spaceflight (GOBBSS), and tin crystal formation.

Fluid Physics and Macromolecular Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

Decades of Data: Extracting Trends from Microgravity Crystallization History

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.; Kephart, Richard; vanderWoerd, Mark; Curreri, Peter A. (Technical Monitor)

2002-01-01

The reduced acceleration environment of an orbiting spacecraft has been posited as an ideal environment for biological crystal growth since buoyancy driven convection and sedimentation are greatly reduced. Since the first sounding rocket flight in 1981 many crystallization experiments have flown with some showing improvement and others not. To further explore macromolecule crystal improvement in microgravity we have accumulated data from published reports and reports submitted by individual investigators to NASA, forming a database called BIOSEArCH (Biological Space Experiment Archive of Crystallization History). To date it contains information from 63 missions including, the Space Shuttle program, unmanned satellites, the Russian Space Station MIR and sounding rocket experiments, containing reports for more than 736 macromolecule experiments. While it is not at this point in time a comprehensive record of all flight crystallization experimental results, there is however sufficient information for emerging trends to be identified. These trends will be highlighted.

Electrical Characteristics CuFe{sub 2}O{sub 4} Thick Film Ceramics Made with Different Screen Size Utilizing Fe{sub 2}O{sub 3} Nanopowder Derived from Yarosite for NTC Thermistor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiendartun,; Syarif, Dani Gustaman

2010-10-24

Fabrication of CuFe{sub 2}O{sub 4} thick film ceramics utilizing Fe{sub 2}O{sub 3} derived from yarosite using screen printing technique for NTC thermistor has been carried out. Effect of thickness variation due to different size of screen (screen 225; 300 and 375 mesh) has been studied. X-ray diffraction analyses (XRD) was done to know crystal structure and phases formation. SEM analyses was carried out to know microstructure of the films. Electrical properties characterization was done through measurement of electrical resistance at various temperatures (room temperature to 100 deg. C). The XRD data showed that the films crystalize in tetragonal spinel. Themore » SEM images showed that the screen with the smaller of the hole size, made the grain size was bigger. Electrical data showed that the larger the screen different size thickness variation (mesh), the larger the resistance, thermistor constant and sensitivity. From the electrical characteristics data, it was known that the electrical characteristics of the CuFe{sub 2}O{sub 4} thick film ceramics followed the NTC characteristic. The value of B and R{sub RT} of the produced CuFe{sub 2}O{sub 4} ceramics namely B = 3241-3484 K and R{sub RT} = 25.6-87.0 M Ohm, fitted market requirement.« less

Isothermal dendritic growth: A low gravity experiment

NASA Technical Reports Server (NTRS)

Glicksman, M. E.; Hahn, R. C.; Lograsso, T. A.; Rubinstein, E. R.; Selleck, M. E.; Winsa, E.

1988-01-01

The Isothermal Dendritic Growth Experiment is an active crystal growth experiment designed to test dendritic growth theory at low undercoolings where convection prohibits such studies at 1 g. The experiment will be essentially autonomous, though limited in-flight interaction through a computer interface is planned. One of the key components of the apparatus will be a crystal growth chamber capable of achieving oriented single crystal dendritic growth. Recent work indicates that seeding the chamber with a crystal of the proper orientation will not, in and of itself, be sufficient to meet this requirement. Additional flight hardware and software required for the STS flight experiment are currently being developed at NASA Lewis Research Center and at Rensselaer Polytechnic Institute.

Investigation of crystal growth in zero gravity environment and investigation of metallic whiskers

NASA Technical Reports Server (NTRS)

Davis, J. H.; Lal, R. B.; Walter, H. U.; Castle, J. G., Jr.

1972-01-01

Theoretical and experimental work reported relates to the effects of near-zero gravity on growths of crystals and metallic whiskers during Skylab and Apollo flight experiments. Studies on growth and characterization of candidate materials for flight experiments cover indium-bismuth compounds, bismuth single crystals, gallium arsenide films and single crystals, and cadmium whiskers.

NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuchs, Martin R., E-mail: mfuchs@bnl.gov; Bhogadi, Dileep K.; Jakoncic, Jean

We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux atmore » 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.« less

Reverse screening methods to search for the protein targets of chemopreventive compounds

NASA Astrophysics Data System (ADS)

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-05-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.

PubMed

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-01-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction.

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds

PubMed Central

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-01-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and grasp the types of calculations used in protein target fishing. In addition, we review the main features of these methods, programs and databases and provide a variety of examples illustrating the application of one or a combination of reverse screening methods for accurate target prediction. PMID:29868550

Construction of High Activity Titanium Dioxide Crystal Surface Heterostructures and Characterization of Its Basic Properties

NASA Astrophysics Data System (ADS)

Wang, Chunxiao; Li, DanQi; Shen, Tingting; Lu, Cheng; Sun, Jing; Wang, Xikui

2018-01-01

Heterogeneous photocatalytic materials, which combine the advantages of photocatalytic materials and heterojunction, have been developed rapidly in the field of environmental pollution control. In this paper, TiO2 surface heterojunction catalysts with different catalytic activity were prepared by controlling the amount of HF, and their XRD characterization was also carried out. In addition, the optimum amount of HF was determined by photocatalytic degradation of simulated dye wastewater by methylene blue solution. And the optimal amount of catalyst and the optimal pH reaction conditions for degradation experiments were used to screen the highly reactive titania surface heterojunction system and its optimum application conditions. It provides the possibility of application in the degradation of industrial wastewater and environmental treatment.

Nonlinear Optical Characterization of Membrane Protein Microcrystals and Nanocrystals.

PubMed

Newman, Justin A; Simpson, Garth J

2016-01-01

Nonlinear optical methods such as second harmonic generation (SHG) and two-photon excited UV fluorescence (TPE-UVF) imaging are promising approaches to address bottlenecks in the membrane protein structure determination pipeline. The general principles of SHG and TPE-UVF are discussed here along with instrument design considerations. Comparisons to conventional methods in high throughput crystallization condition screening and crystal quality assessment prior to X-ray diffraction are also discussed.

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

PubMed Central

Fusco, Diana; Barnum, Timothy J.; Bruno, Andrew E.; Luft, Joseph R.; Snell, Edward H.; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis. PMID:24988076

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

PubMed

Fusco, Diana; Barnum, Timothy J; Bruno, Andrew E; Luft, Joseph R; Snell, Edward H; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

Small molecule inhibitors of mesotrypsin from a structure-based docking screen

DOE PAGES

Kayode, Olumide; Huang, Zunnan; Soares, Alexei S.; ...

2017-05-02

PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active sitemore » residues, and commercial availability. Diminazene (C1D22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (K i) of 3.6±0.3 pM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.« less

Small molecule inhibitors of mesotrypsin from a structure-based docking screen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kayode, Olumide; Huang, Zunnan; Soares, Alexei S.

PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active sitemore » residues, and commercial availability. Diminazene (C1D22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (K i) of 3.6±0.3 pM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.« less

A morphological screening of protein crystals for interferon delivery by metal ion-chelate technology.

PubMed

Jiang, Yanbo; Shi, Kai; Wang, Shuo; Li, Xuefeng; Cui, Fude

2010-12-01

This study presents a preliminary exploration on extending the half-life of therapeutic proteins by crystallization strategy without new molecular entities generation. Recombinant human interferon (rhIFN) α-2b, a model protein drug in this case, was crystallized using a hanging-drop vapor diffusion method. A novel chelating technique with metal ions was employed to promote crystals formation. The effects of key factors such as seeding protein concentration, pH of the hanging drop, ionic strength of the equilibration solution, and precipitants were investigated. Size-exclusion liquid chromatography, antiviral activity determination, and enzyme-linked immunosorbent assay indicated that both the molecular integrity and biological potency of rhIFN were not significantly affected by crystallization process. In addition, the in vitro release behavior of rhIFN from crystal lattice was characterized by an initial fast release, followed by a sustained release up to 48 hour. The work described here suggested an exciting possibility of therapeutic protein crystals as a long-acting formulation.

Demonstration of Crystal Structure.

ERIC Educational Resources Information Center

Neville, Joseph P.

1985-01-01

Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

Screens as light biological variable in microgravitational space environment.

NASA Astrophysics Data System (ADS)

Schlacht, S.; Masali, M.

Foreword The ability of the biological organisms to orient themselves and to synchronize on the variations of the solar rhythms is a fundamental aspect in the planning of the human habitat above all when habitat is confined in the Space the planetary and in satellite outer space settlements In order to simulate the experience of the astronauts in long duration missions one of the dominant characteristics of the Space confined habitats is the absence of the earthlings solar cycles references The Sun is the main references and guidelines of the biological compass and timepiece The organism functions are influenced from the variation of the light in the round of the 24 hours the human circadian rhythms In these habitats it is therefore necessary to reproduce the color and intensity of the solar light variations along the arc of the day according to defined scientific programs assuring a better performance of the human organism subsubsection Multilayer Foldable Screens as biological environmental variable In the project Multilayer Foldable Screens are the monitors posed in the ceiling of an Outer Space habitat and are made of liquid crystals and covered with Kevlar they stand for a modulate and flexible structure for different arrangements and different visions Screens work sout s on all the solar light frequencies and display the images that the subject needs They are characterized from the emission of an environmental light that restores the earthly solar cycle for intensity and color temperature to irradiate

High-pressure hydrogen testing of single crystal superalloys for advanced rocket engine turbopump turbine blades

NASA Technical Reports Server (NTRS)

Alter, W. S.; Parr, R. A.; Johnston, M. H.; Strizak, J. P.

1984-01-01

A screening program to determine the effects of high pressure hydrogen on selected candidate materials for advanced single crystal turbine blade applications is examined. The alloys chosen for the investigation are CM SX-2, CM SX-4C, Rene N-4, and PWA1480. Testing is carried out in hydrogen and helium at 34 MPa and room temperature, with both notched and unnotched single crystal specimens. Results show a significant variation in susceptibility to Hydrogen Environment Embrittlement (HEE) among the four alloys and a marked difference in fracture topography between hydrogen and helium environment specimens.

Solubility Report of 1-Methyl-3,5-Dinitro-1H-1,2,4-Triazole (MDNT) and 2-Methyl-4,5-Dinitro-2H-1,2,3-Triazole 1-Oxide (MDNTO) for Co-Crystallization Screen

DTIC Science & Technology

2015-11-01

New Co-Crystals,” Crystal Growth & Design, Vol. 9, No. 3, pp. 1531-1537, 2009. 2 Landenberger, K., Matzger, A., “ Cocrystal Engineering of a...Y., Li, H., Zhou, Y., Zhou, J., Geo, T., Zhang, H., Jiang, G., “Toward Low- Sensitive and High-Energetic Cocrystal 1: Evaluation of the Power and the...Safety of Observed Energetic Cocrystals ,” CrystEngComm, 15, 4003-4014, 2013. 4 Levinthal, M.L., “Propellant Made With Cocrystals of

Spacelab J experiment descriptions

NASA Technical Reports Server (NTRS)

Miller, Teresa Y. (Editor)

1993-01-01

Brief descriptions of the experiment investigations for the Spacelab J Mission which was launched from the Kennedy Space Center aboard the Endeavour in Sept. 1992 are presented. Experiments cover the following: semiconductor crystals; single crystals; superconducting composite materials; crystal growth; bubble behavior in weightlessness; microgravity environment; health monitoring of Payload Specialists; cultured plant cells; effect of low gravity on calcium metabolism and bone formation; and circadian rhythm.

laboratory studies on the uptake of organic compounds by ice crystals

NASA Astrophysics Data System (ADS)

Fries, E.; Jaeschke, W.

2003-04-01

Anthropogenic aerosols produced from biomass burning are known to increase the number of cloud condensation nuclei in the atmosphere at most latitudes. This reduces cloud droplet size, which prevents raindrop formation at shallower levels in the atmosphere. Vertical convection processes force particles and water vapor to rise up to the upper troposphere. At lower temperatures, ice crystals are formed via heterogeneous freezing of supercooled droplets containing particles known as ice nuclei (IN) and/or via condensation of supercooled water onto IN directly from the vapor, followed by freezing. Ice crystals grow by vapor deposition, by collision of supercooled drops with ice particles and by collision of ice crystals. The grown ice crystals melt on their way down and turn into rain. Most of the precipitation falling to the surface at midlatitudes originates as ice. The adsorption of organic gases emitted from fossil fuel combustion like BTEX may alter particle growth and sublimation rates in the atmosphere. This may also change precipitation rates, which impact the climate world-wide. Considering importance of ice in atmospheric science, laboratory studies are carried out to quantify organic vapor adsorption onto ice. At temperatures between 0 and -40^oC, organic gases at ppb gas levels are allowed to adsorb to the surface of ice crystals with surface properties similar to atmospheric ice. For the experiments, a vertical ice chamber (stainless-steel) with 10 different screen inserts (stainless-steel) was constructed. The chamber is 39 cm in length and 10,5 cm in diameter. The size of the stainless-steel mesh of the screens was chosen by the size of the ice crystals and is 0.14 cm. The ice chamber is located inside a 2x2 m walk-in cold chamber. Prior to the addition of the organic gases, the precleaned carrier gas of synthetic air is humidified to ice saturation in the walk-in cold chamber by passing the carrier stream through a 10 m long and 5 cm in diameter aluminum pipe. Resulting super cooled droplets are removed by stainless-steel-wool. The carrier gas is mixed outside the ice chamber in various proportions with a defined gas mixture of 60 different organic compounds. This mixture is allowed to flow through the ice chamber at defined pressures and temperatures. The concentrations of the compounds in the gas phase are determined at the inlet and the outlet of the ice chamber by a mobile GC (AirmoVoc1020). Additionally, the amount of adsorbed compounds is determined by a very sensitive method based on solid-phase-micro-extraction (SPME) followed by GC/FID. The resulting sorption coefficients for different gas concentrations are plotted vs the reciprocal of the absolute temperature for all substances. First results dealing with the adsorption properties of the investigated organic compounds.

Fragment-based screening of the bromodomain of ATAD2

DOE PAGES

Harner, Mary J.; Chauder, Brian A.; Phan, Jason; ...

2014-10-14

Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. As a result, fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.

Secondary electrons induced by fast ions under channeling conditions. II. Screening of fast heavy ions in solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kudo, H.; Shima, K.; Seki, S.

1991-06-01

Ion-beam shadowing effects have been observed for secondary electrons induced by various ions in the energy range of 1.8--3.8 MeV/amu, under various channeling conditions in Si and GaAs crystals. From a comparison of the energy spectra of electrons induced by ions of equal velocity, we have found reduced shadowing effects for heavy ions (Si, S, and Cl) as compared with light (H, He, C, and O) ions. It is concluded that the reduction results from the screening of the heavy ion's nuclear charge by bound electrons. By analyzing the reduced shadowing effect, the effective nuclear charges for the heavy ionsmore » within the target crystals have been determined.« less

Photonic crystal materials and their application in biomedicine.

PubMed

Chen, Huadong; Lou, Rong; Chen, Yanxiao; Chen, Lili; Lu, Jingya; Dong, Qianqian

2017-11-01

Photonic crystal (PC) materials exhibit unique structural colors that originate from their intrinsic photonic band gap. Because of their highly ordered structure and distinct optical characteristics, PC-based biomaterials have advantages in the multiplex detection, biomolecular screening and real-time monitoring of biomolecules. In addition, PCs provide good platforms for drug loading and biomolecule modification, which could be applied to biosensors and biological carriers. A number of methods are now available to fabricate PC materials with variable structure colors, which could be applied in biomedicine. Emphasis is given to the description of various applications of PC materials in biomedicine, including drug delivery, biodetection and tumor screening. We believe that this article will promote greater communication among researchers in the fields of chemistry, material science, biology, medicine and pharmacy.

Phonons in a magnetized Coulomb crystal of ions with polarizable electron background

NASA Astrophysics Data System (ADS)

Baiko, D. A.; Kozhberov, A. A.

2017-11-01

We have studied phonon modes of a body-centered cubic (bcc) Coulomb crystal of ions in the presence of a uniform magnetic field B taking into account the polarizability of the electron background (electron screening) described by the Thomas-Fermi formalism. For k ≫κTF (k and κTF are the phonon wavevector and Thomas-Fermi wavenumber, respectively), electron polarizability is not important. At k ≪κTF , the electron response results in a pronounced effect. One of the three available modes is acoustic. For orthogonal propagation ( k ⊥B ), its frequency Ω is independent of B and κTF . For k ∥B , Ω∝1 /κTF and is independent of B. Another mode is quadratic. Its frequency is ∝1 /(B κTF) for orthogonal propagation and ∝1 /B and independent of κTF for the parallel case. The third mode is optic with Ω≈ωB ( ωB is the ion cyclotron frequency). A general expression is derived for the dynamic matrix of a Coulomb crystal with a polarizable background and more than one ion in the primitive cell. It is employed for a study of a magnetized hexagonal close-packed Coulomb crystal. We have also presented an analysis of phonon polarization vectors in a magnetized bcc crystal with or without screening. The results obtained can be used for realistic calculations of electron-phonon scattering rates and electron thermal and electrical conductivities in neutron star crusts.

Improving axion detection sensitivity in high purity germanium detector based experiments

NASA Astrophysics Data System (ADS)

Xu, Wenqin; Elliott, Steven

2015-04-01

Thanks to their excellent energy resolution and low energy threshold, high purity germanium (HPGe) crystals are widely used in low background experiments searching for neutrinoless double beta decay, e.g. the MAJORANA DEMONSTRATOR and the GERDA experiments, and low mass dark matter, e.g. the CDMS and the EDELWEISS experiments. A particularly interesting candidate for low mass dark matter is the axion, which arises from the Peccei-Quinn solution to the strong CP problem and has been searched for in many experiments. Due to axion-photon coupling, the postulated solar axions could coherently convert to photons via the Primakeoff effect in periodic crystal lattices, such as those found in HPGe crystals. The conversion rate depends on the angle between axions and crystal lattices, so the knowledge of HPGe crystal axis is important. In this talk, we will present our efforts to improve the HPGe experimental sensitivity to axions by considering the axis orientations in multiple HPGe crystals simultaneously. We acknowledge the support of the U.S. Department of Energy through the LANL/LDRD Program.

Liquid-Crystal Display (LCD) Screen Thermal Testing to Simulate Solar Gain

DTIC Science & Technology

2015-12-01

Display (LCD) Screen Thermal Testing to Simulate Solar Gain 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6 . AUTHOR(S) Steven...Sunlight, Monitor Screen Covered 9 2.6 Test 6 – Bench Test with a 250 W Heat Lamp and Hot Mirror Glass 9 2.7 Test 7 – Bench Test with a 250 W Heat...that was used. The use of a black background with white text was important in creating the worst-case scenario for the absorption of solar radiation

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

PubMed Central

Moeder, Katelyn E.; Ho, Chris M. W.; Zimmerman, Maxwell I.; Frederick, Thomas E.; Bowman, Gregory R.

2017-01-01

Allosteric drugs, which bind to proteins in regions other than their main ligand-binding or active sites, make it possible to target proteins considered “undruggable” and to develop new therapies that circumvent existing resistance. Despite growing interest in allosteric drug discovery, rational design is limited by a lack of sufficient structural information about alternative binding sites in proteins. Previously, we used Markov State Models (MSMs) to identify such “cryptic pockets,” and here we describe a method for identifying compounds that bind in these cryptic pockets and modulate enzyme activity. Experimental tests validate our approach by revealing both an inhibitor and two activators of TEM β-lactamase (TEM). To identify hits, a library of compounds is first virtually screened against either the crystal structure of a known cryptic pocket or an ensemble of structures containing the same cryptic pocket that is extracted from an MSM. Hit compounds are then screened experimentally and characterized kinetically in individual assays. We identify three hits, one inhibitor and two activators, demonstrating that screening for binding to allosteric sites can result in both positive and negative modulation. The hit compounds have modest effects on TEM activity, but all have higher affinities than previously identified inhibitors, which bind the same cryptic pocket but were found, by chance, via a computational screen targeting the active site. Site-directed mutagenesis of key contact residues predicted by the docking models is used to confirm that the compounds bind in the cryptic pocket as intended. Because hit compounds are identified from docking against both the crystal structure and structures from the MSM, this platform should prove suitable for many proteins, particularly targets whose crystal structures lack obvious druggable pockets, and for identifying both inhibitory and activating small-molecule modulators. PMID:28570708

Quality Assurance on Undoped CsI Crystals for the Mu2e Experiment

NASA Astrophysics Data System (ADS)

Atanov, N.; Baranov, V.; Budagov, J.; Davydov, Yu. I.; Glagolev, V.; Tereshchenko, V.; Usubov, Z.; Cervelli, F.; Di Falco, S.; Donati, S.; Morescalchi, L.; Pedreschi, E.; Pezzullo, G.; Raffaelli, F.; Spinella, F.; Colao, F.; Cordelli, M.; Corradi, G.; Diociaiuti, E.; Donghia, R.; Giovannella, S.; Happacher, F.; Martini, M.; Miscetti, S.; Ricci, M.; Saputi, A.; Sarra, I.; Echenard, B.; Hitlin, D. G.; Hu, C.; Miyashita, T.; Porter, F.; Zhang, L.; Zhu, R.-Y.; Grancagnolo, F.; Tassielli, G.; Murat, P.

2018-02-01

The Mu2e experiment is constructing a calorimeter consisting of 1,348 undoped CsI crystals in two disks. Each crystal has a dimension of 34 x 34 x 200 mm, and is readout by a large area silicon PMT array. A series of technical specifications was defined according to physics requirements. Preproduction CsI crystals were procured from three firms: Amcrys, Saint-Gobain and Shanghai Institute of Ceramics. We report the quality assurance on crystal's scintillation properties and their radiation hardness against ionization dose and neutrons. With a fast decay time of 30 ns and a light output of more than 100 p.e./MeV measured with a bi-alkali PMT, undoped CsI crystals provide a cost-effective solution for the Mu2e experiment.

SKYLAB (SL)-3 - EXPERIMENT HARDWARE

NASA Image and Video Library

1973-11-08

S74-19677 (April 1974) --- This crystal of Germanium Selenide (GeSe) was grown under weightless conditions in an electric furnace aboard the Skylab space station. Experiment M556, Vapor Growth of IV-VI Compounds, was conducted as a comparative test of GeSe crystals grown on Earth and those grown in a weightless environment. Skylab postflight results indicate that crystals grown in a zero-gravity situation demonstrate greater growth and better composite structure than those grown in ground-bases laboratories. The GeSe crystal shown here is 20 millimeters long, the largest crystal ever grown on Earth or in space. Principal Investigator for Experiment M556 is Dr. Harry Wiedemaier, Rensselaer Polytechnic Institute, Troy, New York. (See NASA photograph S74-19676 for an example of an Earth-grown Germanium Selenide crystal.) Photo credit: NASA

An experimental study of pyroxene crystallization during rapid cooling in a thermal gradient; applications to komatiites and chondrites

NASA Astrophysics Data System (ADS)

Bouquain, S.; Arndt, N. T.; Faure, F.; Libourel, G.

2013-03-01

To investigate the crystallization of pyroxene in spinifex-textured komatiites and in chondrites we undertook a series of experiments in which compositions in the CMAS system were cooling rapidly in a thermal gradient. Cooling rates were generally between 5 to 10 °C h-1 but some runs were made at 100-200 °C h-1; thermal gradients were between 10 and 20 °C cm-1. These conditions reproduced those at various levels in the crust of komatiitic lava flow. The starting composition was chosen to have pigeonite on the liquidus and a majority of the experiments crystallized zoned pigeonite-diopside crystals like those in komatiite lavas. A~conspicuous aspect of the experimental results was their lack of reproduceability. Some experiments crystallized forsterite whereas others that were run under similar conditions crystallized two pyroxenes and no forsterite; some experiments were totally glassy but others totally crystallized to pyroxene. The degree of supercooling at the onset of pyroxene crystallization was variable, from less than 25 °C to more than 110 °C. We attribute these results to the difficulty of nucleation of pyroxene. In some cases forsterite crystallized metastably and modified the liquid composition to inhibit pyroxene crystallization; in others no nucleation took place until a large degree of supercooling was achieved, then pyroxene crystallized rapidly. Pigeonite crystallized under a wide range of conditions, at cooling rates from 3 to 100 °C h-1. The notion that this mineral only forms at low cooling rates is not correct.

Identifying, studying and making good use of macromolecular crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.

2014-07-25

As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources moremore » intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.« less

Screening and structural elucidation of the zwitterionic cocrystal o-picolinic acid with p-nitro aniline

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.; Sangeetha, K.

2017-04-01

The cocrystal was screened by solvent drop grinding method and the crystals were grown by slow evaporation method at ambient conditions. The cocrystal formation of o-picolinic acid with p-nitro aniline was initially analysed by powder X-ray diffraction. Further the structural properties of the grown crystal were confirmed by the single X-ray diffraction which indicates that the cocrystal were connected by the strong N+sbnd H-⋯O hydrogen bond interaction. The cell parameters of the grown crystal were a = 14.2144(5) Å, b = 5.7558(2) Å, c = 16.0539(6) Å. The functional groups were identified using Fourier transform infrared and Raman spectral analysis. The excitation and emission state of the sample was analysed by the UV-Visible and Fluorescence studies. The red emission was observed from the Fluorescence studies. NMR studies revealed the chemical shift of the cocrystal. Thermal stability and its melting behaviour were studied by TGA and DSC analytical techniques. Electrical behaviour was studied using the dielectric studies. The intermolecular charge transfer within the molecule were analysed using HOMO- LUMO plots.

Large Area Microencapsulated Reflective Guest-Host Liquid Crystal Displays and Their Applications

NASA Astrophysics Data System (ADS)

Nakai, Yutaka; Tanaka, Masao; Enomoto, Shintaro; Iwanaga, Hiroki; Hotta, Aira; Kobayashi, Hitoshi; Oka, Toshiyuki; Kizaki, Yukio; Kidzu, Yuko; Naito, Katsuyuki

2002-07-01

We have developed reflective liquid crystal displays using microencapsulated guest-host liquid crystals, whose size was sufficiently large for viewing documents. A high-brightness image can be realized because there is no need for polarizers. Easy fabrication processes, consisting of screen-printing of microencapsulated liquid crystal and film adhesion, have enabled the realization of thinner and lighter cell structures. It has been confirmed that the display is tolerant of the pressures to which it would be subject in actual use. The optimization of fabrication processes has enabled the realization of reflectance uniformity in the display area and reduction of the driving voltage. Our developed display is suitable for portable information systems, such as electronic book applications.

A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caffrey, Martin, E-mail: martin.caffrey@tcd.ie

A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challengesmore » and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.« less

First results from the PROTEIN experiment on board the International Space Station

NASA Astrophysics Data System (ADS)

Decanniere, Klaas; Potthast, Lothar; Pletser, Vladimir; Maes, Dominique; Otalora, Fermin; Gavira, Jose A.; Pati, Luis David; Lautenschlager, Peter; Bosch, Robert

On March 15 2009 Space Shuttle Discovery was launched, carrying the Process Unit of the Protein Crystallization Diagnostics Facility (PCDF) to the International Space Station. It contained the PROTEIN experiment, aiming at the in-situ observation of nucleation and crystal growth behaviour of proteins. After installation in the European Drawer Rack (EDR) and connection to the PCDF Electronics Unit, experiment runs were performed continuously for 4 months. It was the first time that protein crystallization experiments could be modified on-orbit in near real-time, based on data received on ground. The data included pseudo-dark field microscope images, interferograms, and Dynamic Light Scattering data. The Process Unit with space grown crystals was returned to ground on July 31 2009. Results for the model protein glucose isomerase (Glucy) from Streptomyces rubiginosus crystallized with ammonium sulfate will be reported concerning nucleation and the growth from Protein and Impurities Depletion Zones (PDZs). In addition, results of x-ray analyses for space-grown crystals will be given.

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

PubMed Central

Baba, Seiki; Hoshino, Takeshi; Ito, Len; Kumasaka, Takashi

2013-01-01

Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection. PMID:23999307

Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.

PubMed

Strecker, Claas; Meyer, Bernd

2018-05-29

Protein flexibility poses a major challenge to docking of potential ligands in that the binding site can adopt different shapes. Docking algorithms usually keep the protein rigid and only allow the ligand to be treated as flexible. However, a wrong assessment of the shape of the binding pocket can prevent a ligand from adapting a correct pose. Ensemble docking is a simple yet promising method to solve this problem: Ligands are docked into multiple structures, and the results are subsequently merged. Selection of protein structures is a significant factor for this approach. In this work we perform a comprehensive and comparative study evaluating the impact of structure selection on ensemble docking. We perform ensemble docking with several crystal structures and with structures derived from molecular dynamics simulations of renin, an attractive target for antihypertensive drugs. Here, 500 ns of MD simulations revealed binding site shapes not found in any available crystal structure. We evaluate the importance of structure selection for ensemble docking by comparing binding pose prediction, ability to rank actives above nonactives (screening utility), and scoring accuracy. As a result, for ensemble definition k-means clustering appears to be better suited than hierarchical clustering with average linkage. The best performing ensemble consists of four crystal structures and is able to reproduce the native ligand poses better than any individual crystal structure. Moreover this ensemble outperforms 88% of all individual crystal structures in terms of screening utility as well as scoring accuracy. Similarly, ensembles of MD-derived structures perform on average better than 75% of any individual crystal structure in terms of scoring accuracy at all inspected ensembles sizes.

Processing materials in space - The history and the future

NASA Technical Reports Server (NTRS)

Chassay, Roger; Carswell, Bill

1987-01-01

The development of materials processing in space, and some of the Soyuz, Apollo, Skylab, and Shuttle orbital materials experiments are reviewed. Consideration is given to protein crystal growth, electrophoresis, low-gravity isoelectric focusing, phase partitioning, a monodisperse latex reactor, semiconductor crystal growth, solution crystal growth, the triglycine sulfate experiment, vapor crystal growth experiments, the mercuric iodide experiment, electronic and electrooptical materials, organic thin films and crystalline solids, deep undercooling of metals and alloys, magnetic materials, immiscible materials, metal solidification research, reluctant glass-forming materials, and containerless glass formation. The space processing apparatuses and ground facilities, for materials processing are described. Future facilities for commercial research, development, and manufacturing in space are proposed.

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.

Synthesis and Physical Properties of Liquid Crystals: An Interdisciplinary Experiment

ERIC Educational Resources Information Center

Van Hecke, Gerald R.; Karukstis, Kerry K.; Hanhan Li; Hendargo, Hansford C.; Cosand, Andrew J.; Fox, Marja M.

2005-01-01

A study involves multiple chemistry and physics concepts applied to a state of matter that has biological relevance. An experiment involving the synthesis and physical properties of liquid crystals illustrates the interdisciplinary nature of liquid crystal research and the practical devices derived from such research.

Quality Assurance on Undoped CsI Crystals for the Mu2e Experiment

DOE PAGES

Atanov, N.; Baranov, V.; Budagov, J.; ...

2017-12-21

The Mu2e experiment is constructing a calorimeter consisting of 1,348 undoped CsI crystals in two disks. Each crystal has a dimension of 34 x 34 x 200 mm 3, and is readout by a large area silicon PMT array. A series of technical specifications was defined according to physics requirements. Preproduction CsI crystals were procured from three firms: Amcrys, Saint-Gobain and Shanghai Institute of Ceramics. We report the quality assurance on crystal's scintillation properties and their radiation hardness against ionization dose and neutrons. With a fast decay time of 30 ns and a light output of more than 100 p.e./MeVmore » measured with a bi-alkali PMT, undoped CsI crystals provide a cost-effective solution for the Mu2e experiment.« less

Quality Assurance on Undoped CsI Crystals for the Mu2e Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atanov, N.; Baranov, V.; Budagov, J.

The Mu2e experiment is constructing a calorimeter consisting of 1,348 undoped CsI crystals in two disks. Each crystal has a dimension of 34 x 34 x 200 mm 3, and is readout by a large area silicon PMT array. A series of technical specifications was defined according to physics requirements. Preproduction CsI crystals were procured from three firms: Amcrys, Saint-Gobain and Shanghai Institute of Ceramics. We report the quality assurance on crystal's scintillation properties and their radiation hardness against ionization dose and neutrons. With a fast decay time of 30 ns and a light output of more than 100 p.e./MeVmore » measured with a bi-alkali PMT, undoped CsI crystals provide a cost-effective solution for the Mu2e experiment.« less

Novel approaches for targeting the adenosine A2A receptor.

PubMed

Yuan, Gengyang; Gedeon, Nicholas G; Jankins, Tanner C; Jones, Graham B

2015-01-01

The adenosine A2A receptor (A2AR) represents a drug target for a wide spectrum of diseases. Approaches for targeting this membrane-bound protein have been greatly advanced by new stabilization techniques. The resulting X-ray crystal structures and subsequent analyses provide deep insight to the A2AR from both static and dynamic perspectives. Application of this, along with other biophysical methods combined with fragment-based drug design (FBDD), has become a standard approach in targeting A2AR. Complementarities of in silico screening based- and biophysical screening assisted- FBDD are likely to feature in future approaches in identifying novel ligands against this key receptor. This review describes evolution of the above approaches for targeting A2AR and highlights key modulators identified. It includes a review of: adenosine receptor structures, homology modeling, X-ray structural analysis, rational drug design, biophysical methods, FBDD and in silico screening. As a drug target, the A2AR is attractive as its function plays a role in a wide spectrum of diseases including oncologic, inflammatory, Parkinson's and cardiovascular diseases. Although traditional approaches such as high-throughput screening and homology model-based virtual screening (VS) have played a role in targeting A2AR, numerous shortcomings have generally restricted their applications to specific ligand families. Using stabilization methods for crystallization, X-ray structures of A2AR have greatly accelerated drug discovery and influenced development of biophysical-in silico hybrid screening methods. Application of these new methods to other ARs and G-protein-coupled receptors is anticipated in the future.

Anisotropic nanocolloids: self-assembly, interfacial adsorption, and electrostatic screening

NASA Astrophysics Data System (ADS)

de Graaf, J.

2012-06-01

In this thesis we consider the influence of anisotropy on the behaviour of colloids using theory and simulations. The recent increase in the ability to synthesize anisotropic particles (cubes, caps, octapods, etc.) has led to samples of sufficient quality to perform self-assembly experiments. Our investigation is therefore particularly relevant to current and future experimental studies of colloids. We examine several topics for which shape anisotropy plays an important role: (1.) - Interfacial adsorption. We introduced the triangular-tessellation technique to approximate the surface areas and line length which are associated with a plane-particle intersection. Our method allowed us to determine the free energy of adsorption for a single irregular colloid with heterogeneous surface properties adsorbed at a flat liquid-liquid interface in the Pieranski approximation. Ellipsoids only adsorbed at the interface perpendicular to the interfacial normal. However, for cylinders we could find a metastable adsorption minimum corresponding to parallel adsorption. We also considered the possible time dependence of the adsorption process using simple dynamics. Finally, we studied the adsorption of truncated nanocubes with a contact-angle surface pattern and we observed that there are three prototypical equilibrium adsorption configurations for these particles. (2.) - Crystal-structure prediction. We extended an existing crystal-structure-prediction algorithm to predict structures for systems comprised of irregular hard particles. Using this technique we examined the high-density crystal structures for 17 irregular nonconvex shapes and we confirmed several mathematical conjectures for the packings of a large set of 142 convex polyhedra. We also proved that we have obtained the densest configurations for rhombicuboctahedra and rhombic enneacontrahedra, respectively. Moreover, we considered a family of truncated cubes, which interpolates between a cube and an octahedron, for which we obtained a fascinating richness in crystal structures. For the octahedron we determined the equation of state and we obtained a liquid, a (metastable) body-centred-cubic rotator phase, and a crystal phase. (3.) - Octapod hierarchical self-assembly. We analysed the recently observed hierarchical self-assembly of octapod-shaped nanocrystals (octapods) into three-dimensional (3D) superstructures. We constructed an empirical simulation model capable of reproducing the initial chain-formation step of the self-assembly. The van-der-Waals (vdW) interactions between octapods suspended in an (a)polar medium were obtained by means of a Hamaker-de-Boer-type integration and the nature of these interactions allowed us to justify elements of our empirical model. We used the theoretical vdW calculation, together with the experimental and simulation results, to formulate a mechanism which explained the observed self-assembly in terms of the solvent-dependence and directionality of the octapod-octapod interactions. (4.) - Ionic screening of charged Janus particles. We studied the screening of charged Janus particles in an electrolyte by primitive-model Monte Carlo (MC) simulations for a wide variety of parameters. We also introduced a method to compare these results to the predictions of nonlinear Poisson-Boltzmann (PB) theory. The comparison of MC and PB results allowed us to probe the range of validity of the PB approximation. This range of validity corresponds well to the range that was predicted by field-theoretical studies of homogeneously charged flat surfaces.

Ground Based Experiments in Support of Microgravity Research Results-Vapor Growth of Organic Nonlinear Optical Thin Film

NASA Technical Reports Server (NTRS)

Zugrav, M. Ittu; Carswell, William E.; Haulenbeek, Glen B.; Wessling, Francis C.

2001-01-01

This work is specifically focused on explaining previous results obtained for the crystal growth of an organic material in a reduced gravity environment. On STS-59, in April 1994, two experiments were conducted with N,N-dimethyl-p-(2,2-dicyanovinyl) aniline (DCVA), a promising nonlinear optical (NLO) material. The space experiments were set to reproduce laboratory experiments that yielded small, bulk crystals of DCVA. The results of the flight experiment, however, were surprising. Rather than producing a bulk single crystal, the result was the production of two high quality, single crystalline thin films. This result was even more intriguing when it is considered that thin films are more desirable for NLO applications than are bulk single crystals. Repeated attempts on the ground to reproduce these results were fruitless. A second set of flight experiments was conducted on STS-69 in September 1995. This time eight DCVA experiments were flown, with each of seven experiments containing a slight change from the first reference experiment. The reference experiment was programmed with growth conditions identical to those of the STS-59 mission. The slight variations in each of the other seven were an attempt to understand what particular parameter was responsible for the preference of thin film growth over bulk crystal growth in microgravity. Once again the results were surprising. In all eight cases thin films were grown again, albeit with varying quality. So now we were faced with a phenomenon that not only takes place in microgravity, but also is very robust, resisting all attempts to force the growth of bulk single crystals.

Colorimetric photonic hydrogel aptasensor for the screening of heavy metal ions.

PubMed

Ye, Bao-Fen; Zhao, Yuan-Jin; Cheng, Yao; Li, Ting-Ting; Xie, Zhuo-Ying; Zhao, Xiang-Wei; Gu, Zhong-Ze

2012-09-28

We have developed a robust method for the visual detection of heavy metal ions (such as Hg(2+) and Pb(2+)) by using aptamer-functionalized colloidal photonic crystal hydrogel (CPCH) films. The CPCHs were derived from a colloidal crystal array of monodisperse silica nanoparticles, which were polymerized within the polyacrylamide hydrogel. The heavy metal ion-responsive aptamers were then cross-linked in the hydrogel network. During detection, the specific binding of heavy metal ions and cross-linked single-stranded aptamers in the hydrogel network caused the hydrogel to shrink, which was detected as a corresponding blue shift in the Bragg diffraction peak position of the CPCHs. The shift value could be used to estimate, quantitatively, the amount of the target ion. It was demonstrated that our CPCH aptasensor could screen a wide concentration range of heavy metal ions with high selectivity and reversibility. In addition, these aptasensors could be rehydrated from dried gels for storage and aptamer protection. It is anticipated that our technology may also be used in the screening of a broad range of metal ions in food, drugs and the environment.

Shuttle Mission STS-50: Orbital Processing of High-Quality CdTe Compound Semiconductors Experiment: Final Flight Sample Characterization Report

NASA Technical Reports Server (NTRS)

Larson, David J.; Casagrande, Luis G.; DiMarzio, Don; Alexander, J. Iwan D.; Carlson, Fred; Lee, Taipo; Dudley, Michael; Raghathamachar, Balaji

1998-01-01

The Orbital Processing of High-Quality Doped and Alloyed CdTe Compound Semiconductors program was initiated to investigate, quantitatively, the influences of gravitationally dependent phenomena on the growth and quality of bulk compound semiconductors. The objective was to improve crystal quality (both structural and compositional) and to better understand and control the variables within the crystal growth production process. The empirical effort entailed the development of a terrestrial (one-g) experiment baseline for quantitative comparison with microgravity (mu-g) results. This effort was supported by the development of high-fidelity process models of heat transfer, fluid flow and solute redistribution, and thermo-mechanical stress occurring in the furnace, safety cartridge, ampoule, and crystal throughout the melting, seeding, crystal growth, and post-solidification processing. In addition, the sensitivity of the orbital experiments was analyzed with respect to the residual microgravity (mu-g) environment, both steady state and g-jitter. CdZnTe crystals were grown in one-g and in mu-g. Crystals processed terrestrially were grown at the NASA Ground Control Experiments Laboratory (GCEL) and at Grumman Aerospace Corporation (now Northrop Grumman Corporation). Two mu-g crystals were grown in the Crystal Growth Furnace (CGF) during the First United States Microgravity Laboratory Mission (USML-1), STS-50, June 24 - July 9, 1992.

Growth of InSb and InI Crystals on Earth and in Microgravity

NASA Technical Reports Server (NTRS)

Ostrogorsky, A. G.; Churilov, A.; Volz, M. P.; Riabov, V.; Van den Berg, L.

2015-01-01

During the past 40 years, dozens of semiconductor crystal growth experiments have been conducted in space laboratories. The subsequent analysis of the space-grown crystals revealed (i) that weak convection existed in virtually all melt-growth experiments, (ii) de-wetting significantly reduced the level of stress-induced defects, and (iii) particularly encouraging results were obtained in vapor-growth experiments. In 2002, following a decade of ground based research in growing doped Ge and GaSb crystals, a series of crystal growth experiments was performed at the ISS, within the SUBSA (Solidification Using a Baffle in Sealed Ampoules) investigation. Te- and Zn-doped InSb crystals were grown from the melt. The specially designed furnace provided a side-view of the melt and precise seeding measurement of the growth rate. At present, under sponsorship of CASIS (Center for the Advancement of Science in Space, www.iss-casis.org), we are conducting ground-based experiments with indium mono-iodide (InI) in preparation for the "SUBSA II" ISS investigation, planned for 2017. The experiments include: i) Horizontal Bridgman (HB) growth and ii) Vapor Transport (VT) growth. Finite element modeling will also be conducted, to optimize the design of the flight ampoules, for vapor and melt growth.

An experimental study of pyroxene crystallization during rapid cooling in a thermal gradient: application to komatiites

NASA Astrophysics Data System (ADS)

Bouquain, S.; Arndt, N. T.; Faure, F.; Libourel, G.

2014-07-01

To investigate the crystallization of pyroxene in spinifex-textured komatiites, we undertook a series of experiments in which compositions in the CaO-MgO-Al2O3-SiO2 CMAS system were cooled rapidly in a thermal gradient. Cooling rates were generally between 5 and 10 °C h-1, but some runs were made at 100-200 °C h-1; thermal gradients were between 10 and 20 °C cm-1. These conditions reproduced those at various depths in the crust of komatiite lava flow. The starting composition was chosen to have pigeonite on the liquidus, and most of the experimental charges crystallized zoned pigeonite-diopside crystals like those in komatiite lavas. An intriguing aspect of the experimental results was their lack of reproducibility. Some experiments crystallized forsterite, whereas others that were run under similar conditions crystallized two pyroxenes and no forsterite; some experiments were totally glassy, but others crystallized entirely to pyroxene. The degree of supercooling at the onset of pyroxene crystallization was variable, from less than 25 °C to more than 110 °C. We attribute these results to the difficulty of nucleation of pyroxene under the conditions of the experiments. In some cases forsterite crystallized metastably and modified the liquid composition to inhibit pyroxene crystallization; in others no nucleation took place until a large degree of supercooling was achieved, and then pyroxene crystallized rapidly. Pigeonite crystallized under a wide range of conditions, at cooling rates from 3 to 100 °C h-1. The notion that this mineral only forms at low cooling rates is not correct.

Crystalline heterogeneities and instabilities in thermally convecting magma chamber

NASA Astrophysics Data System (ADS)

Culha, C.; Suckale, J.; Qin, Z.

2016-12-01

A volcanic vent can supply different densities of crystals over an eruption time period. This has been seen in Hawai'i's Kilauea Iki 1959 eruption; however it is not common for all Kilauea or basaltic eruptions. We ask the question: Under what conditions can homogenous magma chamber cultivate crystalline heterogeneities? In some laboratory experiments and numerical simulations, a horizontal variation is observed. The region where crystals reside is identified as a retention zone: convection velocity balances settling velocity. Simulations and experiments that observe retention zones assume crystals do not alter the convection in the fluid. However, a comparison of experiments and simulations of convecting magma with crystals suggest that large crystal volume densities and crystal sizes alter fluid flow considerably. We introduce a computational method that fully resolves the crystalline phase. To simulate basaltic magma chambers in thermal convection, we built a numerical solver of the Navier-Stoke's equation, continuity equation, and energy equation. The modeled magma is assumed to be a viscous, incompressible fluid with a liquid and solid phase. Crystals are spherical, rigid bodies. We create Rayleigh-Taylor instability through a cool top layer and hot bottom layer and update magma density while keeping crystal temperature and size constant. Our method provides a detailed picture of magma chambers, which we compare to other models and experiments to identify when and how crystals alter magma chamber convection. Alterations include stratification, differential settling and instabilities. These characteristics are dependent on viscosity, convection vigor, crystal volume density and crystal characteristics. We reveal that a volumetric crystal density variation may occur over an eruption time period, if right conditions are met to form stratifications and instabilities in magma chambers. These conditions are realistic for Kilauea Iki's 1959 eruption.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander

Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s -1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away frommore » the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.« less

A Physical Chemistry Experiment in Polymer Crystallization Kinetics

ERIC Educational Resources Information Center

Singfield, Kathy L.; Chisholm, Roderick A.; King, Thomas L.

2012-01-01

A laboratory experiment currently used in an undergraduate physical chemistry lab to investigate the rates of crystallization of a polymer is described. Specifically, the radial growth rates of typical disc-shaped crystals, called spherulites, growing between microscope glass slides are measured and the data are treated according to polymer…

Zeolite crystal growth in space - What has been learned

NASA Technical Reports Server (NTRS)

Sacco, A., Jr.; Thompson, R. W.; Dixon, A. G.

1993-01-01

Three zeolite crystal growth experiments developed at WPI have been performed in space in last twelve months. One experiment, GAS-1, illustrated that to grow large, crystallographically uniform crystals in space, the precursor solutions should be mixed in microgravity. Another experiment evaluated the optimum mixing protocol for solutions that chemically interact ('gel') on contact. These results were utilized in setting the protocol for mixing nineteen zeolite solutions that were then processed and yielded zeolites A, X and mordenite. All solutions in which the nucleation event was influenced produced larger, more 'uniform' crystals than did identical solutions processed on earth.

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

NASA Technical Reports Server (NTRS)

Herren, B.

1992-01-01

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Cumulant Green's function calculations of plasmon satellites in bulk sodium: Influence of screening and the crystal environment

NASA Astrophysics Data System (ADS)

Zhou, Jianqiang Sky; Gatti, Matteo; Kas, J. J.; Rehr, J. J.; Reining, Lucia

2018-01-01

We present ab initio calculations of the photoemission spectra of bulk sodium using different flavors of the cumulant expansion approximation for the Green's function. In particular, we study the dispersion and intensity of the plasmon satellites. We show that the satellite spectrum is much more sensitive to many details than the quasiparticle spectrum, which suggests that the experimental investigation of satellites could yield additional information beyond the usual studies of the band structure. In particular, a comparison to the homogeneous electron gas shows that the satellites are influenced by the crystal environment, although the crystal potential in sodium is weak. Moreover, the temperature dependence of the lattice constant is reflected in the position of the satellites. Details of the screening also play an important role; in particular, the contribution of transitions from 2 s and 2 p semicore levels influences the satellites, but not the quasiparticle. Moreover, inclusion of contributions to the screening beyond the random-phase approximation has an effect on the satellites. Finally, we elucidate the importance of the coupling of electrons and holes by comparing the results of the time-ordered and the retarded cumulant expansion approximations. Again, we find small but noticeable differences. Since all the small effects add up, our most advanced calculation yields a satellite position which is improved with respect to previous calculations by almost 1 eV. This stresses the fact that the calculation of satellites is much more delicate than the calculation of a quasiparticle band structure.

Synthesis, characterization, antimicrobial screening and in silico studies of Schiff bases derived from trans-para-methoxycinnamaldehyde

NASA Astrophysics Data System (ADS)

Obasi, N. L.; Kaior, G. U.; Ibezim, A.; Ochonogor, Alfred E.; Rhyman, Lydia; Uahengo, Veikko; Lutter, Michael; Jurkschat, Klaus; Ramasami, Ponnadurai

2017-12-01

Two Schiff bases namely N,N‧-Bis-[3-(4-metoxy-phenyl)-allylidene]ethane-1,2-diamine (TPMC/EDA) and [3-(4-methoxy-phenyl)-allylidene]-phenyl-amine (TPMC/AN) were synthesized. They were characterized using elemental microanalysis, IR, NMR, UV and mass spectroscopies. Single crystals of TPMC/AN were also analyzed by X-ray diffraction and the compound was examined using B3LYP/6-311++G(d,p) method. A Monoclinic crystal system and space groups of P21/c were obtained for the crystal. Docking calculations on the compounds showed they interacted with fungal N-myristoyltransferase and bacteria DNA gyrase at 2.62-2.95 and 190.26-98.99 μM ranges. The predicted docked poses identified unique binding modes of the compounds and vital intermolecular interactions. The anti-microbial screening of the compounds were carried out against Escherichia coli, Bacillus subtillis, Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans and Aspergillus niger using agar well diffusion method. The standard drugs used were the anti-bacterial ciprofloxacin and the anti-fungal fluconazole. The compounds showed activity against all the microorganisms comparable to the used standard drugs. TPMC/EDA was more active than the standard fungal drug in the screening against the fungi strain, Aspergillus niger. It showed the MIC and IZD of 1.3 mg/ml and 9.0 mm respectively. These suggest that the compounds are potential bactericidal and fungicidal candidates.

Surrogate Seeds For Growth Of Crystals

NASA Technical Reports Server (NTRS)

Shlichta, Paul J.

1989-01-01

Larger crystals of higher quality grown. Alternative method for starting growth of crystal involves use of seed crystal of different material instead of same material as solution. Intended for growing single-crystal proteins for experiments but applicable in general to growth of crystals from solutions and to growth of semiconductor or other crystals from melts.

Microgravity

NASA Image and Video Library

2001-01-24

Experiments with colloidal solutions of plastic microspheres suspended in a liquid serve as models of how molecules interact and form crystals. For the Dynamics of Colloidal Disorder-Order Transition (CDOT) experiment, Paul Chaikin of Princeton University has identified effects that are attributable to Earth's gravity and demonstrated that experiments are needed in the microgravity of orbit. Space experiments have produced unexpected dendritic (snowflake-like) structures. To date, the largest hard sphere crystal grown is a 3 mm single crystal grown at the cool end of a ground sample. At least two more additional flight experiments are plarned aboard the International Space Station. This image is from a video downlink.

Concentration and structure inhomogeneities in GaSb(Si) single crystals grown at different heat and mass transfer conditions

NASA Astrophysics Data System (ADS)

Serebryakov, Yu. A.; Prokhorov, I. A.; Vlasov, V. N.; Korobeynikova, E. N.; Zakharov, B. G.; Shul'pina, I. L.; Marchenko, M. P.; Fryazinov, I. V.

2007-06-01

Results of ground-based experiments on crystallization of gallium antimonide on the POLIZON facility carried out within the framework of space experiment preparation aboard FOTON satellite are submitted. Technical and technological opportunities of suppression of disturbing factors for improvement of quality of grown crystals in space are substantiated. Features of formation of concentration and structure inhomogeneities in GaSb:Si crystals grown under non-stationary and stationary convection conditions are investigated. Experimental data about structure and dopant distribution inhomogeneities are discussed taking into account results of numerical researches of GaSb:Si crystallization. Also earlier received results of modeling of GaSb:Te crystallization under close temperature conditions are used. Correlation between computational and experimental data is shown. The data on intensity of flows close to crystallization front are received at which non-stationary or stationary conditions of crystallization are realized. The forecast for space conditions is made. The influence of a rotating magnetic field on convection in melt for application in space experiment projected is investigated.

Radial integrals 4f and nephelauxetic effect of Nd3+ in crystals.

PubMed

Petrov, D; Angelov, B

2014-01-24

The radial expectation values 4f,k=2, 4, 6, for oxygen- or halogen- coordinated Nd(3+) ions in 25 crystals have been obtained from experimental Slater parameter shifts ΔFk=Fk (free ion) - Fk (crystal) by means of the dielectric screening model. The 4f values found by this new approach are compatible with those computed by relativistic 4f wave functions. The nephelauxetic ratios βk in respect to the free ion Nd IV have been also determined and related to covalency and bonding parameters. Copyright © 2013 Elsevier B.V. All rights reserved.

Fluorescence Approaches to Growing Macromolecule Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

Trace fluorescent labeling, typically < 1%, can be a powerful aid in macromolecule crystallization. Precipitation concentrates a solute, and crystals are the most densely packed solid form. The more densely packed the fluorescing material, the more brightly the emission from it, and thus fluorescence intensity of a solid phase is a good indication of whether one has crystals or not. The more brightly fluorescing crystalline phase is easily distinguishable, even when embedded in an amorphous precipitate. This approach conveys several distinct advantages: one can see what the protein is doing in response to the imposed conditions, and distinguishing between amorphous and microcrystalline precipitated phases are considerably simpler. The higher fluorescence intensity of the crystalline phase led us to test if we could derive crystallization conditions from screen outcomes which had no obvious crystalline material, but simply "bright spots" in the precipitated phase. Preliminary results show that the presence of these bright spots, not observable under white light, is indeed a good indicator of potential crystallization conditions.

fcc-bcc phase transition in plasma crystals using time-resolved measurements

NASA Astrophysics Data System (ADS)

Dietz, C.; Bergert, R.; Steinmüller, B.; Kretschmer, M.; Mitic, S.; Thoma, M. H.

2018-04-01

Three-dimensional plasma crystals are often described as Yukawa systems for which a phase transition between the crystal structures fcc and bcc has been predicted. However, experimental investigations of this transition are missing. We use a fast scanning video camera to record the crystallization process of 70 000 microparticles and investigate the existence of the fcc-bcc phase transition at neutral gas pressures of 30, 40, and 50 Pa. To analyze the crystal, robust phase diagrams with the help of a machine learning algorithm are calculated. This work shows that the phase transition can be investigated experimentally and makes a comparison with numerical results of Yukawa systems. The phase transition is analyzed in dependence on the screening parameter and structural order. We suggest that the transition is an effect of gravitational compression of the plasma crystal. Experimental investigations of the fcc-bcc phase transition will provide an opportunity to estimate the coupling strength Γ by comparison with numerical results of Yukawa systems.

In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michalska, Karolina; Tan, Kemin; Chang, Changsoo

A prototype of a 96-well plate scanner forin situdata collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection atT= 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-coolingmore » can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software,in situdata collection will become available for the SBC user program including remote access.« less

A compact disk-like centrifugal microfluidic system for high-throughput nanoliter-scale protein crystallization screening.

PubMed

Li, Gang; Chen, Qiang; Li, Junjun; Hu, Xiaojian; Zhao, Jianlong

2010-06-01

A centrifuge-based microfluidic system has been developed that enables automated high-throughput and low-volume protein crystallizations. In this system, protein solution was automatically and accurately metered and dispensed into nanoliter-sized multiple reaction chambers, and it was mixed with various types of precipitants using a combination of capillary effect and centrifugal force. It has the advantages of simple fabrication, easy operation, and extremely low waste. To demonstrate the feasibility of this system, we constructed a chip containing 24 units and used it to perform lysozyme and cyan fluorescent protein (CyPet) crystallization trials. The results demonstrate that high-quality crystals can be grown and harvested from such a nanoliter-volume microfluidic system. Compared to other microfluidic technologies for protein crystallization, this microfluidic system allows zero waste, simple structure and convenient operation, which suggests that our microfluidic disk can be applied not only to protein crystallization, but also to the miniaturization of various biochemical reactions requiring precise nanoscale control.

Magnetotransport Properties in High-Quality Ultrathin Two-Dimensional Superconducting Mo2C Crystals.

PubMed

Wang, Libin; Xu, Chuan; Liu, Zhibo; Chen, Long; Ma, Xiuliang; Cheng, Hui-Ming; Ren, Wencai; Kang, Ning

2016-04-26

Ultrathin transition metal carbides are a class of developing two-dimensional (2D) materials with superconductivity and show great potentials for electrical energy storage and other applications. Here, we report low-temperature magnetotransport measurements on high-quality ultrathin 2D superconducting α-Mo2C crystals synthesized by a chemical vapor deposition method. The magnetoresistance curves exhibit reproducible oscillations at low magnetic fields for temperature far below the superconducting transition temperature of the crystals. We interpret the oscillatory magnetoresistance as a consequence of screening currents circling around the boundary of triangle-shaped terraces found on the surface of ultrathin Mo2C crystals. As the sample thickness decreases, the Mo2C crystals exhibit negative magnetoresistance deep in the superconducting transition regime, which reveals strong phase fluctuations of the superconducting order parameters associated with the superconductor-insulator transition. Our results demonstrate that the ultrathin superconducting Mo2C crystals provide an interesting system for studying rich transport phenomena in a 2D crystalline superconductor with enhanced quantum fluctuations.

Modeling of dislocation dynamics in germanium Czochralski growth

NASA Astrophysics Data System (ADS)

Artemyev, V. V.; Smirnov, A. D.; Kalaev, V. V.; Mamedov, V. M.; Sidko, A. P.; Podkopaev, O. I.; Kravtsova, E. D.; Shimansky, A. F.

2017-06-01

Obtaining very high-purity germanium crystals with low dislocation density is a practically difficult problem, which requires knowledge and experience in growth processes. Dislocation density is one of the most important parameters defining the quality of germanium crystal. In this paper, we have performed experimental study of dislocation density during 4-in. germanium crystal growth using the Czochralski method and comprehensive unsteady modeling of the same crystal growth processes, taking into account global heat transfer, melt flow and melt/crystal interface shape evolution. Thermal stresses in the crystal and their relaxation with generation of dislocations within the Alexander-Haasen model have been calculated simultaneously with crystallization dynamics. Comparison to experimental data showed reasonable agreement for the temperature, interface shape and dislocation density in the crystal between calculation and experiment.

Monomer-dependent secondary nucleation in amyloid formation.

PubMed

Linse, Sara

2017-08-01

Secondary nucleation of monomers on the surface of an already existing aggregate that is formed from the same kind of monomers may lead to autocatalytic amplification of a self-assembly process. Such monomer-dependent secondary nucleation occurs during the crystallization of small molecules or proteins and self-assembled materials, as well as in protein self-assembly into fibrous structures. Indications of secondary nucleation may come from analyses of kinetic experiments starting from pure monomers or monomers supplemented with a low concentration of pre-formed aggregates (seeds). More firm evidence requires additional experiments, for example those employing isotope labels to distinguish new aggregates arising from the monomer from those resulting from fragmentation of the seed. In cases of amyloid formation, secondary nucleation leads to the formation of toxic oligomers, and inhibitors of secondary nucleation may serve as starting points for therapeutic developments. Secondary nucleation displays a high degree of structural specificity and may be enhanced by mutations or screening of electrostatic repulsion.

A Method for Identifying Small-Molecule Aggregators Using Photonic Crystal Biosensor Microplates

PubMed Central

Chan, Leo L.; Lidstone, Erich A.; Finch, Kristin E.; Heeres, James T.; Hergenrother, Paul J.; Cunningham, Brian T.

2010-01-01

Small molecules identified through high-throughput screens are an essential element in pharmaceutical discovery programs. It is now recognized that a substantial fraction of small molecules exhibit aggregating behavior leading to false positive results in many screening assays, typically due to nonspecific attachment to target proteins. Therefore, the ability to efficiently identify compounds within a screening library that aggregate can streamline the screening process by eliminating unsuitable molecules from further consideration. In this work, we show that photonic crystal (PC) optical biosensor microplate technology can be used to identify and quantify small-molecule aggregation. A group of aggregators and nonaggregators were tested using the PC technology, and measurements were compared with those gathered by three alternative methods: dynamic light scattering (DLS), an α-chymotrypsin colorimetric assay, and scanning electron microscopy (SEM). The PC biosensor measurements of aggregation were confirmed by visual observation using SEM, and were in general agreement with the α-chymotrypsin assay. DLS measurements, in contrast, demonstrated inconsistent readings for many compounds that are found to form aggregates in shapes, very different from the classical spherical particles assumed in DLS modeling. As a label-free detection method, the PC biosensor aggregation assay is simple to implement and provides a quantitative direct measurement of the mass density of material adsorbed to the transducer surface, whereas the microplate-based sensor format enables compatibility with high-throughput automated liquid-handling methods used in pharmaceutical screening. PMID:20930952

Single-drop optimization of protein crystallization.

PubMed

Meyer, Arne; Dierks, Karsten; Hilterhaus, Dierk; Klupsch, Thomas; Mühlig, Peter; Kleesiek, Jens; Schöpflin, Robert; Einspahr, Howard; Hilgenfeld, Rolf; Betzel, Christian

2012-08-01

A completely new crystal-growth device has been developed that permits charting a course across the phase diagram to produce crystalline samples optimized for diffraction experiments. The utility of the device is demonstrated for the production of crystals for the traditional X-ray diffraction data-collection experiment, of microcrystals optimal for data-collection experiments at a modern microbeam insertion-device synchrotron beamline and of nanocrystals required for data collection on an X-ray laser beamline.

Scientist prepare Lysozyme Protein Crystal

NASA Technical Reports Server (NTRS)

1996-01-01

Dan Carter and Charles Sisk center a Lysozyme Protein crystal grown aboard the USML-2 shuttle mission. Protein isolated from hen egg-white and functions as a bacteriostatic enzyme by degrading bacterial cell walls. First enzyme ever characterized by protein crystallography. It is used as an excellent model system for better understanding parameters involved in microgravity crystal growth experiments. The goal is to compare kinetic data from microgravity experiments with data from laboratory experiments to study the equilibrium.

Purification, crystallization and initial crystallographic characterization of the Ginkgo biloba 11S seed globulin ginnacin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Tengchuan; Chen, Yu-Wei; Howard, Andrew

2008-07-01

The crystallization of ginnacin, the 11S seed storage protein from G. biloba, is reported. Ginkgo biloba, a well known ‘living fossil’ native to China, is grown worldwide as an ornamental shade plant. Medicinal and nutritional uses of G. biloba in Asia have a long history. However, ginkgo seed proteins have not been well studied at the biochemical and molecular level. In this study, the G. biloba 11S seed storage protein ginnacin was purified by sequential anion-exchange and gel-filtration chromatography. A crystallization screen was performed and well diffracting single crystals were obtained by the vapor-diffusion method. A molecular-replacement structural solution hasmore » been obtained. There are six protomers in an asymmetric unit. Structure refinement is currently in progress.« less

Crystallization of M-CSF.alpha.

DOEpatents

Pandit, Jayvardhan; Jancarik, Jarmila; Kim, Sung-Hou; Koths, Kirston; Halenbeck, Robert; Fear, Anna Lisa; Taylor, Eric; Yamamoto, Ralph; Bohm, Andrew

1999-01-01

The present invention is directed to methods for crystallizing macrophage colony stimulating factor (M-CSF) and to a crystalline M-CSF produced thereby. The present invention is also directed to methods for designing and producing M-CSF agonists and antagonists using information derived from the crystallographic structure of M-CSF. The invention is also directed to methods for screening M-CSF agonists and antagonists. In addition, the present invention is directed to an isolated, purified, soluble and functional M-CSF receptor.

Honouring Stories: Mi'kmaq Women's Experiences with Pap Screening in Eastern Canada.

PubMed

MacDonald, Catherine; Martin-Misener, Ruth; Steenbeek, Audrey; Browne, Annette

2015-03-01

Mi'kmaq women are reported to have lower rates of Papanicolaou (Pap) screening and higher rates of cervical cancer than non-Aboriginal women. This qualitative participatory study used postcolonial feminist perspectives and Indigenous principles to explore Mi'kmaq women's experiences with Pap screening within the contexts that shaped their experiences. Community facilitators assisted with the research process. Talking circles and individual in-depth interviews were conducted with 16 Mi'kmaq women. Also, health-care providers were interviewed in 2 Mi'kmaq communities. The findings indicate that historical and social contexts are shaping Mi'kmaq women's screening experiences and that these experiences are diverse, as are their understandings about screening. Some women were accessing regular screening despite challenging personal circumstances. The results highlight the need for nurses and other health-care providers to understand the uniqueness of each woman's experiences with Pap screening. Improvements in screening rates depend on multifaceted nursing approaches developed in partnership with Mi'kmaq women. Copyright© by Ingram School of Nursing, McGill University.

Skylab experiment performance evaluation manual. Appendix J: Experiment M555 gallium arsenide single crystal growth (MSFC)

NASA Technical Reports Server (NTRS)

Byers, M. S.

1973-01-01

Analyses for Experiment M555, Gallium Arsenide Single Crystal Growth (MSFC), to be used for evaluating the performance of the Skylab corollary experiments under preflight, inflight, and post-flight conditions are presented. Experiment contingency plan workaround procedure and malfunction analyses are presented in order to assist in making the experiment operationally successful.

Inexpensive Electrooptic Experiments on Liquid Crystal Displays.

ERIC Educational Resources Information Center

Ciferno, Thomas M.; And Others

1995-01-01

Describes the construction and use of an electrooptic apparatus that can be incorporated into the classroom to test liquid crystal displays (LCDs) and introduce students to experiments of an applied physics nature with very practical implications. Presents experiments that give students hands-on experience with technologies of current interest to…

Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

NASA Technical Reports Server (NTRS)

Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

1994-01-01

One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

X-ray studies of recombinant anti-testosterone Fab fragments: the use of PEG 3350 in crystallization.

PubMed

Valjakka, J; Hemminki, A; Teerinen, T; Takkinen, K; Rouvinen, J

2000-02-01

Recombinant anti-testosterone wild-type Fab fragment and mutant Fab fragments with high binding selectivity developed by protein engineering have been crystallized with and without ligands. Crystals of these Fab fragments were obtained by the vapour-diffusion technique at room temperature using solutions of PEG 3350 with various biological buffers and with a wide pH range. So far, five data sets have been collected from crystals of three Fab-antigen complexes and from two uncomplexed Fab fragments, with resolutions ranging from 2.10 to 3.1 A. Crystallization conditions for Fab fragments were found by using modifications of the low ionic strength PEG 3350 series. Suitable concentrations of PEG 400, MPD and glycerol solutions for use as cryoprotectants in PEG 3350 solutions have been determined. One useful observation was that PEG 3350 is able to work alone as a cryoprotectant. The screening protocol used requires a smaller amount of protein material to achieve auspicious pre-crystals than previously. Results support the claim that PEG 3350 is more suitable for the crystallization of Fab fragments than higher molecular weight PEGs.

Growth of triglycine sulfate (TGS) crystals by solution technique

NASA Technical Reports Server (NTRS)

Lal, R. B.; Kroes, R. L.; Wilcox, W. R.

1982-01-01

The growth of crystals from solution is greatly influenced by buoyancy driven convection. In a low-g environment, convection is greatly suppressed and diffusion becomes the predominant mechanism for thermal and mass transport. An experiment to grow TGS crystals by solution technique during the orbital Spacelab III mission has been designed. Crystals are grown by a new and unique technique of extracting heat from the crystal through a sting. The cooling at the sting tip is responsible for the desired supersaturation near the growing crystal. Calculations indicate that the cooled sting technique for solution crystal growth is necessary in low-g to maintain a maximum growth rate of 1 mm/day. Results of groundbased work in support of the flight experiment are discussed.

Analytics of crystal growth in space

NASA Technical Reports Server (NTRS)

Wilcox, W. R.; Chang, C. E.; Shlichta, P. J.; Chen, P. S.; Kim, C. K.

1974-01-01

Two crystal growth processes considered for spacelab experiments were studied to anticipate and understand phenomena not ordinarily encountered on earth. Computer calculations were performed on transport processes in floating zone melting and on growth of a crystal from solution in a spacecraft environment. Experiments intended to simulate solution growth at micro accelerations were performed.

Fabrication and Characterization of Colloidal Crystal Thin Films

ERIC Educational Resources Information Center

Rodriguez, I.; Ramiro-Manzano, F.; Meseguer, F.; Bonet, E.

2011-01-01

We present a laboratory experiment that allows undergraduate or graduate students to get introduced to colloidal crystal research concepts in an interesting way. Moreover, such experiments and studies can also be useful in the field of crystallography or solid-state physics. The work concerns the growth of colloidal crystal thin films obtained…

The cubicon method for concentrating membrane proteins in the cubic mesophase.

PubMed

Ma, Pikyee; Weichert, Dietmar; Aleksandrov, Luba A; Jensen, Timothy J; Riordan, John R; Liu, Xiangyu; Kobilka, Brian K; Caffrey, Martin

2017-09-01

The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to concentrate certain membrane proteins and complexes to values suitable for in meso crystallization and structure determination. The cubicon method described here exploits the amphiphilic nature of membrane proteins and their natural tendency to partition preferentially into lipid bilayers from aqueous solution. Using several rounds of reconstitution, the protein concentration in the bilayer of the cubic mesophase can be ramped up stepwise from less than a milligram per milliliter to tens of milligrams per milliliter for crystallogenesis. The general applicability of the method is demonstrated with five integral membrane proteins: the β 2 -adrenergic G protein-coupled receptor (β 2 AR), the peptide transporter (PepT St ), diacylglycerol kinase (DgkA), the alginate transporter (AlgE) and the cystic fibrosis transmembrane conductance regulator (CFTR). In the cases of β 2 AR, PepT St , DgkA and AlgE, an effective 20- to 45-fold concentration was realized, resulting in a protein-laden mesophase that allowed the formation of crystals using the in meso method and structure determination to resolutions ranging from 2.4 Å to 3.2 Å. In addition to opening up in meso crystallization to a broader range of integral membrane protein targets, the cubicon method should find application in situations that require membrane protein reconstitution in a lipid bilayer at high concentrations. These applications include functional and biophysical characterization studies for ligand screening, drug delivery, antibody production and protein complex formation. A typical cubicon experiment can be completed in 3-5 h.

[Development of opened instrument for generating and measuring physiological signal].

PubMed

Chen, Longcong; Hu, Guohu; Gao, Bin

2004-12-01

An opened instrument with liquid crystal display (LCD) for generating and measuring physiological signal is introduced in this paper. Based on a single-chip microcomputer. the instrument uses the technique of LCD screen to display signal wave and information, and it realizes man-machine interaction by keyboard. This instrument can produce not only defined signal in common use by utilizing important saved data and relevant arithmetic, but also user-defined signal. Therefore, it is open to produce signal. In addition, this instrument has strong extension because of its modularized design as computer, which has much function such as displaying, measuring and saving physiological signal, and many features such as low power consumption, small volume, low cost and portability. Hence this instrument is convenient for experiment teaching, clinic examining, maintaining of medical instrument.

Rapid gas hydrate formation processes: Will they work?

DOE PAGES

Brown, Thomas D.; Taylor, Charles E.; Bernardo, Mark P.

2010-06-07

Researchers at DOE’s National Energy Technology Laboratory (NETL) have been investigating the formation of synthetic gas hydrates, with an emphasis on rapid and continuous hydrate formation techniques. The investigations focused on unconventional methods to reduce dissolution, induction, nucleation and crystallization times associated with natural and synthetic hydrates studies conducted in the laboratory. Numerous experiments were conducted with various high-pressure cells equipped with instrumentation to study rapid and continuous hydrate formation. The cells ranged in size from 100 mL for screening studies to proof-of-concept studies with NETL’s 15-Liter Hydrate Cell. The results from this work demonstrate that the rapid and continuousmore » formation of methane hydrate is possible at predetermined temperatures and pressures within the stability zone of a Methane Hydrate Stability Curve.« less

Viscosity measurements of crystallizing andesite from Tungurahua volcano (Ecuador).

PubMed

Chevrel, Magdalena Oryaëlle; Cimarelli, Corrado; deBiasi, Lea; Hanson, Jonathan B; Lavallée, Yan; Arzilli, Fabio; Dingwell, Donald B

2015-03-01

Viscosity has been determined during isothermal crystallization of an andesite from Tungurahua volcano (Ecuador). Viscosity was continuously recorded using the concentric cylinder method and employing a Pt-sheathed alumina spindle at 1 bar and from 1400°C to subliquidus temperatures to track rheological changes during crystallization. The disposable spindle was not extracted from the sample but rather left in the sample during quenching thus preserving an undisturbed textural configuration of the crystals. The inspection of products quenched during the crystallization process reveals evidence for heterogeneous crystal nucleation at the spindle and near the crucible wall, as well as crystal alignment in the flow field. At the end of the crystallization, defined when viscosity is constant, plagioclase is homogeneously distributed throughout the crucible (with the single exception of experiment performed at the lowest temperature). In this experiments, the crystallization kinetics appear to be strongly affected by the stirring conditions of the viscosity determinations. A TTT (Time-Temperature-Transformation) diagram illustrating the crystallization "nose" for this andesite under stirring conditions and at ambient pressure has been constructed. We further note that at a given crystal content and distribution, the high aspect ratio of the acicular plagioclase yields a shear-thinning rheology at crystal contents as low as 13 vol %, and that the relative viscosity is higher than predicted from existing viscosity models. These viscosity experiments hold the potential for delivering insights into the relative influences of the cooling path, undercooling, and deformation on crystallization kinetics and resultant crystal morphologies, as well as their impact on magmatic viscosity.

Viscosity measurements of crystallizing andesite from Tungurahua volcano (Ecuador)

PubMed Central

Cimarelli, Corrado; deBiasi, Lea; Hanson, Jonathan B.; Lavallée, Yan; Arzilli, Fabio; Dingwell, Donald B.

2015-01-01

Abstract Viscosity has been determined during isothermal crystallization of an andesite from Tungurahua volcano (Ecuador). Viscosity was continuously recorded using the concentric cylinder method and employing a Pt‐sheathed alumina spindle at 1 bar and from 1400°C to subliquidus temperatures to track rheological changes during crystallization. The disposable spindle was not extracted from the sample but rather left in the sample during quenching thus preserving an undisturbed textural configuration of the crystals. The inspection of products quenched during the crystallization process reveals evidence for heterogeneous crystal nucleation at the spindle and near the crucible wall, as well as crystal alignment in the flow field. At the end of the crystallization, defined when viscosity is constant, plagioclase is homogeneously distributed throughout the crucible (with the single exception of experiment performed at the lowest temperature). In this experiments, the crystallization kinetics appear to be strongly affected by the stirring conditions of the viscosity determinations. A TTT (Time‐Temperature‐Transformation) diagram illustrating the crystallization “nose” for this andesite under stirring conditions and at ambient pressure has been constructed. We further note that at a given crystal content and distribution, the high aspect ratio of the acicular plagioclase yields a shear‐thinning rheology at crystal contents as low as 13 vol %, and that the relative viscosity is higher than predicted from existing viscosity models. These viscosity experiments hold the potential for delivering insights into the relative influences of the cooling path, undercooling, and deformation on crystallization kinetics and resultant crystal morphologies, as well as their impact on magmatic viscosity. PMID:27656114

Experimental Study of Sr Partitioning into Calcite at Various Linear Growth Rates and Temperatures: Preliminary Results.

NASA Astrophysics Data System (ADS)

Gabitov, R. I.; Watson, B. E.

2004-05-01

The surface of a crystal in equilibrium with surrounding fluid can have a composition that differs from the bulk crystal. If growth rate of the crystal exceeds a minimum value at which partitioning-equilibrium can be maintained, then the crystal surface composition may be "captured" by the newly-formed lattice. The degree of this entrapment increases with increasing crystal growth rate. Non-equlibrium partitioning of Sr into calcite probably occurs by this entrapment mechanism. Sr and calcite are geochemically significant in understanding the thermal history of the ocean because the substitution of Sr for Ca in calcite is temperature dependent. To improve our understanding of the partitioning of Sr into calcite, we conducted two different types of experiment: 1) calcite growth from Sr-bearing solution with analysis of the crystal cross-section by electron microprobe (bulk crystal-liquid runs); and 2) treatment of calcite cleavage surfaces with Sr-bearing solutions and examination of the top few nm surface layer by X-ray photoelectron spectroscopy (surface-liquid runs). In the series of bulk-liquid experiments crystals were grown by three different procedures: 1) precipitation on glass slide (pre-coated with calcite), where a steady flow of CaCl2 - SrCl2 and Na2CO3 solutions were mixed just before passage through a tube and allowed to drip onto a slide ("cave"-type experiments, ionic strength I=0.01); 2) growth from a CaCl2 - NH4Cl - SrCl2 solution by diffusion of CO2 from an ammonium carbonate source ("drift" experiments, I=0.52); 3) coarsening of small calcite crystals in the CaCO3-SrCO3-NaCl-H2O system at 800-950° C and 0.5-1 kb in a cold seal apparatus. The growth rate of individual crystals was determined by periodic monitoring of crystal size with time or roughly by comparison of final size with duration of the experiment. Surface-liquid experiments were performed by treatment of cleavage surfaces of natural calcite fragments in a Sr(ClO4)2 solution for 1 minute. After treatment the remaining solution was blown out by a stream of nitrogen to preclude the precipitation of Sr phase. We observed that the precipitated calcite crystals can be very different in size even if the runs have the same input rate of calcite components. The cave-type and cold-seal runs yielded 15-40 μ m calcites, but in the drift experiments crystal size varied between 60 μ m and 1 mm. Electron microprobe analysis across the large crystals show that the concentration of Sr is higher in the center and decreases toward the edge. This is probably due to the cube-root dependence of radial growth on the volume change of the growing crystals. Like previous workers who measured bulk uptake of Sr as a function of precipitation rate, we observed that increased growth rate (V, nm/s) enhances Sr uptake into the crystal, raising Kdbulk/liquid=(Sr/Ca)bulk/(Sr/Ca)liquid. Kdbulk/liquid = 0.03 to 0.06 when log(V)=-1.1 to -0.6 at 25° C in the cave-type runs (I=0.01). At higher ionic strength (I=0.52) and T=55° C, Kdbulk/liquid=0.11 to 0.15 when log(V)=-0.6 to 0.4 in the drift experiments. XPS analysis of surface-liquid experiments yielded higher Kdsurface/liquid=(Sr/Ca)surface/(Sr/Ca)liquid values compared with Kdbulk/liquid. This combined evidence supports the idea that Sr is enriched at the calcite surface relative to the bulk crystal during crystal growth.

Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology.

PubMed

Horst, Reto; Wüthrich, Kurt

2015-07-20

Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [ 2 H, 15 N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al ., 2013). 2D [ 15 N, 1 H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

Protein crystal growth results from shuttle flight 51-F

NASA Technical Reports Server (NTRS)

Bugg, C. E.

1985-01-01

The protein crystal growth (PCG) experiments run on 51-F were analyzed. It was found that: (1) sample stability is increased over that observed during the experiments on flight 51-D; (2) the dialysis experiments produced lysozyme crystals that were significantly larger than those obtained in our identical ground-based studies; (3) temperature fluctuations apparently caused problems during the crystallization experiments on 51-F; (4) it is indicated that teflon tape stabilizes droplets on the syringe tips; (5) samples survived during the reentry and landing in glass tips that were not stoppered with plungers; (6) from the ground-based studies, it was expected that equilibration should be complete within 2 to 4 days for all of these vapor-diffusion experiments, thus it appears that the vapor diffusion rates are somewhat slower under microgravity conditions; (7) drop tethering was highly successful, all four of the tethered drops were stable, even though they contained MPD solutions; (8) the PCG experiments on 51-F were done to assess the hardware and experimental procedures that are developed for future flights, when temperature control will be available. Lysozyme crystals obtained by microdialysis are considerably larger than those obtained on the ground, using the identical apparatus and procedures.

Te-and Zn-Doped InSb Crystals Grown in Microgravity

NASA Technical Reports Server (NTRS)

Ostrogorsky, A. G.; Marin, C.; Volz, M.; Bonner, W. A.; Duffar, T.

2004-01-01

In 2002, within the SUBSA (Solidification Using a Baffle in Sealed Ampoules) investigation, seven doped InSb crystals were grown in microgravity at the International Space Station. The key goals of the SUBSA investigation are: (a) to clarify the origin of the melt convection in space laboratories; (b) to reduce melt convection to the level which allows reproducible diffusion-controlled segregation; (e) to explore the submerged baffle process and liquid encapsulation in microgravity. 30 crystal growth experiments were conducted in the ground unit, to optimize the design of flight ampoules and to test the transparent SUBSA furnace developed by TecMasters Inc. The specially designed furnace, allowed observation of the crystal growth process (melting, seeding, motion of the solid-liquid interface, etc.). In the summer of 2002, eight crystal growth experiments were conducted in the Microgravity Science Glovebox (MSG) facility at the ISS. Four Te-doped (k = 0.5) and three Zn-doped (k2.9) crystals were grown on undoped seeds. In one experiment, we were not able to seed and grow. The seven grown crystals were sectioned and analyzed using SIMS. The design of the SUBSA ampoules, the segregation data and the video images obtained during the SUBSA flight experiments will be presented and discussed.

Valuing experience factors in the provision of Chlamydia screening: an application to women attending the family planning clinic.

PubMed

Watson, Verity; Ryan, Mandy; Watson, Emma

2009-06-01

To examine women's preferences for characteristics of chlamydia screening. Chlamydia trachomatis is the most common curable sexually transmitted disease. To design effective screening programs, it is important to fully capture the benefits of screening to patients. Thus, the value of experience factors must be considered alongside health outcomes. A self-complete discrete choice experiment questionnaire was administered to women attending a family planning clinic. Chlamydia screening was described by five characteristics: location of screening; type of screening test; cost of screening test; risk of developing pelvic inflammatory disease if chlamydia is untreated; and support provided when receiving results. One hundred twenty-six women completed the questionnaire. Respondents valued characteristics of the care experience. Screening was valued at 15 pound; less invasive screening tests increase willingness to pay by 7 pound, and more invasive tests reduce willingness to pay by 3.50 pound. The most preferred screening location was the family planning clinic, valued at 5 pound. The support of a trained health-care professional when receiving results was valued at 4 pound. Respondents under 25 years and those in a casual relationship were less likely to be screened. Women valued experience factors in the provision of chlamydia screening. To correctly value these screening programs and to predict uptake, cost-effectiveness studies should take such values into account. Failure to do this may result in incorrect policy recommendations.

Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering.

PubMed

Loschen, Christoph; Klamt, Andreas

2015-06-01

The fact that novel drug candidates are becoming increasingly insoluble is a major problem of current drug development. Computational tools may address this issue by screening for suitable solvents or by identifying potential novel cocrystal formers that increase bioavailability. In contrast to other more specialized methods, the fluid phase thermodynamics approach COSMO-RS (conductor-like screening model for real solvents) allows for a comprehensive treatment of drug solubility, solvate and cocrystal formation and many other thermodynamics properties in liquids. This article gives an overview of recent COSMO-RS developments that are of interest for drug development and contains several new application examples for solubility prediction and solvate/cocrystal screening. For all property predictions COSMO-RS has been used. The basic concept of COSMO-RS consists of using the screening charge density as computed from first principles calculations in combination with fast statistical thermodynamics to compute the chemical potential of a compound in solution. The fast and accurate assessment of drug solubility and the identification of suitable solvents, solvate or cocrystal formers is nowadays possible and may be used to complement modern drug development. Efficiency is increased by avoiding costly quantum-chemical computations using a database of previously computed molecular fragments. COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use. © 2015 Royal Pharmaceutical Society.

Decades of Data: Extracting Trends from Microgravity Crystallization History

NASA Technical Reports Server (NTRS)

Judge, R. A.; Snell, E. H.; Kephart, R.; vanderWoerd, M.

2004-01-01

The reduced acceleration environment of an orbiting spacecraft has been proposed as an ideal environment for biological crystal growth as the first sounding rocket flight in 1981 many crystallization experiments have flown with some showing improvement and others not. To further explore macromolecule crystal improvement in microgravity we have accumulated data from published reports and reports submitted by 63 missions including the Space Shuttle program, unmanned satellites, the Russian Space Station MIR and sounding rocket experiments. While it is not at this point in time a comprehensive record of all flight crystallization experimental results, there is however sufficient information for emerging trends to be identified. In this study the effects of the acceleration environment, the techniques of crystallization, sample molecular weight and the response of individual macromolecules to microgravity crystallization will be investigated.

Application Of Empirical Phase Diagrams For Multidimensional Data Visualization Of High Throughput Microbatch Crystallization Experiments.

PubMed

Klijn, Marieke E; Hubbuch, Jürgen

2018-04-27

Protein phase diagrams are a tool to investigate cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphological features, such as crystal size, as well as kinetic features, such as crystal growth time. Common used data visualization techniques include individual line graphs or symbols-based phase diagrams. These techniques have limitations in terms of handling large datasets, comprehensiveness or completeness. To eliminate these limitations, morphological and kinetic features obtained from crystallization images generated with high throughput microbatch experiments have been visualized with radar charts in combination with the empirical phase diagram (EPD) method. Morphological features (crystal size, shape, and number, as well as precipitate size) and kinetic features (crystal and precipitate onset and growth time) are extracted for 768 solutions with varying chicken egg white lysozyme concentration, salt type, ionic strength and pH. Image-based aggregation morphology and kinetic features were compiled into a single and easily interpretable figure, thereby showing that the EPD method can support high throughput crystallization experiments in its data amount as well as its data complexity. Copyright © 2018. Published by Elsevier Inc.

Selective and reusable iron(II)-based molecular sensor for the vapor-phase detection of alcohols.

PubMed

Naik, Anil D; Robeyns, Koen; Meunier, Christophe F; Léonard, Alexandre F; Rotaru, Aurelian; Tinant, Bernard; Filinchuk, Yaroslav; Su, Bao Lian; Garcia, Yann

2014-02-03

A mononuclear iron(II) neutral complex (1) is screened for sensing abilities for a wide spectrum of chemicals and to evaluate the response function toward physical perturbation like temperature and mechanical stress. Interestingly, 1 precisely detects methanol among an alcohol series. The sensing process is visually detectable, fatigue-resistant, highly selective, and reusable. The sensing ability is attributed to molecular sieving and subsequent spin-state change of iron centers, after a crystal-to-crystal transformation.

Nucleation, crystallization, and melting of atactic polystyrene

NASA Astrophysics Data System (ADS)

Chai, Yu; Forrest, James

Here we present the study of using low molecular weight atactic polystyrene (aPS) as the model system to understand the nucleation, crystallization, and meting behaviors of the stereo-regular polymer chains in aPS. The result is consistent with the theoretical calculation proposed by Semenov. In addition, both the crystallization and melting experiments indicate that all crystals are on or near the surface. Finally, the nucleation experiment below the glass transition temperature provides another piece of evidence of the enhanced surface dynamics in glassy polymers.

Packaging consideration of two-dimensional polymer-based photonic crystals for laser beam steering

NASA Astrophysics Data System (ADS)

Dou, Xinyuan; Chen, Xiaonan; Chen, Maggie Yihong; Wang, Alan Xiaolong; Jiang, Wei; Chen, Ray T.

2009-02-01

In this paper, we report the theoretical study of polymer-based photonic crystals for laser beam steering which is based on the superprism effect as well as the experiment fabrication of the two dimensional photonic crystals for the laser beam steering. Superprism effect, the principle for beam steering, was separately studied in details through EFC (Equifrequency Contour) analysis. Polymer based photonic crystals were fabricated through double exposure holographic interference method using SU8-2007. The experiment results were also reported.

Contortionist bubbles in andesitic enclaves: implications for gas migration and phase segregation in crystal-rich magmas.

NASA Astrophysics Data System (ADS)

Oppenheimer, J. C.; Cashman, K. V.; Rust, A.; Dobson, K. J.; Bacon, C. R.; Dingwell, D. B.

2016-12-01

In order to constrain gas migration behaviors in crystal-rich magmas, we compare results of analogue experiments to frozen structures in andesitic enclaves. In the analogue experiments air was injected into mixtures of syrup and particles sandwiched between glass plates. We observed a significant increase in bubble deformation and coalescence when particle fractions increased beyond a critical value (the random loose packing). At high particle fractions, bubble growth re-organized (compacted) the particles adjacent to the bubble walls. This caused liquid segregation into patches within the particle suspension and into large void spaces near the outer edge of experiments. We compare these experiments to void morphologies in a 58 x 70 x 73 cm andesitic enclave from silicic-andesite lava flows of Mt Mazama, Oregon (Bacon, 1986). This enclave is zoned, with a vesicle-rich center and a glass-rich rim, suggesting gas-driven melt segregation from the center to the rim. We use both 2D (optical microscopy and SEM) and 3D (X-ray tomography) techniques to image crystal textures and bubble shapes. The center of the enclave bears scattered patches of groundmass in the main phenocryst framework. These patches are similar to those observed in experiments, and thus melt segregation in the enclave may have occurred both toward the rim and toward these patches. Bubble morphologies reveal two main types of bubbles. (1) Lobate and finger-like bubbles, similar to the deformed bubbles in experiments, are found exclusively in the groundmass patches. They are also often associated with compacted crystal structures at the bubble walls. (2) Diktytaxitic textures - angular bubbles flattened against phenocrysts - are abundant in the crystal networks. These voids are entirely connected in 3D and formed the gas-rich center of the enclave. They likely represent a gas migration regime where the expanding gas front cannot deform the crystal structure but instead invades the pore-space between crystals, pushing out residual melt (filter pressing). The switch between regimes appears to depend on crystal size and aspect ratio. The similar features between bubbles in the enclave and in experiments are encouraging, and suggest that crystal-induced bubble deformation, and gas-driven melt segregation, may be common in crystal-rich magmas.

On the equivalence between Young's double-slit and crystal double-refraction interference experiments.

PubMed

Ossikovski, Razvigor; Arteaga, Oriol; Vizet, Jérémy; Garcia-Caurel, Enric

2017-08-01

We show, both analytically and experimentally, that under common experimental conditions the interference pattern produced in a classic Young's double-slit experiment is indistinguishable from that generated by means of a doubly refracting uniaxial crystal whose optic axis makes a skew angle with the light propagation direction. The equivalence between diffraction and crystal optics interference experiments, taken for granted by Arago and Fresnel in their pioneering research on the interference of polarized light beams, is thus rigorously proven.

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

DOE PAGES

Dao, E. Han; Sierra, Raymond G.; Laksmono, Hartawan; ...

2015-04-30

In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecondmore » X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.« less

Dual Telecentric Lens System For Projection Onto Tilted Toroidal Screen

NASA Technical Reports Server (NTRS)

Gold, Ronald S.; Hudyma, Russell M.

1995-01-01

System of two optical assemblies for projecting image onto tilted toroidal screen. One projection lens optimized for red and green spectral region; other for blue. Dual-channel approach offers several advantages which include: simplified color filtering, simplified chromatic aberration corrections, less complex polarizing prism arrangement, and increased throughput of blue light energy. Used in conjunction with any source of imagery, designed especially to project images formed by reflection of light from liquid-crystal light valve (LCLV).

Electrostatic interactions between ions near Thomas-Fermi substrates and the surface energy of ionic crystal at imperfect metals

PubMed Central

Kaiser, V.; Comtet, J.; Niguès, A.; Siria, A.; Coasne, B.; Bocquet, L.

2017-01-01

The electrostatic interaction between two charged particles is strongly modified in the vicinity of a metal. This situation is usually accounted for by the celebrated image charges approach, which was further extended to account for the electronic screening properties of the metal at the level of the Thomas-Fermi description. In this paper we build upon the approach by [Kornyshev et al. Zh. Eksp. Teor. Fiz., 78(3):1008–1019, 1980] and successive works to calculate the 1-body and 2-body electrostatic energy of ions near a metal in terms of the Thomas-Fermi screening length. We propose workable approximations suitable for molecular simulations of ionic systems close to metallic walls. Furthermore, we use this framework to calculate analytically the electrostatic contribution to the surface energy of a one dimensional crystal at a metallic wall and its dependence on the Thomas-Fermi screening length. These calculations provide a simple interpretation for the surface energy in terms of image charges, which allow for an estimate of interfacial properties in more complex situations of a disordered ionic liquid close to a metal surface. A counterintuitive outcome is that electronic screening, as characterized by a molecular Thomas-Fermi length ℓTF, profoundly affects the wetting of ionic systems close to a metal, in line with the recent experimental observation of capillary freezing of ionic liquids in metallic confinement. PMID:28436506

Survey Analysis of Materials Processing Experiments Aboard STS-47: Spacelab J

NASA Technical Reports Server (NTRS)

Sharpe, R. J.; Wright, M. D.

2009-01-01

This Technical Memorandum (TM) is a survey outline of materials processing experiments aboard Space Shuttle Mission STS-47: Spacelab J, a joint venture between NASA and the National Space Development Agency of Japan. The mission explored materials processing experiments including electronics and crystal growth materials, metals and alloys, glasses and ceramics, and fluids. Experiments covered include Growth of Silicone Spherical Crystals and Surface Oxidation, Growth Experiment of Narrow Band-Gap Semiconductor Lead-Tin-Tellurium Crystals in Space, Study on Solidification of Immiscible Alloys, Fabrication of Very-Low-Density, High-Stiffness Carbon Fiber/Aluminum Hybridized Composites, High Temperature Behavior of Glass, and Study of Bubble Behavior. The TM underscores the historical significance of these experiments in the context of materials processing in space.

Experiments with Cholesteric Liquid Crystals

ERIC Educational Resources Information Center

Fergason, James L.

1970-01-01

Describes laboratory experiments designed to demonstrate (1) the properties of cholesteric liquid crystals, (2) thermal mapping, (3) thermal diffusivity, (4) adiabatic expansion of rubber, and (5) measurement of radiated energy by a point source. Contains all of the information on materials and apparatus needed to perform the experiments.…

Crystal growth of artificial snow

NASA Technical Reports Server (NTRS)

Kimura, S.; Oka, A.; Taki, M.; Kuwano, R.; Ono, H.; Nagura, R.; Narimatsu, Y.; Tanii, J.; Kamimiytat, Y.

1984-01-01

Snow crystals were grown onboard the space shuttle during STS-7 and STS-8 to facilitate the investigation of crystal growth under conditions of weightlessness. The experimental design and hardware are described. Space-grown snow crystals were polyhedrons looking like spheres, which were unlike snow crystals produced in experiments on Earth.

An Apparatus for Growth of Small Crystals From Solutions.

ERIC Educational Resources Information Center

Mitrovic, Mico M.

1995-01-01

Describes an apparatus for crystal growth that was designed to study growth kinetics of small crystals from solutions and to obtain crystals of various substances. Describes the use of the apparatus in laboratory practical experiments in the field of crystal growth physics within the course "Solid State Physics". (JRH)

Coulomb crystallization in classical and quantum systems

NASA Astrophysics Data System (ADS)

Bonitz, Michael

2007-11-01

Coulomb crystallization occurs in one-component plasmas when the average interaction energy exceeds the kinetic energy by about two orders of magnitude. A simple road to reach such strong coupling consists in using external confinement potentials the strength of which controls the density. This has been succsessfully realized with ions in traps and storage rings and also in dusty plasma. Recently a three-dimensional spherical confinement could be created [1] which allows to produce spherical dust crystals containing concentric shells. I will give an overview on our recent results for these ``Yukawa balls'' and compare them to experiments. The shell structure of these systems can be very well explained by using an isotropic statically screened pair interaction. Further, the thermodynamic properties of these systems, such as the radial density distribution are discussed based on an analytical theory [3]. I then will discuss Coulomb crystallization in trapped quantum systems, such as mesoscopic electron and electron hole plasmas in coupled layers [4,5]. These systems show a very rich correlation behavior, including liquid and solid like states and bound states (excitons, biexcitons) and their crystals. On the other hand, also collective quantum and spin effects are observed, including Bose-Einstein condensation and superfluidity of bound electron-hole pairs [4]. Finally, I consider Coulomb crystallization in two-component neutral plasmas in three dimensions. I discuss the necessary conditions for crystals of heavy charges to exist in the presence of a light component which typically is in the Fermi gas or liquid state. It can be shown that their exists a critical ratio of the masses of the species of the order of 80 [5] which is confirmed by Quantum Monte Carlo simulations [6]. Familiar examples are crystals of nuclei in the core of White dwarf stars, but the results also suggest the existence of other crystals, including proton or α-particle crystals in dense matter and of hole crystals in semiconductors. [1] O. Arp, D. Block, A. Piel, and A. Melzer, Phys. Rev. Lett. 93, 165004 (2004). [2] M. Bonitz, D. Block, O. Arp, V. Golubnychiy, H. Baumgartner, P. Ludwig, A. Piel, and A. Filinov, Phys. Rev. Lett. 96, 075001 (2006). [3] C. Henning, H. Baumgartner, A. Piel, P. Ludwig, V. Golubnychiy, M. Bonitz, and D. Block, Phys. Rev. E 74, 056403 (2006) and Phys. Rev. E (2007). [4] A. Filinov, M. Bonitz, and Yu. Lozovik, Phys. Rev. Lett. 86, 3851 (2001). [5] M. Bonitz, V. Filinov, P. Levashov, V. Fortov, and H. Fehske, Phys. Rev. Lett. 95, 235006 (2005) and J. Phys. A: Math. Gen. 39, 4717 (2006). [6] Introduction to Computational Methods for Many-Body Systems, M. Bonitz and D. Semkat (eds.), Rinton Press, Princeton (2006)

Experiment 3: Zeolite Crystal Growth in Microgravity- The USML-2 Mission

NASA Technical Reports Server (NTRS)

Bac, Nurcan; Warzywoda, Juliusz; Sacco, Albert, Jr.

1998-01-01

The extensive use of zeolites and their impact on the world's economy leads to many efforts to characterize their structure, and to improve the knowledge base for nucleation and growth of these crystals. The Zeolite Crystal Growth (ZCG) experiment on USML-2 aims to enhance the understanding of nucleation and growth of zeolite crystals while attempting to provide a means of controlling the defect concentration in microgravity. Zeolites A, X, Beta, and Silicalite were grown during the 16-day USML-2 mission. The solutions where the nucleation event was controlled yielded larger and more uniform crystals of better morphology and purity than their terrestrial/control counterparts. Space-grown Beta crystals were free of line defects while terrestrial/controls had substantial defects.

Real-time optical image processing techniques

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang

1988-01-01

Nonlinear real-time optical processing on spatial pulse frequency modulation has been pursued through the analysis, design, and fabrication of pulse frequency modulated halftone screens and the modification of micro-channel spatial light modulators (MSLMs). Micro-channel spatial light modulators are modified via the Fabry-Perot method to achieve the high gamma operation required for non-linear operation. Real-time nonlinear processing was performed using the halftone screen and MSLM. The experiments showed the effectiveness of the thresholding and also showed the needs of higher SBP for image processing. The Hughes LCLV has been characterized and found to yield high gamma (about 1.7) when operated in low frequency and low bias mode. Cascading of two LCLVs should also provide enough gamma for nonlinear processing. In this case, the SBP of the LCLV is sufficient but the uniformity of the LCLV needs improvement. These include image correlation, computer generation of holograms, pseudo-color image encoding for image enhancement, and associative-retrieval in neural processing. The discovery of the only known optical method for dynamic range compression of an input image in real-time by using GaAs photorefractive crystals is reported. Finally, a new architecture for non-linear multiple sensory, neural processing has been suggested.

Utilization of oriented crystal growth for screening of aromatic carboxylic acids cocrystallization with urea

NASA Astrophysics Data System (ADS)

Przybyłek, Maciej; Ziółkowska, Dorota; Kobierski, Mirosław; Mroczyńska, Karina; Cysewski, Piotr

2016-01-01

The possibility of molecular complex formation in the solid state of urea with benzoic acid analogues was measured directly on the crystallite films deposited on the glass surface using powder X-ray diffractometry (PXRD). Obtained solid mixtures were also analyzed using Fourier transform infrared spectroscopy (FTIR). The simple droplet evaporation method was found to be efficient, robust, fast and cost-preserving approach for first stage cocrystal screening. Additionally, the application of orientation effect to cocrystal screening simplifies the analysis due to damping of majority of diffraction signals coming from coformers. During validation phase the proposed approach successfully reproduced both positive cases of cocrystallization (urea:salicylic acid and urea:4-hydroxy benzoic acid) as well as pairs of co-formers immiscible in the solid state (urea:benzoic acid and urea:acetylsalicylic acids). Based on validated approach new cocrystals of urea were identified in complexes with 3-hydroxybenzoic acid, 2,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid, 2,6-dihydroxybenzoic acid and 3,5-dihydroxybenzoic acid. In all cases formation of multicomponent crystal phase was confirmed by the appearance of new reflexes on the diffraction patterns and FTIR absorption band shifts of O-H and N-H groups.

Physical Vapor Transport of Mercurous Chloride Crystals: Design of a Microgravity Experiment

NASA Technical Reports Server (NTRS)

Duval, W, M. B.; Singh, N. B.; Glicksman, M. E.

1997-01-01

Flow field characteristics predicted from a computational model show that the dynamical state of the flow, for practical crystal growth conditions of mercurous chloride, can range from steady to unsteady. Evidence that the flow field can be strongly dominated by convection for ground-based conditions is provided by the prediction of asymmetric velocity profiles bv the model which show reasonable agreement with laser Doppler velocimetry experiments in both magnitude and planform. Unsteady flow is shown to be correlated with a degradation of crystal quality as quantified by light scattering pattern measurements, A microgravity experiment is designed to show that an experiment performed with parameters which yield an unsteady flow becomes steady (diffusive-advective) in a microgravity environment of 10(exp -3) g(sub 0) as predicted by the model, and hence yields crystals with optimal quality.

Ground state of a confined Yukawa plasma including correlation effects

NASA Astrophysics Data System (ADS)

Henning, C.; Ludwig, P.; Filinov, A.; Piel, A.; Bonitz, M.

2007-09-01

The ground state of an externally confined one-component Yukawa plasma is derived analytically using the local density approximation (LDA). In particular, the radial density profile is computed. The results are compared with the recently obtained mean-field (MF) density profile [Henning , Phys. Rev. E 74, 056403 (2006)]. While the MF results are more accurate for weak screening, the LDA with correlations included yields the proper description for large screening. By comparison with first-principles simulations for three-dimensional spherical Yukawa crystals, we demonstrate that the two approximations complement each other. Together they accurately describe the density profile in the full range of screening parameters.

Improving the apo-state detergent stability of NTS1 with CHESS for pharmacological and structural studies.

PubMed

Scott, Daniel J; Kummer, Lutz; Egloff, Pascal; Bathgate, Ross A D; Plückthun, Andreas

2014-11-01

The largest single class of drug targets is the G protein-coupled receptor (GPCR) family. Modern high-throughput methods for drug discovery require working with pure protein, but this has been a challenge for GPCRs, and thus the success of screening campaigns targeting soluble, catalytic protein domains has not yet been realized for GPCRs. Therefore, most GPCR drug screening has been cell-based, whereas the strategy of choice for drug discovery against soluble proteins is HTS using purified proteins coupled to structure-based drug design. While recent developments are increasing the chances of obtaining GPCR crystal structures, the feasibility of screening directly against purified GPCRs in the unbound state (apo-state) remains low. GPCRs exhibit low stability in detergent micelles, especially in the apo-state, over the time periods required for performing large screens. Recent methods for generating detergent-stable GPCRs, however, offer the potential for researchers to manipulate GPCRs almost like soluble enzymes, opening up new avenues for drug discovery. Here we apply cellular high-throughput encapsulation, solubilization and screening (CHESS) to the neurotensin receptor 1 (NTS1) to generate a variant that is stable in the apo-state when solubilized in detergents. This high stability facilitated the crystal structure determination of this receptor and also allowed us to probe the pharmacology of detergent-solubilized, apo-state NTS1 using robotic ligand binding assays. NTS1 is a target for the development of novel antipsychotics, and thus CHESS-stabilized receptors represent exciting tools for drug discovery. Copyright © 2014 Elsevier B.V. All rights reserved.

A historical perspective on protein crystallization from 1840 to the present day.

PubMed

Giegé, Richard

2013-12-01

Protein crystallization has been known since 1840 and can prove to be straightforward but, in most cases, it constitutes a real bottleneck. This stimulated the birth of the biocrystallogenesis field with both 'practical' and 'basic' science aims. In the early years of biochemistry, crystallization was a tool for the preparation of biological substances. Today, biocrystallogenesis aims to provide efficient methods for crystal fabrication and a means to optimize crystal quality for X-ray crystallography. The historical development of crystallization methods for structural biology occurred first in conjunction with that of biochemical and genetic methods for macromolecule production, then with the development of structure determination methodologies and, recently, with routine access to synchrotron X-ray sources. Previously, the identification of conditions that sustain crystal growth occurred mostly empirically but, in recent decades, this has moved progressively towards more rationality as a result of a deeper understanding of the physical chemistry of protein crystal growth and the use of idea-driven screening and high-throughput procedures. Protein and nucleic acid engineering procedures to facilitate crystallization, as well as crystallization methods in gelled-media or by counter-diffusion, represent recent important achievements, although the underlying concepts are old. The new nanotechnologies have brought a significant improvement in the practice of protein crystallization. Today, the increasing number of crystal structures deposited in the Protein Data Bank could mean that crystallization is no longer a bottleneck. This is not the case, however, because structural biology projects always become more challenging and thereby require adapted methods to enable the growth of the appropriate crystals, notably macromolecular assemblages. © 2013 FEBS.

Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

DOE PAGES

Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; ...

2015-06-27

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here in this study, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallizationmore » conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.« less

Protein Crystallization.

PubMed

McPherson, Alexander

2017-01-01

Protein crystallization was discovered by chance nearly 200 years ago and was developed in the late nineteenth century as a powerful purification tool, and a demonstration of chemical purity. The crystallization of proteins, nucleic acids, and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule, but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by manipulation of various parameters that include temperature, ionic strength, and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors, or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch, and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years due to the advent of practical, easy-to-use screening kits, and the application of laboratory robotics.

Liquid crystal foil for the detection of breast cancer

NASA Astrophysics Data System (ADS)

Biernat, Michał; Trzyna, Marcin; Byszek, Agnieszka; Jaremek, Henryk

2016-09-01

Breast cancer is the most common malignant tumor in females around the world, representing 25.2% of all cancers in women. About 1.7 million women were diagnosed with breast cancer worldwide in 2012 with a death rate of about 522,0001,2. The most frequently used methods in breast cancer screening are imaging methods, i.e. ultrasonography and mammography. A common feature of these methods is that they inherently involve the use of expensive and advanced equipment. The development of advanced computer systems allowed for the continuation of research started already in the 1980s3 and the use of contact thermography in breast cancer screening. The physiological basis for the application of thermography in medical imaging diagnostics is the so-called dermothermal effect related to higher metabolism rate around focal neoplastic lesion. This phenomenon can occur on breast surface as localized temperature anomalies4. The device developed by Braster is composed of a detector that works on the basis of thermotropic liquid crystals, image acquisition device and a computer system for image data processing and analysis. Production of the liquid crystal detector was based on a proprietary CLCF technology (Continuous Liquid Crystal Film). In 2014 Braster started feasibility study to prove that there is a potential for artificial intelligence in early breast cancer detection using Braster's proprietary technology. The aim of this study was to develop a computer system, using a client-server architecture, to an automatic interpretation of thermographic pictures created by the Braster devices.

Investigation of the linear and second-order nonlinear optical properties of molecular crystals within the local field theory.

PubMed

Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

2013-09-21

In this paper it is shown that modest calculations combining first principles evaluations of the molecular properties with electrostatic interaction schemes to account for the crystal environment effects are reliable for predicting and interpreting the experimentally measured electric linear and second-order nonlinear optical susceptibilities of molecular crystals within the experimental error bars. This is illustrated by considering two molecular crystals, namely: 2-methyl-4-nitroaniline and 4-(N,N-dimethylamino)-3-acetamidonitrobenzene. Three types of surrounding effects should be accounted for (i) the polarization due to the surrounding molecules, described here by static electric fields originating from their electric dipoles or charge distributions, (ii) the intermolecular interactions, which affect the geometry and particularly the molecular conformation, and (iii) the screening of the external electric field by the constitutive molecules. This study further highlights the role of electron correlation on the linear and nonlinear responses of molecular crystals and the challenge of describing frequency dispersion.

Reticular synthesis of porous molecular 1D nanotubes and 3D networks.

PubMed

Slater, A G; Little, M A; Pulido, A; Chong, S Y; Holden, D; Chen, L; Morgan, C; Wu, X; Cheng, G; Clowes, R; Briggs, M E; Hasell, T; Jelfs, K E; Day, G M; Cooper, A I

2017-01-01

Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal-organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of 'reticular synthesis', in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the 'node and strut' principles of reticular synthesis to molecular crystals.

Reticular synthesis of porous molecular 1D nanotubes and 3D networks

NASA Astrophysics Data System (ADS)

Slater, A. G.; Little, M. A.; Pulido, A.; Chong, S. Y.; Holden, D.; Chen, L.; Morgan, C.; Wu, X.; Cheng, G.; Clowes, R.; Briggs, M. E.; Hasell, T.; Jelfs, K. E.; Day, G. M.; Cooper, A. I.

2017-01-01

Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal-organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of 'reticular synthesis', in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the 'node and strut' principles of reticular synthesis to molecular crystals.

Growth of single crystals of mercuric iodide (HgI/sub 2/) in spacelab III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Den Berg, L.; Schnepple, W.F.

1981-01-01

Continued development of a system designed to grow crystals by physical vapor transport in the environment of Spacelab III will be described, with special emphasis on simulation of expected space conditions, adjustment of crystal growth parameters, and on board observation and control of the experiment by crew members and ground personnel. A critical factor in the use of mercuric iodide for semiconductor detectors of x-rays and gamma-rays is the crystalline quality of the material. The twofold purpose of the Spacelab III experiment is therefore to grow single crystals with superior electronic properties as an indirect result of the greatly reducedmore » gravity field during the growth, and to obtain data which will lead to improved understanding of the vapor transport mechanism. The experiments planned to evaluate the space crystals, including gamma-ray diffractometry and measurements of stoichiometry, lattice dimensions, mechanical strength, luminescense, and detector performance are discussed.« less

A Differential Scanning Calorimetry Method for Construction of Continuous Cooling Transformation Diagram of Blast Furnace Slag

NASA Astrophysics Data System (ADS)

Gan, Lei; Zhang, Chunxia; Shangguan, Fangqin; Li, Xiuping

2012-06-01

The continuous cooling crystallization of a blast furnace slag was studied by the application of the differential scanning calorimetry (DSC) method. A kinetic model describing the correlation between the evolution of the degree of crystallization with time was obtained. Bulk cooling experiments of the molten slag coupled with numerical simulation of heat transfer were conducted to validate the results of the DSC methods. The degrees of crystallization of the samples from the bulk cooling experiments were estimated by means of the X-ray diffraction (XRD) and the DSC method. It was found that the results from the DSC cooling and bulk cooling experiments are in good agreement. The continuous cooling transformation (CCT) diagram of the blast furnace slag was constructed according to crystallization kinetic model and experimental data. The obtained CCT diagram characterizes with two crystallization noses at different temperature ranges.

Characterization of PbWO4 crystals for high-energy physics experiments

NASA Astrophysics Data System (ADS)

Kim, M. J.; Park, H.; Kim, H. J.

2016-09-01

High-energy physics (HEP) experiments have employed many new types of scintillators. Specifically, bismuth germanate, thallium-doped cesium iodide, and lead tungstate (PbWO4, PWO) have been used for the L3 experiment; CLEO II, Belle and BES-III; and CMS, respectively. PWO has particularly beneficial properties, such as high density, fast decay time, short radiation length and radiation hardness. In this study, we tested the PWO crystals at low temperatures to determine their applicability in future calorimeters. Various crystals from the Proton Antiproton Annihilations at Darmstadt (PANDA) experiment in Giessen, the Bogoroditsk Techno-Chemical Plant (BTCP) in Russia and by Shanghai Institute of Ceramics, Chinese Academy of Sciences (SICCAS) in China were investigated. We studied the scintillation properties of PWO crystals, such as their X-ray luminescence, relative light yields, absolute light yields, energy resolutions, decay times and longitudinal uniformities of their light yields. In addition, we measured the temperature dependences of the light yields and decay times by using a 137Cs γ-ray source. The emission spectra of the PWO crystals consisted of a broad band from 350 nm to 700 nm, and the peak emission wavelength in each spectrum was 420 nm. The emission spectra of the PWO crystals from SICCAS were slightly shifted to longer wavelengths compared with those of the crystals from the other institutions.

Post-flight analyses of the crystals from the M0003-14 quartz crystal microbalance experiment

NASA Technical Reports Server (NTRS)

Stuckey, W. K.; Radhakrishnan, G.; Wallace, D.

1993-01-01

Quartz Crystal Microbalances constructed by QCM Research were flown on the leading and trailing edges of LDEF as one of the sub-experiments of M0003. Response of the crystals coated with 150 A of In2O3 was recorded during the first 424 days of the mission. A second QCM with crystals coated with 150 A of ZnS was also flown but not monitored. After the flight, the QCM's were disassembled and analyzed in The Aerospace Corporation laboratories. The samples included the crystals from the leading and trailing edge samples of both types of coatings along with the reference crystals, which were inside the QCM housing. Analyses were performed by scanning electron microscopy, energy dispersive x-ray analyses, x-ray photoelectron spectroscopy, ion microprobe mass analysis, and reflectance spectroscopy in the infrared and UV/visible regions. The crystals are contaminated predominantly with silicone compounds. The contamination is higher on the leading edge than on the trailing edge and higher on the exposed crystals than on the reference crystals.

Evolution of the Shape of Detached GeSi Crystals in Microgravity

NASA Technical Reports Server (NTRS)

Volz, M. P.; Mazuruk, K.

2013-01-01

A series of GeSi crystal growth experiments are planned to be conducted in the Low Gradient Furnace (LGF) onboard the International Space Station. An objective of these experiments is to understand the mechanisms of detached Bridgman growth, a process in which a gap exists between the growing semiconductor crystal and the crucible wall. Crystals grown without wall contact have superior quality to otherwise similar crystals grown in direct contact with a container, especially with respect to impurity incorporation, formation of dislocations, and residual stress in crystals. Numerical calculations are used to determine the conditions in which a gap can exist. According to crystal shape stability theory, only some of these gap widths will be dynamically stable. Beginning with a crystal diameter that differs from stable conditions, the transient crystal growth process is analyzed. In microgravity, dynamic stability depends only on capillary effects and is decoupled from heat transfer. Depending on the initial conditions and growth parameters, the crystal shape will evolve towards the crucible wall, towards a stable gap width, or towards the center of the crucible, collapsing the meniscus.

Highly Non-Linear Optical (NLO) organic crystals

NASA Technical Reports Server (NTRS)

Harris, J. Milton

1987-01-01

This research project involves the synthesis and characterization of organic materials having powerful nonlinear optical (NLO) properties and the growth of highly ordered crystals and monomolecular films of these materials. Research in four areas is discussed: theoretical design of new materials, characterization of NLO materials, synthesis of new materials and development of coupling procedures for forming layered films, and improvement of the techniques for vapor phase and solution phase growth of high quality organic crystals. Knowledge gained from these experiments will form the basis for experiments in the growth of these crystals.

Ultra-compact laser beam steering device using holographically formed two dimensional photonic crystal.

PubMed

Dou, Xinyuan; Chen, Xiaonan; Chen, Maggie Yihong; Wang, Alan Xiaolong; Jiang, Wei; Chen, Ray T

2010-03-01

In this paper, we report the theoretical study of polymer-based photonic crystals for laser beam steering which is based on the superprism effect as well as the experiment fabrication of the two dimensional photonic crystals for the laser beam steering. Superprism effect, the principle for beam steering, was separately studied in details through EFC (Equifrequency Contour) analysis. Polymer based photonic crystals were fabricated through double exposure holographic interference method using SU8-2007. The experiment results showed a beam steering angle of 10 degree for 30 nm wavelength variation.

Fabrication and Characterization of Three Dimensional Photonic Crystals Generated by Multibeam Interference Lithography

DTIC Science & Technology

2009-01-01

and J. A. Lewis, "Microperiodic structures - Direct writing of three-dimensional webs ," Nature, vol. 428, pp. 386-386, 2004. [9] M. Campbell, D. N...of Applied Physics Part 1-Regular Papers Brief Communications & Review Papers , vol. 44, pp. 6355-6367, 2005. [75] P. Cloetens, W. Ludwig, J... paper screen on the sample holder and marking the beam position. If the central beam is properly aligned, the spot on the screen remains at the

The future of crystallography in drug discovery

PubMed Central

Zheng, Heping; Hou, Jing; Zimmerman, Matthew D; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Introduction X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule–ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. Areas covered This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of ‘Big Data’ analysis, biochemical experimental design and structure-based drug discovery. Expert opinion Although X-ray crystallography is one of the most detailed ‘microscopes’ available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify these hypotheses. X-ray crystallography will find its future application in drug discovery by the development of specific tools that would allow realistic interpretation of the outcome coordinates and/or support testing of these hypotheses. PMID:24372145

Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment

DOE PAGES

Cha, Wonsuk; Liu, Wenjun; Harder, Ross; ...

2016-07-26

A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible with in situ sample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifyingin situchamber design. This approach was demonstrated with Au nanoparticles and will enable,more » for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.« less

Cobalt adatoms on graphene: Effects of anisotropies on the correlated electronic structure

NASA Astrophysics Data System (ADS)

Mozara, R.; Valentyuk, M.; Krivenko, I.; Şaşıoǧlu, E.; Kolorenč, J.; Lichtenstein, A. I.

2018-02-01

Impurities on surfaces experience a geometric symmetry breaking induced not only by the on-site crystal-field splitting and the orbital-dependent hybridization, but also by different screening of the Coulomb interaction in different directions. We present a many-body study of the Anderson impurity model representing a Co adatom on graphene, taking into account all anisotropies of the effective Coulomb interaction, which we obtained by the constrained random-phase approximation. The most pronounced differences are naturally displayed by the many-body self-energy projected onto the single-particle states. For the solution of the Anderson impurity model and analytical continuation of the Matsubara data, we employed new implementations of the continuous-time hybridization expansion quantum Monte Carlo and the stochastic optimization method, and we verified the results in parallel with the exact diagonalization method.

Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment.

PubMed

Cha, Wonsuk; Liu, Wenjun; Harder, Ross; Xu, Ruqing; Fuoss, Paul H; Hruszkewycz, Stephan O

2016-09-01

A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible with in situ sample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifying in situ chamber design. This approach was demonstrated with Au nanoparticles and will enable, for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.

Flight Experiments of Physical Vapor Transport of ZnSe: Growth of Crystals in Various Convective Conditions

NASA Technical Reports Server (NTRS)

Su, Ching-Hua

2015-01-01

A low gravity material experiment will be performed in the Material Science Research Rack (MSRR) on International Space Station (ISS). The flight experiment will conduct crystal growths of ZnSe and related ternary compounds, such as ZnSeS and ZnSeTe, by physical vapor transport (PVT). The main objective of the project is to determine the relative contributions of gravity-driven fluid flows to the compositional distribution, incorporation of impurities and defects, and deviation from stoichiometry observed in the grown crystals as results of buoyancy-driven convection and growth interface fluctuations caused by irregular fluid-flows on Earth. The investigation consists of extensive ground-based experimental and theoretical research efforts and concurrent flight experimentation. The objectives of the ground-based studies are (1) obtain the experimental data and conduct the analyses required to define the optimum growth parameters for the flight experiments, (2) perfect various characterization techniques to establish the standard procedure for material characterization, (3) quantitatively establish the characteristics of the crystals grown on Earth as a basis for subsequent comparative evaluations of the crystals grown in a low-gravity environment and (4) develop theoretical and analytical methods required for such evaluations. ZnSe and related ternary compounds have been grown by vapor transport technique with real time in-situ non-invasive monitoring techniques. The grown crystals have been characterized extensively by various techniques to correlate the grown crystal properties with the growth conditions. This talk will focus on the ground-based studies on the PVT crystal growth of ZnSe and related ternary compounds, especially the effects of different growth orientations related to gravity direction on the grown crystals.

A study of crystal growth by solution technique

NASA Technical Reports Server (NTRS)

Lal, R. B.

1981-01-01

The mechanism of crystal growth by solution technique was studied. A low temperature solution crystal growth setup was developed. Crystals of triglycine sulfate (TGS) were grown using this arrangement. Some additional tasks were performed toward fabrication of experiments for future space flight.

Solid Xenon Project

NASA Astrophysics Data System (ADS)

Balakishiyeva, Durdana N.; Mahapatra, Rupak; Saab, Tarek; Yoo, Jonghee

2010-08-01

Crystals like Germanium and Silicon need to be grown in specialized facilities which is time and money costly. It takes many runs to test the detector once it's manufactured and mishaps are very probable. It is of a great challenge to grow big germanium crystals and that's why stacking them up in a tower is the only way at the moment to increase testing mass. Liquid Noble gas experiments experiencing contamination problems, their predicted energy resolution at 10 keV and lower energy range is not as good as predicted. Every experiment is targeting one specific purpose, looking for one thing. Why not to design an experiment that is diverse and build a detector that can search for Dark Matter, Solar Axions, Neutrinoless Double Beta decay, etc. Solid Xenon detector is such detector. We designed a simple Xenon crystal growing chamber that was put together at Fermi National Accelerator Laboratory. The first phase of this experiment was to demonstrate that a good, crack free Xenon crystal can be grown (regardless of many failed attempts by various groups) and our first goal, 1 kg crystal, was successful.

A hetero-micro-seeding strategy for readily crystallizing closely related protein variants.

PubMed

Islam, Mohammad M; Kuroda, Yutaka

2017-11-04

Protein crystallization remains difficult to rationalize and screening for optimal crystallization conditions is a tedious and time consuming procedure. Here, we report a hetero-micro-seeding strategy for producing high resolution crystals of closely related protein variants, where micro crystals from a readily crystallized variant are used as seeds to develop crystals of other variants less amenable to crystallization. We applied this strategy to Bovine Pancreatic Trypsin Inhibitor (BPTI) variants, which would not crystallize using standard crystallization practice. Out of six variants in our analysis, only one called BPTI-[5,55]A14G formed well behaving crystals; and the remaining five (A14GA38G, A14GA38V, A14GA38L, A14GA38I, and A14GA38K) could be crystallized only using micro-seeds from the BPTI-[5,55]A14G crystal. All hetero-seeded crystals diffracted at high resolution with minimum mosaicity, retaining the same space group and cell dimension. Moreover, hetero-micro-seeding did not introduce any biases into the mutant's structure toward the seed structure, as demonstrated by A14GA38I structures solved using micro-seeds from A14GA38G, A14GA38L and A14GA38I. Though hetero-micro-seeding is a simple and almost naïve strategy, this is the first direct demonstration of its workability. We believe that hetero-micro-seeding, which is contrasting with the popular idea that crystallization requires highly purified proteins, could contribute a new tool for rapidly solving protein structures in mutational analysis studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Kotov works with Plasma Crystal-3+ Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-25

ISS022-E-035436 (25 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, works with the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Kotov works with Plasma Crystal-3+ Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-25

ISS022-E-035434 (25 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, works with the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Structural Biology of Proteins of the Multi-enzyme Assembly Human Pyruvate Dehydrogenase Complex

NASA Technical Reports Server (NTRS)

2003-01-01

Objectives and research challenges of this effort include: 1. Need to establish Human Pyruvate Dehydrogenase Complex protein crystals; 2. Need to test value of microgravity for improving crystal quality of Human Pyruvate Dehydrogenase Complex protein crystals; 3. Need to improve flight hardware in order to control and understand the effects of microgravity on crystallization of Human Pyruvate Dehydrogenase Complex proteins; 4. Need to integrate sets of national collaborations with the restricted and specific requirements of flight experiments; 5. Need to establish a highly controlled experiment in microgravity with a rigor not yet obtained; 6. Need to communicate both the rigor of microgravity experiments and the scientific value of results obtained from microgravity experiments to the national community; and 7. Need to advance the understanding of Human Pyruvate Dehydrogenase Complex structures so that scientific and commercial advance is identified for these proteins.

Using Magnetic Field Gradients to Simulate Variable Gravity in Fluids and Materials Experiments

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan

2006-01-01

Fluid flow due to a gravitational field is caused by sedimentation, thermal buoyancy, or solutal buoyancy induced convection. During crystal growth, for example, these flows are undesirable and can lead to crystal imperfections. While crystallization in microgravity can approach diffusion limited growth conditions (no convection), terrestrially strong magnetic fields can be used to control fluid flow and sedimentation effects. In this work, a theory is presented on the stability of solutal convection of a magnetized fluid(weak1y paramagnetic) in the presence of a magnetic field. The requirements for stability are developed and compared to experiments performed within the bore of a superconducting magnet. The theoretical predictions are in good agreement with the experiments. Extension of the technique can also be applied to study artificial gravity requirements for long duration exploration missions. Discussion of this application with preliminary experiments and application of the technique to crystal growth will be provided.

Adaptation of in-situ microscopy for crystallization processes

NASA Astrophysics Data System (ADS)

Bluma, A.; Höpfner, T.; Rudolph, G.; Lindner, P.; Beutel, S.; Hitzmann, B.; Scheper, T.

2009-08-01

In biotechnological and pharmaceutical engineering, the study of crystallization processes gains importance. An efficient analytical inline sensor could help to improve the knowledge about these processes in order to increase efficiency and yields. The in-situ microscope (ISM) is an optical sensor developed for the monitoring of bioprocesses. A new application for this sensor is the monitoring in downstream processes, e.g. the crystallization of proteins and other organic compounds. This contribution shows new aspects of using in-situ microscopy to monitor crystallization processes. Crystals of different chemical compounds were precipitated from supersaturated solutions and the crystal growth was monitored. Exemplified morphological properties and different forms of crystals could be distinguished on the basis of offline experiments. For inline monitoring of crystallization processes, a special 0.5 L stirred tank reactor was developed and equipped with the in-situ microscope. This reactor was utilized to carry out batch experiments for crystallizations of O-acetylsalicyclic acid (ASS) and hen egg white lysozyme (HEWL). During the whole crystallization process, the in-situ microscope system acquired images directly from the crystallization broth. For the data evaluation, an image analysis algorithm was developed and implemented in the microscope analysis software.

Curved crystals for high-resolution focusing of X and gamma rays through a Laue lens

NASA Astrophysics Data System (ADS)

Guidi, Vincenzo; Bellucci, Valerio; Camattari, Riccardo; Neri, Ilaria

2013-08-01

Crystals with curved diffracting planes have been investigated as high-efficiency optical components for the realization of a Laue lens for satellite-borne experiments in astrophysics. At Sensor and Semiconductor Laboratory (Ferrara, Italy) a research and development plan to implement Si and Ge curved crystals by surface grooving technique has been undertaken. The method of surface grooving allows obtaining Si and Ge curved crystals with self-standing curvature, i.e., with no need for external bending device, which is a mandatory issue in satellite-borne experiments. Si and Ge grooved crystals have been characterized by X-ray diffraction at ESRF and ILL to prove their functionality for a high-reflectivity Laue lens.

Crystal structure of spinach plastocyanin at 1.7 A resolution.

PubMed Central

Xue, Y.; Okvist, M.; Hansson, O.; Young, S.

1998-01-01

The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins. PMID:9792096

Liquid crystal thermography and true-colour digital image processing

NASA Astrophysics Data System (ADS)

Stasiek, J.; Stasiek, A.; Jewartowski, M.; Collins, M. W.

2006-06-01

In the last decade thermochromic liquid crystals (TLC) and true-colour digital image processing have been successfully used in non-intrusive technical, industrial and biomedical studies and applications. Thin coatings of TLCs at surfaces are utilized to obtain detailed temperature distributions and heat transfer rates for steady or transient processes. Liquid crystals also can be used to make visible the temperature and velocity fields in liquids by the simple expedient of directly mixing the liquid crystal material into the liquid (water, glycerol, glycol, and silicone oils) in very small quantities to use as thermal and hydrodynamic tracers. In biomedical situations e.g., skin diseases, breast cancer, blood circulation and other medical application, TLC and image processing are successfully used as an additional non-invasive diagnostic method especially useful for screening large groups of potential patients. The history of this technique is reviewed, principal methods and tools are described and some examples are also presented.

Holographic data storage crystals for LDEF (A0044)

NASA Technical Reports Server (NTRS)

Callen, W. R.; Gaylord, T. K.

1984-01-01

Electro-optic holographic recording systems were developed. The spaceworthiness of electro-optic crystals for use in ultrahigh capacity space data storage and retrieval systems are examined. The crystals for this experiment are included with the various electro-optical components of LDEF experiment. The effects of long-duration exposure on active optical system components is investigated. The concept of data storage in an optical-phase holographic memory is illustrated.

Crystallization of Calcium Carbonate in a Large Scale Field Study

NASA Astrophysics Data System (ADS)

Ueckert, Martina; Wismeth, Carina; Baumann, Thomas

2017-04-01

The long term efficiency of geothermal facilities and aquifer thermal energy storage in the carbonaceous Malm aquifer in the Bavarian Molasse Basin is seriously affected by precipitations of carbonates. This is mainly caused by pressure and temperature changes leading to oversaturation during production. Crystallization starts with polymorphic nuclei of calcium carbonate and is often described as diffusion-reaction controlled. Here, calcite crystallization is favoured by high concentration gradients while aragonite crystallization is occurring at high reaction rates. The factors affecting the crystallization processes have been described for simplified, well controlled laboratory experiments, the knowledge about the behaviour in more complex natural systems is still limited. The crystallization process of the polymorphic forms of calcium carbonate were investigated during a heat storage test at our test site in the eastern part of the Bavarian Molasse Basin. Complementary laboratory experiments in an autoclave were run. Both, field and laboratory experiments were conducted with carbonaceous tap water. Within the laboratory experiments additionally ultra pure water was used. To avoid precipitations of the tap water, a calculated amount of {CO_2} was added prior to heating the water from 45 - 110°C (laboratory) resp. 65 - 110°C (field). A total water volume of 0.5 L (laboratory) resp. 1 L (field) was immediately sampled and filtrated through 10 - 0.1

Novel Hybrid Virtual Screening Protocol Based on Molecular Docking and Structure-Based Pharmacophore for Discovery of Methionyl-tRNA Synthetase Inhibitors as Antibacterial Agents

PubMed Central

Liu, Chi; He, Gu; Jiang, Qinglin; Han, Bo; Peng, Cheng

2013-01-01

Methione tRNA synthetase (MetRS) is an essential enzyme involved in protein biosynthesis in all living organisms and is a potential antibacterial target. In the current study, the structure-based pharmacophore (SBP)-guided method has been suggested to generate a comprehensive pharmacophore of MetRS based on fourteen crystal structures of MetRS-inhibitor complexes. In this investigation, a hybrid protocol of a virtual screening method, comprised of pharmacophore model-based virtual screening (PBVS), rigid and flexible docking-based virtual screenings (DBVS), is used for retrieving new MetRS inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen the Specs (202,408 compounds) database, a structurally diverse chemical database. Fifteen hit compounds were selected from the final hits and shifted to experimental studies. These results may provide important information for further research of novel MetRS inhibitors as antibacterial agents. PMID:23839093

Performance evaluation of structure based and ligand based virtual screening methods on ten selected anti-cancer targets.

PubMed

Ramasamy, Thilagavathi; Selvam, Chelliah

2015-10-15

Virtual screening has become an important tool in drug discovery process. Structure based and ligand based approaches are generally used in virtual screening process. To date, several benchmark sets for evaluating the performance of the virtual screening tool are available. In this study, our aim is to compare the performance of both structure based and ligand based virtual screening methods. Ten anti-cancer targets and their corresponding benchmark sets from 'Demanding Evaluation Kits for Objective In silico Screening' (DEKOIS) library were selected. X-ray crystal structures of protein-ligand complexes were selected based on their resolution. Openeye tools such as FRED, vROCS were used and the results were carefully analyzed. At EF1%, vROCS produced better results but at EF5% and EF10%, both FRED and ROCS produced almost similar results. It was noticed that the enrichment factor values were decreased while going from EF1% to EF5% and EF10% in many cases. Published by Elsevier Ltd.

Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitors

PubMed Central

2013-01-01

We describe and apply a scaffold-focused virtual screen based upon scaffold trees to the mitotic kinase TTK (MPS1). Using level 1 of the scaffold tree, we perform both 2D and 3D similarity searches between a query scaffold and a level 1 scaffold library derived from a 2 million compound library; 98 compounds from 27 unique top-ranked level 1 scaffolds are selected for biochemical screening. We show that this scaffold-focused virtual screen prospectively identifies eight confirmed active compounds that are structurally differentiated from the query compound. In comparison, 100 compounds were selected for biochemical screening using a virtual screen based upon whole molecule similarity resulting in 12 confirmed active compounds that are structurally similar to the query compound. We elucidated the binding mode for four of the eight confirmed scaffold hops to TTK by determining their protein–ligand crystal structures; each represents a ligand-efficient scaffold for inhibitor design. PMID:23672464

Expression and X-Ray Structural Determination of the Nucleoprotein of Lassa Fever Virus.

PubMed

Qi, Xiaoxuan; Wang, Wenjian; Dong, Haohao; Liang, Yuying; Dong, Changjiang; Ly, Hinh

2018-01-01

We describe methods to express the nucleoprotein (NP) of Lassa fever virus (LASV) in E. coli, to purify and crystallize it using the sitting-drop vapor diffusion method. The crystals were screened using Rigaku micro-007 X-ray generator and a dataset was collected at a resolution of 2.36 Å. The crystals belong to space group P3, with the unit cell parameters a = b = 176.35 Å, c = 56.40 Å, α = β = 90°, and γ = 120°. Using the X-ray diffraction method, we constructed a three-dimensional structure of the LASV NP that should aid in the development of novel therapeutic strategies against this virus, for which vaccine and effective treatment modalities are currently unavailable.

One-step model of photoemission from single-crystal surfaces

DOE PAGES

Karkare, Siddharth; Wan, Weishi; Feng, Jun; ...

2017-02-28

In our paper, we present a three-dimensional one-step photoemission model that can be used to calculate the quantum efficiency and momentum distributions of electrons photoemitted from ordered single-crystal surfaces close to the photoemission threshold. Using Ag(111) as an example, we also show that the model can not only calculate the quantum efficiency from the surface state accurately without using any ad hoc parameters, but also provides a theoretical quantitative explanation of the vectorial photoelectric effect. This model in conjunction with other band structure and wave function calculation techniques can be effectively used to screen single-crystal photoemitters for use as electronmore » sources for particle accelerator and ultrafast electron diffraction applications.« less

Optimization of crystallization conditions for biological macromolecules.

PubMed

McPherson, Alexander; Cudney, Bob

2014-11-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Optimization of crystallization conditions for biological macromolecules

PubMed Central

McPherson, Alexander; Cudney, Bob

2014-01-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success. PMID:25372810

Establish an automated flow injection ESI-MS method for the screening of fragment based libraries: Application to Hsp90.

PubMed

Riccardi Sirtori, Federico; Caronni, Dannica; Colombo, Maristella; Dalvit, Claudio; Paolucci, Mauro; Regazzoni, Luca; Visco, Carlo; Fogliatto, Gianpaolo

2015-08-30

ESI-MS is a well established technique for the study of biopolymers (nucleic acids, proteins) and their non covalent adducts, due to its capacity to detect ligand-target complexes in the gas phase and allows inference of ligand-target binding in solution. In this article we used this approach to investigate the interaction of ligands to the Heat Shock Protein 90 (Hsp90). This enzyme is a molecular chaperone involved in the folding and maturation of several proteins which has been subjected in the last years to intensive drug discovery efforts due to its key role in cancer. In particular, reference compounds, with a broad range of dissociation constants from 40pM to 100μM, were tested to assess the reliability of ESI-MS for the study of protein-ligand complexes. A good agreement was found between the values measured with a fluorescence polarization displacement assay and those determined by mass spectrometry. After this validation step we describe the setup of a medium throughput screening method, based on ESI-MS, suitable to explore interactions of therapeutic relevance biopolymers with chemical libraries. Our approach is based on an automated flow injection ESI-MS method (AFI-MS) and has been applied to screen the Nerviano Medical Sciences proprietary fragment library of about 2000 fragments against Hsp90. In order to discard false positive hits and to discriminate those of them interacting with the N-terminal ATP binding site, competition experiments were performed using a reference inhibitor. Gratifyingly, this group of hits matches with the ligands previously identified by NMR FAXS techniques and confirmed by X-ray co-crystallization experiments. These results support the use of AFI-MS for the screening of medium size libraries, including libraries of small molecules with low affinity typically used in fragment based drug discovery. AFI-MS is a valid alternative to other techniques with the additional opportunities to identify compounds interacting with unpredicted or allosteric sites, without the need of any binding probes. Copyright © 2015 Elsevier B.V. All rights reserved.

The role of superheating in the formation of Glass Mountain obsidians (Long Valley, CA) inferred through crystallization of sanidine

NASA Astrophysics Data System (ADS)

Waters, Laura E.; Andrews, Benjamin J.

2016-10-01

The Glass Mountain obsidians (Long Valley, CA) are crystal poor (<8 vol%) and highly evolved (high SiO2, low Sr), and therefore, their formation required extremely efficient separation of melts from a crystal-rich source. A petrologic and experimental investigation of the mineral phases in Glass Mountain lavas identifies conditions under which phenocrysts grew and the driving mechanism for crystallization, which places constraints on the possible processes that generated the obsidians. The obsidian in this study (GM-11) is saturated in nine phases (sanidine + quartz + plagioclase + titanomagnetite + ilmenite + zircon + apatite + allanite + biotite), and results of high-resolution SEM compositional mapping and electron microprobe analysis reveal that individual sanidine crystals are normally zoned and span a range of compositions (Or40-78). Sanidines have a "granophyric" texture, characterized by intergrowths of quartz and sanidine. Mineral phases in the natural sample are compared to H2O-saturated phase equilibrium experiments conducted in cold-seal pressure vessels, over a range of conditions (700-850 °C; 75-225 MPa), and all are found to be plausible phenocrysts. Comparison of sanidine compositions from the natural sample with those grown in phase equilibrium experiments demonstrates that sanidine in the natural sample occurs in a reduced abundance. Further comparison with phase equilibrium experiments suggests that sanidine compositions track progressive loss of dissolved melt water (±cooling), suggesting that crystallization in the natural obsidian was driven predominantly by degassing resulting from decompression. It is paradoxical that an effusively (slowly) erupted lava should contain multiple phenocryst phases, including sanidine crystals that span a range of compositions with granophyric textures, and yet remain so crystal poor. To resolve this paradox, it is necessary that the solidification mechanism (degassing or cooling) that produced the sanidine crystals (and other mineral phases) must have an associated kinetic effect(s) that efficiently hinders crystal nucleation and growth. Decompression experiments conducted in this study and from the literature collectively demonstrate that the simplest way to inhibit nucleation during degassing-induced crystallization is to initiate degassing ± cooling from superliquidus conditions, and therefore, the Glass Mountain obsidians were superheated prior to crystallization.

The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

DOE PAGES

Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; ...

2016-02-24

The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. As a result, sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.

The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russi, Silvia; Song, Jinhu; McPhillips, Scott E.

The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. As a result, sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.

Studies on Aspirin Crystals Generated by a Modified Vapor Diffusion Method.

PubMed

Mittal, Amit; Malhotra, Deepak; Jain, Preeti; Kalia, Anupama; Shunmugaperumal, Tamilvanan

2016-08-01

The objectives of the current investigation were (1) to study the influence of selected two different non-solvents (diethylether and dichloromethane) on the drug crystal formation of a model drug, aspirin (ASP-I) by the modified vapor diffusion method and (2) to characterize and compare the generated crystals (ASP-II and ASP-III) using different analytical techniques with that of unprocessed ASP-I. When compared to the classical vapor diffusion method which consumes about 15 days to generate drug crystals, the modified method needs only 12 h to get the same. Fourier transform-infrared spectroscopy (FT-IR) reveals that the internal structures of ASP-II and ASP-III crystals were identical when compared with ASP-I. Although the drug crystals showed a close similarity in X-ray diffraction patterns, the difference in the relative intensities of some of the diffraction peaks (especially at 2θ values of around 7.7 and 15.5) could be attributed to the crystal habit or crystal size modification. Similarly, the differential scanning calorimetry (DSC) study speculates that only the crystal habit modifications might occur but without involving any change in internal structure of the generated drug polymorphic form I. This is further substantiated from the scanning electron microscopy (SEM) pictures that indicated the formation of platy shape for the ASP-II crystals and needle shape for the ASP-III crystals. In addition, the observed slow dissolution of ASP crystals should indicate polymorph form I formation. Thus, the modified vapor diffusion method could routinely be used to screen and legally secure all possible forms of other drug entities too.

(PCG) Protein Crystal Growth Horse Serum Albumin

NASA Technical Reports Server (NTRS)

1995-01-01

Horse Serum Albumin crystals grown during the USML-1 (STS-50) mission's Protein Crystal Growth Glovebox Experiment. These crystals were grown using a vapor diffusion technique at 22 degrees C. The crystals were allowed to grow for nine days while in orbit. Crystals of 1.0 mm in length were produced. The most abundant blood serum protein, regulates blood pressure and transports ions, metabolites, and therapeutic drugs. Principal Investigator was Edward Meehan.

Modeling of Macroscopic/Microscopic Transport and Growth Phenomena in Zeolite Crystal Solutions Under Microgravity Conditions

NASA Technical Reports Server (NTRS)

Gatsonis, Nikos A.; Alexandrou, Andreas; Shi, Hui; Ongewe, Bernard; Sacco, Albert, Jr.

1999-01-01

Crystals grown from liquid solutions have important industrial applications. Zeolites, for instance, a class of crystalline aluminosilicate materials, form the backbone of the chemical process industry worldwide, as they are used as adsorbents and catalysts. Many of the phenomena associated with crystal growth processes are not well understood due to complex microscopic and macroscopic interactions. Microgravity could help elucidate these phenomena and allow the control of defect locations, concentration, as well as size of crystals. Microgravity in an orbiting spacecraft could help isolate the possible effects of natural convection (which affects defect formation) and minimize sedimentation. In addition, crystals will stay essentially suspended in the nutrient pool under a diffusion-limited growth condition. This is expected to promote larger crystals by allowing a longer residence time in a high-concentration nutrient field. Among other factors, the crystal size distribution depends on the nucleation rate and crystallization. These two are also related to the "gel" polymerization/depolymerization rate. Macroscopic bulk mass and flow transport and especially gravity, force the crystals down to the bottom of the reactor, thus forming a sedimentation layer. In this layer, the growth rate of the crystals slows down as crystals compete for a limited amount of nutrients. The macroscopic transport phenomena under certain conditions can, however, enhance the nutrient supply and therefore, accelerate crystal growth. Several zeolite experiments have been performed in space with mixed results. The results from our laboratory have indicated an enhancement in size of 30 to 70 percent compared to the best ground based controls, and a reduction of lattice defects in many of the space grown crystals. Such experiments are difficult to interpret, and cannot be easily used to derive empirical or other laws since many physical parameters are simultaneously involved in the process. At the same time, however, there is increased urgency to develop such an understanding in order to more accurately quantify the process. In order to better understand the results obtained from our prior space experiments, and design future experiments, a detailed fluid dynamic model simulating the crystal growth mechanism is required. This will not only add to the fundamental knowledge on the crystallization of zeolites, but also be useful in predicting the limits of size and growth of these important industrial materials. Our objective is to develop macro/microscopic theoretical and computational models to study the effect of transport phenomena in the growth of crystals grown in solutions. Our effort has concentrated so far in the development of separate macroscopic and microscopic models. The major highlights of our accomplishments are described.

Effect of surface site interactions on potentiometric titration of hematite (α-Fe2O3) crystal faces.

PubMed

Chatman, Shawn; Zarzycki, P; Preočanin, T; Rosso, K M

2013-02-01

Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well-defined hematite/electrolyte interfaces. Our recently proposed thermodynamic model [1,25] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 min. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly-, doubly-, and triply-coordinated surface sites on each face. Strongly non-linear hysteretic pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly- and triply-coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals. Copyright © 2012 Elsevier Inc. All rights reserved.

Fast ultrasonic wavelength tuning in X-ray experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blagov, A. E., E-mail: blagov-ae@mail.ru; Pisarevskii, Yu. V.; Koval’chuk, M. V.

2016-03-15

A method of tuning (scanning) X-ray beam wavelength based on modulation of the lattice parameter of X-ray optical crystal by an ultrasonic standing wave excited in it has been proposed and experimentally implemented. The double-crystal antiparallel scheme of X-ray diffraction, in which an ultrasonic wave is excited in the second crystal, is used in the experiment. The profile of characteristic line k{sub α1} of an X-ray tube with a molybdenum anode is recorded using both the proposed tuning scheme and conventional mechanical rotation of crystal. The results obtained by both techniques are in good agreement.

Timing and tracking for the Crystal Barrel detector

NASA Astrophysics Data System (ADS)

Beck, Reinhard; Brinkmann, Kai; Novotny, Rainer

2017-01-01

The aim of the project D.3 is the upgrade of several detector components used in the CBELSA/TAPS experiment at ELSA. The readout of the Crystal Barrel Calorimeter will be extended by a timing branch in order to gain trigger capability for the detector, which will allow to measure completely neutral final states in photoproduction reactions (see projects A.1 and C.5). Additionally, the readout of the inner crystals of the TAPS detector, which covers the forward opening of the Crystal Barrel Calorimeter, will be modified to be capable of high event rates due to the intensity upgrade of ELSA. Furthermore, a full-scale prototype Time Projection Chamber (TPC) has been built to be used as a new central tracker for the CBELSA/TAPS experiment at ELSA and the FOPI experiment at GSI.

High-Temperature Controlled Redox Crystallization Studies

NASA Technical Reports Server (NTRS)

Williams, R. J.

1985-01-01

The crystallization of silicates containing redox sensitive ions (e.g., Fe, Ti, Ce) must be performed under controlled and known redox conditions in order to obtain the maximum scientific benefit from experimental study. Furthermore, many compositions crystallize dense phases which settle during ground-based experiments. This settling influences the texture and chemical evolution of the crystallizing system. The purpose of this investigation is to develop a test system in which controlled redox experiments can be performed in the microgravity environment. The system will use solid ceramic oxygen electrolyte cells for control, measurements, and production of the required redox conditions. A preliminary design for a prototype is developed, the electrolyte and furnace tested, and a tentative protocol for experiment developed. The control parameter is to be established and a laboratory prototype built.

Astronaut Scott Parazynski works with PCG experiment on middeck

NASA Image and Video Library

1994-11-14

STS066-13-029 (3-14 Nov 1994) --- On the Space Shuttle Atlantis' mid-deck, astronaut Scott E. Parazynski, mission specialist, works at one of two areas onboard the Shuttle which support the Protein Crystal Growth (PCG) experiment. This particular section is called the Vapor Diffusion Apparatus (VDA), housed in a Single Locker Thermal Enclosure (STES). Together with the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES) the VDA represents the continuing research into the structures of proteins and other macromolecules such as viruses. In addition to using the microgravity of space to grow high-quality protein crystals for structural analyses, the experiments are expected to help develop technologies and methods to improve the protein crystallization process on Earth as well as in space.

Inverse Band Structure Design via Materials Database Screening: Application to Square Planar Thermoelectrics

DOE PAGES

Isaacs, Eric B.; Wolverton, Chris

2018-02-26

Electronic band structure contains a wealth of information on the electronic properties of a solid and is routinely computed. However, the more difficult problem of designing a solid with a desired band structure is an outstanding challenge. In order to address this inverse band structure design problem, we devise an approach using materials database screening with materials attributes based on the constituent elements, nominal electron count, crystal structure, and thermodynamics. Our strategy is tested in the context of thermoelectric materials, for which a targeted band structure containing both flat and dispersive components with respect to crystal momentum is highly desirable.more » We screen for thermodynamically stable or metastable compounds containing d 8 transition metals coordinated by anions in a square planar geometry in order to mimic the properties of recently identified oxide thermoelectrics with such a band structure. In doing so, we identify 157 compounds out of a total of over half a million candidates. After further screening based on electronic band gap and structural anisotropy, we explicitly compute the band structures for the several of the candidates in order to validate the approach. We successfully find two new oxide systems that achieve the targeted band structure. Electronic transport calculations on these two compounds, Ba 2PdO 3 and La 4PdO 7, confirm promising thermoelectric power factor behavior for the compounds. This methodology is easily adapted to other targeted band structures and should be widely applicable to a variety of design problems.« less

Inverse Band Structure Design via Materials Database Screening: Application to Square Planar Thermoelectrics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isaacs, Eric B.; Wolverton, Chris

Electronic band structure contains a wealth of information on the electronic properties of a solid and is routinely computed. However, the more difficult problem of designing a solid with a desired band structure is an outstanding challenge. In order to address this inverse band structure design problem, we devise an approach using materials database screening with materials attributes based on the constituent elements, nominal electron count, crystal structure, and thermodynamics. Our strategy is tested in the context of thermoelectric materials, for which a targeted band structure containing both flat and dispersive components with respect to crystal momentum is highly desirable.more » We screen for thermodynamically stable or metastable compounds containing d 8 transition metals coordinated by anions in a square planar geometry in order to mimic the properties of recently identified oxide thermoelectrics with such a band structure. In doing so, we identify 157 compounds out of a total of over half a million candidates. After further screening based on electronic band gap and structural anisotropy, we explicitly compute the band structures for the several of the candidates in order to validate the approach. We successfully find two new oxide systems that achieve the targeted band structure. Electronic transport calculations on these two compounds, Ba 2PdO 3 and La 4PdO 7, confirm promising thermoelectric power factor behavior for the compounds. This methodology is easily adapted to other targeted band structures and should be widely applicable to a variety of design problems.« less

Electrostatic interactions between ions near Thomas-Fermi substrates and the surface energy of ionic crystals at imperfect metals.

PubMed

Kaiser, V; Comtet, J; Niguès, A; Siria, A; Coasne, B; Bocquet, L

2017-07-01

The electrostatic interaction between two charged particles is strongly modified in the vicinity of a metal. This situation is usually accounted for by the celebrated image charges approach, which was further extended to account for the electronic screening properties of the metal at the level of the Thomas-Fermi description. In this paper we build upon a previous approach [M. A. Vorotyntsev and A. A. Kornyshev, Zh. Eksp. Teor. Fiz., 1980, 78(3), 1008-1019] and successive works to calculate the 1-body and 2-body electrostatic energy of ions near a metal in terms of the Thomas-Fermi screening length. We propose workable approximations suitable for molecular simulations of ionic systems close to metallic walls. Furthermore, we use this framework to calculate analytically the electrostatic contribution to the surface energy of a one dimensional crystal at a metallic wall and its dependence on the Thomas-Fermi screening length. These calculations provide a simple interpretation for the surface energy in terms of image charges, which allows for an estimation of the interfacial properties in more complex situations of a disordered ionic liquid close to a metal surface. The counter-intuitive outcome is that electronic screening, as characterized by a molecular Thomas-Fermi length l TF , profoundly affects the wetting of ionic systems close to a metal, in line with the recent experimental observation of capillary freezing of ionic liquids in metallic confinement.

Calibrated LCD/TFT stimulus presentation for visual psychophysics in fMRI.

PubMed

Strasburger, H; Wüstenberg, T; Jäncke, L

2002-11-15

Standard projection techniques using liquid crystal (LCD) or thin-film transistor (TFT) technology show drastic distortions in luminance and contrast characteristics across the screen and across grey levels. Common luminance measurement and calibration techniques are not applicable in the vicinity of MRI scanners. With the aid of a fibre optic, we measured screen luminances for the full space of screen position and image grey values and on that basis developed a compensation technique that involves both luminance homogenisation and position-dependent gamma correction. By the technique described, images displayed to a subject in functional MRI can be specified with high precision by a matrix of desired luminance values rather than by local grey value.

Screening for Traumatic Experiences and Mental Health Distress Among Women in HIV Care in Cape Town, South Africa.

PubMed

Yemeke, Tatenda T; Sikkema, Kathleen J; Watt, Melissa H; Ciya, Nonceba; Robertson, Corne; Joska, John A

2017-07-01

Traumatic events can negatively affect clinical outcomes among HIV positive women, particularly when those events result in ongoing psychological distress. Consequently, there have been calls to integrate screening and treatment of traumatic experiences and associated mental health disorders into HIV care. In South Africa, screening for traumatic experiences and mental health is not a routine part of HIV care. The goal of this study was to examine the prevalence of traumatic experiences and mental health distress among women in an HIV clinic in Cape Town, South Africa, and to explore the acceptability of routine screening in this setting. Seventy HIV positive women were screened following referral from health care workers in the clinic. Among the participants, 51% reported a history of sexual abuse and 75% reported physical intimate partner violence (physical IPV). Among all participants, 36% met screening criteria for depression; among those with traumatic experiences ( n = 57), 70% met screening criteria for posttraumatic stress disorder (PTSD). Compared with reporting no sexual abuse or physical IPV, having experienced both sexual abuse and physical IPV was significantly associated with higher odds of depression, while reporting either sexual abuse or physical IPV individually was not significantly associated with increased odds of depression. Among women reporting sexual abuse, 61% were disclosing their experience for the first time during the screening; 31% of women with physical IPV experience were disclosing for the first time. Overall, 98% of participants thought screening should be routine and extended to all women as part of clinic care. Screening women for sexual abuse and physical IPV may be an important component of ensuring HIV care engagement.

Changes in copper sulfate crystal habit during cooling crystallization

NASA Astrophysics Data System (ADS)

Giulietti, M.; Seckler, M. M.; Derenzo, S.; Valarelli, J. V.

1996-09-01

The morphology of technical grade copper(II) sulfate pentahydrate crystals produced from batch cooling experiments in the temperature range of 70 to 30°C is described and correlated with the process conditions. A slow linear cooling rate (batch time of 90 min) predominantly caused the appearance of well-formed crystals. Exponential cooling (120 min) resulted in the additional formation of agglomerates and twins. The presence of seeds for both cooling modes led to round crystals, agglomerates and twins. Fast linear cooling (15 min) gave rise to a mixture of the former types. Broken crystals and adhering fragments were often found. Growth zoning was pronounced in seeded and linear cooling experiments. Fluid inclusions were always found and were more pronounced for larger particles. The occurrence of twinning, zoning and fluid inclusions was qualitatively explained in terms of fundamental principles.

CRYSTAL: The Cirrus Regional Study of Tropical Anvils and Layers

NASA Technical Reports Server (NTRS)

Delnore, Victor E.; Cox, Stephen K.; Curran, Robert J.

1999-01-01

CRYSTAL the Cirrus Regional Study of Tropical Anvils and Layers is part of the ongoing series of field experiments to study clouds and their impact on world weather and climate, and will attempt to improve the application of cloud effects in global climate models. CRYSTAL is being planned as two parts: a limited CRYSTAL field campaign in 2001 to examine towering clouds and anvil genesis over the Everglades of Florida, and the main CRYSTAL field campaign in the summer of 2003 in the Tropical Western Pacific. The latter is timed to take advantage of several cloud measurement satellites that will be operational at that time. This paper discusses some of the issues to be addressed in CRYSTAL, gives a brief description of the research plan, and describes its relationship to other important field experiments.

Ice forming experiment

NASA Technical Reports Server (NTRS)

Vali, G.

1982-01-01

A low gravity experiment to assess the effect of the presence of supercooled cloud droplets on the diffusional growth rate of ice crystals is described. The theoretical work and the feasibility studies are summarized. The nucleation of ice crystals in supercooled clouds is also discussed.

Plasma Crystal-3 Plus experiment Chamber Leak Check

NASA Image and Video Library

2010-07-01

ISS024-E-007144 (1 July 2010) --- Russian cosmonaut Alexander Skvortsov, Expedition 24 commander, performs chamber leak checks on the new Plasma Crystal-3 Plus experiment in the Poisk Mini-Research Module 2 (MRM2) of the International Space Station.

Kotov works with Plasma Crystal-3+ Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-28

ISS022-E-040614 (28 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, is pictured while working with the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Kotov works with Plasma Crystal-3 Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-25

ISS022-E-035439 (25 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, is pictured while working with the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Kotov works with Plasma Crystal-3 Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-25

ISS022-E-035438 (25 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, uses a computer while servicing the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Kotov works with Plasma Crystal-3+ Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-28

ISS022-E-040617 (28 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, is pictured while working with the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Kotov works with Plasma Crystal-3+ Experiment in the SM during Expedition 22

NASA Image and Video Library

2010-01-28

ISS022-E-040615 (28 Jan. 2010) --- Russian cosmonaut Oleg Kotov, Expedition 22 flight engineer, uses a computer while servicing the Plasma Crystal-3 experiment in the Zvezda Service Module of the International Space Station.

Skylab M518 multipurpose furnace convection analysis

NASA Technical Reports Server (NTRS)

Bourgeois, S. V.; Spradley, L. W.

1975-01-01

An analysis was performed of the convection which existed on ground tests and during skylab processing of two experiments: vapor growth of IV-VI compounds growth of spherical crystals. A parallel analysis was also performed on Skylab experiment indium antimonide crystals because indium antimonide (InSb) was used and a free surface existed in the tellurium-doped Skylab III sample. In addition, brief analyses were also performed of the microsegregation in germanium experiment because the Skylab crystals indicated turbulent convection effects. Simple dimensional analysis calculations and a more accurate, but complex, convection computer model, were used in the analysis.

KSC-97PC1382

NASA Image and Video Library

1997-09-08

United States Microgravity Payload-4 (USMP-4) experiments are prepared to be flown on Space Shuttle mission STS-87 in the Space Station Processing Facility at Kennedy Space Center (KSC). This horizontal tube is known as MEPHISTO, the French acronym for a cooperative American-French investigation of the fundamentals of crystal growth. This experiment, designed for the study of solidification (or freezing) during the growth cycle of liquid materials used for semiconductor crystals, aims to aid in the development of techniques for growing higher quality crystals on Earth. All STS-87 experiments are scheduled for launch on Nov. 19 from KSC

Sensing Coulomb impurities with 1/f noise in 3D Topological Insulator

NASA Astrophysics Data System (ADS)

Bhattacharyya, Semonti; Banerjee, Mitali; Nhalil, Hariharan; Elizabeth, Suja; Ghosh, Arindam

2015-03-01

Electrical transport in the non-trivial surface states of bulk Topological Insulator (TI) reveal several intriguing properties ranging from bipolar field effect transistor action, weak antilocalization in quantum transport, to the recently discovered quantum anomalous Hall effect. Many of these phenomena depend crucially on the nature of disorder and its screening by the Dirac Fermions at the TI surface. We have carried out a systematic study of low-frequency 1/f noise in Bi1.6Sb0.4Te2Se1 single crystals, to explore the dominant source of scattering of surface electrons and monitor relative contributions of the surface and bulk channels. Our results reveal that while trapped coulomb impurities at the substrate-TI interface are dominating source of scattering for thin (10 nm) TI, charged crystal disorder contribute strongly in thick TI (110 nm) channels. An unexpected maximum at 25K in noise from thick TI devices indicate scattering of the surface states by a cooperative charge dynamics in the bulk of the TI, possibly associated with the Selenium vacancies. Our experiment demonstrates, for the first time, impact of the bulk charge distribution on the surface state transport in TIs that could be crucial to the implementation of these materials in electronic applications.

Vertical dielectric screening of few-layer van der Waals semiconductors.

PubMed

Koo, Jahyun; Gao, Shiyuan; Lee, Hoonkyung; Yang, Li

2017-10-05

Vertical dielectric screening is a fundamental parameter of few-layer van der Waals two-dimensional (2D) semiconductors. However, unlike the widely-accepted wisdom claiming that the vertical dielectric screening is sensitive to the thickness, our first-principles calculation based on the linear response theory (within the weak field limit) reveals that this screening is independent of the thickness and, in fact, it is the same as the corresponding bulk value. This conclusion is verified in a wide range of 2D paraelectric semiconductors, covering narrow-gap ones and wide-gap ones with different crystal symmetries, providing an efficient and reliable way to calculate and predict static dielectric screening of reduced-dimensional materials. Employing this conclusion, we satisfactorily explain the tunable band gap in gated 2D semiconductors. We further propose to engineer the vertical dielectric screening by changing the interlayer distance via vertical pressure or hybrid structures. Our predicted vertical dielectric screening can substantially simplify the understanding of a wide range of measurements and it is crucial for designing 2D functional devices.

Synthesis and Screening of Phase Change Chalcogenide Thin Film Materials for Data Storage.

PubMed

Guerin, Samuel; Hayden, Brian; Hewak, Daniel W; Vian, Chris

2017-07-10

A combinatorial synthetic methodology based on evaporation sources under an ultrahigh vacuum has been used to directly synthesize compositional gradient thin film libraries of the amorphous phases of GeSbTe alloys at room temperature over a wide compositional range. An optical screen is described that allows rapid parallel mapping of the amorphous-to-crystalline phase transition temperature and optical contrast associated with the phase change on such libraries. The results are shown to be consistent with the literature for compositions where published data are available along the Sb 2 Te 3 -GeTe tie line. The results reveal a minimum in the crystallization temperature along the Sb 2 Te 3 -Ge 2 Te 3 tie line, and the method is able to resolve subsequent cubic-to-hexagonal phase transitions in the GST crystalline phase. HT-XRD has been used to map the phases at sequentially higher temperatures, and the results are reconciled with the literature and trends in crystallization temperatures. The results clearly delineate compositions that crystallize to pure GST phases and those that cocrystallize Te. High-throughput measurement of the resistivity of the amorphous and crystalline phases has allowed the compositional and structural correlation of the resistivity contrast associated with the amorphous-to-crystalline transition, which range from 5-to-8 orders of magnitude for the compositions investigated. The results are discussed in terms of the compromises in the selection of these materials for phase change memory applications and the potential for further exploration through more detailed secondary screening of doped GST or similar classes of phase change materials designed for the demands of future memory devices.

Structure and crystallization of SiO2 and B2O3 doped lithium disilicate glasses from theory and experiment.

PubMed

Erlebach, Andreas; Thieme, Katrin; Sierka, Marek; Rüssel, Christian

2017-09-27

Solid solutions of SiO 2 and B 2 O 3 in Li 2 O·2SiO 2 are synthesized and characterized for the first time. Their structure and crystallization mechanisms are investigated employing a combination of simulations at the density functional theory level and experiments on the crystallization of SiO 2 and B 2 O 3 doped lithium disilicate glasses. The remarkable agreement of calculated and experimentally determined cell parameters reveals the preferential, kinetically controlled incorporation of [SiO 4 ] and [BO 4 ] at the Li + lattice sites of the Li 2 O·2SiO 2 crystal structure. While the addition of SiO 2 increases the glass viscosity resulting in lower crystal growth velocities, glasses containing B 2 O 3 show a reduction of both viscosities and crystal growth velocities. These observations could be rationalized by a change of the chemical composition of the glass matrix surrounding the precipitated crystal phase during the course of crystallization, which leads to a deceleration of the attachment of building units required for further crystal growth at the liquid-crystal interface.

STS-34: Mission Overview Briefing

NASA Technical Reports Server (NTRS)

1989-01-01

Live footage shows Milt Heflin, the Lead Flight Director participating in the STS-34 Mission Briefing. He addresses the primary objective, and answered questions from the audience and other NASA Centers. Heflin also mentions the Shuttle Solar Backscatter Ultraviolet secondary payload, and several experiments. These experiments include Growth Hormone Crystal Distribution (Plants), Polymer Morphology, Sensor Technology Experiment, Mesoscale Lightning Experiment, Shuttle Student Involvement Program "Ice Crystals", and the Air Force Maui Optical Site.

Molecular dynamic simulation of weakly magnetized complex plasmas

NASA Astrophysics Data System (ADS)

Funk, Dylan; Konopka, Uwe; Thomas, Edward

2017-10-01

A complex plasma consists of the usual plasma components (electrons, ions and neutrals), as well as a heavier component made of solid, micrometer-sized particles. The particles are in general highly charged as a result of the interaction with the other plasma components. The static and dynamic properties of a complex plasma such as its crystal structure or wave properties are influenced by many forces acting on the individual particles such as the dust particle interaction (a screened Coulomb interaction), neutral (Epstein) drag, the particle inertia and various plasma drag or thermophoretic forces. To study the behavior of complex plasmas we setup an experiment accompanying molecular dynamic simulation. We will present the approach taken in our simulation and give an overview of experimental situations that we want to cover with our simulation such as the particle charge under microgravity condition as performed on the PK-4 space experiment, or to study the detailed influences of high magnetic fields. This work was supported by the US Dept. of Energy (DE-SC0016330), NSF (PHY-1613087) and JPL/NASA (JPL-RSA 1571699).

How the ESRF helps industry and how they help the ESRF

PubMed Central

Malbet-Monaco, Stéphanie; Leonard, Gordon A.; Mitchell, Edward P.; Gordon, Elspeth J.

2013-01-01

The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-­ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF’s industrial clients have been a major driving force in the evolution of the ESRF’s macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments. This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry. PMID:23793155

Electro-optic control of photographic imaging quality through ‘Smart Glass’ windows in optics demonstrations

NASA Astrophysics Data System (ADS)

Ozolinsh, Maris; Paulins, Paulis

2017-09-01

An experimental setup allowing the modeling of conditions in optical devices and in the eye at various degrees of scattering such as cataract pathology in human eyes is presented. The scattering in cells of polymer-dispersed liquid crystals (PDLCs) and ‘Smart Glass’ windows is used in the modeling experiments. Both applications are used as optical obstacles placed in different positions of the optical information flow pathway either directly on the stimuli demonstration computer screen or mounted directly after the image-formation lens of a digital camera. The degree of scattering is changed continuously by applying an AC voltage of up to 30-80 V to the PDLC cell. The setup uses a camera with 14 bit depth and a 24 mm focal length lens. Light-emitting diodes and diode-pumped solid-state lasers emitting radiation of different wavelengths are used as portable small-divergence light sources in the experiments. Image formation, optical system point spread function, modulation transfer functions, and system resolution limits are determined for such sample optical systems in student optics and optometry experimental exercises.

Liquid Crystals: The Phase of the Future.

ERIC Educational Resources Information Center

Ondris-Crawford, Renate; And Others

1992-01-01

Liquid crystal displays are currently utilized to convey information via graphic displays. Presents experiments and explanations that employ the concept of liquid crystals to learn concepts related to the various states of matter, electric and magnetic forces, refraction of light, and optics. Discusses applications of liquid crystal technology.…

Cohesive finite element modeling of the delamination of HTPB binder and HMX crystals under tensile loading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walters, David J.; Luscher, Darby J.; Yeager, John D.

Accurately modeling the mechanical behavior of the polymer binders and the degradation of interfaces between binder and crystal is important to science-based understanding of the macro-scale response of polymer bonded explosives. The paper presents a description of relatively a simple bi-crystal HMX-HTPB specimen and associated tensile loading experiment including computed tomography imaging, the pertinent constitutive theory, and details of numerical simulations used to infer the behavior of the material during the delamination process. Within this work, mechanical testing and direct numerical simulation of this relatively simple bi-crystal system enabled reasonable isolation of binder-crystal interface delamination, in which the effects ofmore » the complicated thermomechanical response of explosive crystals were minimized. Cohesive finite element modeling of the degradation and delamination of the interface between a modified HTPB binder and HMX crystals was used to reproduce observed results from tensile loading experiments on bi-crystal specimens. Several comparisons are made with experimental measurements in order to identify appropriate constitutive behavior of the binder and appropriate parameters for the cohesive traction-separation behavior of the crystal-binder interface. This research demonstrates the utility of directly modeling the delamination between binder and crystal within crystal-binder-crystal tensile specimen towards characterizing the behavior of these interfaces in a manner amenable to larger scale simulation of polycrystalline PBX materials. One critical aspect of this approach is micro computed tomography imaging conducted during the experiments, which enabled comparison of delamination patterns between the direct numerical simulation and actual specimen. In addition to optimizing the cohesive interface parameters, one important finding from this investigation is that understanding and representing the strain-hardening plasticity of HTPB binder is important within the context of using a cohesive traction-separation model for the delamination of a crystal-binder system.« less

Cohesive finite element modeling of the delamination of HTPB binder and HMX crystals under tensile loading

DOE PAGES

Walters, David J.; Luscher, Darby J.; Yeager, John D.; ...

2018-02-27

Accurately modeling the mechanical behavior of the polymer binders and the degradation of interfaces between binder and crystal is important to science-based understanding of the macro-scale response of polymer bonded explosives. The paper presents a description of relatively a simple bi-crystal HMX-HTPB specimen and associated tensile loading experiment including computed tomography imaging, the pertinent constitutive theory, and details of numerical simulations used to infer the behavior of the material during the delamination process. Within this work, mechanical testing and direct numerical simulation of this relatively simple bi-crystal system enabled reasonable isolation of binder-crystal interface delamination, in which the effects ofmore » the complicated thermomechanical response of explosive crystals were minimized. Cohesive finite element modeling of the degradation and delamination of the interface between a modified HTPB binder and HMX crystals was used to reproduce observed results from tensile loading experiments on bi-crystal specimens. Several comparisons are made with experimental measurements in order to identify appropriate constitutive behavior of the binder and appropriate parameters for the cohesive traction-separation behavior of the crystal-binder interface. This research demonstrates the utility of directly modeling the delamination between binder and crystal within crystal-binder-crystal tensile specimen towards characterizing the behavior of these interfaces in a manner amenable to larger scale simulation of polycrystalline PBX materials. One critical aspect of this approach is micro computed tomography imaging conducted during the experiments, which enabled comparison of delamination patterns between the direct numerical simulation and actual specimen. In addition to optimizing the cohesive interface parameters, one important finding from this investigation is that understanding and representing the strain-hardening plasticity of HTPB binder is important within the context of using a cohesive traction-separation model for the delamination of a crystal-binder system.« less

Monitoring and modeling of ultrasonic wave propagation in crystallizing mixtures

NASA Astrophysics Data System (ADS)

Marshall, T.; Challis, R. E.; Tebbutt, J. S.

2002-05-01

The utility of ultrasonic compression wave techniques for monitoring crystallization processes is investigated in a study of the seeded crystallization of copper II sulfate pentahydrate from aqueous solution. Simple models are applied to predict crystal yield, crystal size distribution and the changing nature of the continuous phase. A scattering model is used to predict the ultrasonic attenuation as crystallization proceeds. Experiments confirm that modeled attenuation is in agreement with measured results.

Containerless processing of single crystals in low-G environment

NASA Technical Reports Server (NTRS)

Walter, H. U.

1974-01-01

Experiments on containerless crystal growth from the melt were conducted during Skylab missions SL3 and SL4 (Skylab Experiment M-560). Six samples of InSb were processed, one of them heavily doped with selenium. The concept of the experiment is discussed and related to general crystal growth methods and their merits as techniques for containerless processing in space. The morphology of the crystals obtained is explained in terms of volume changes associated with solidification and wetting conditions during solidification. All samples exhibit extremely well developed growth facets. Analysis by X-ray topographical methods and chemical etching shows that the crystals are of high structural perfection. Average dislocation density as revealed by etching is of the order of 100 per sq cm; no dislocation clusters could be observed in the space-grown samples. A sequence of striations that is observed in the first half of the selenium-doped sample is explained as being caused by periodic surface breakdown.

Preliminary Work in Obtaining Site-Directed Mutants of Hen Egg White Lysozyme

NASA Technical Reports Server (NTRS)

Holmes, Leonard D.

1996-01-01

Protein crystal growth studies are recognized as a critical endeavor in the field of molecular biotechnology. The scientific applications of this field include the understanding of how enzymes function and the accumulation of accurate information of atomic structures, a key factor in the process of rational drug design. NASA has committed substantial investment and resources to the field of protein crystal growth and has conducted many microgravity protein crystal growth experiments aboard shuttle flights. Crystals grown in space tend to be larger, denser and have a more perfect habit and geometry. These improved properties gained in the microgravity environment of space result largely from the reduction of solutal convection, and the elimination of sedimentation at the growing crystal surface. Shuttle experiments have yielded many large, high quality crystals that are suitable for high resolution X-ray diffraction analysis. Examples of biologically important macromolecules which have been successfully crystallized during shuttle missions include: lysozyme, isocitrate lyase, gamma-interferon, insulin, human serum albumin and canavalin. Numerous other examples are also available. In addition to obtaining high quality crystals, investigators are also interested in learning the mechanisms by which the growth events take place. Crystallization experiments indicate that for the enzyme HEWL, measured growth rates do not follow mathematical models for 2D nucleation and dislocation-led growth of tetragonal protein crystals. As has been suggested by the laboratory of Marc L. Pusey, a possible explanation for the disagreement between observation and data is that HEWL tetraconal crystals form by aggregated units of lysozyme in supersaturated solutions. Surface measurement data was shown to fit very well with a model using an octamer unit cell as the growth unit. According to this model, the aggregation pathway and subsequent crystal growth is described by: monomer < ------ > dimer < ------- > tetramer < ------ > octamer < ------ > higher order. It is believed that multimer aggregation of lysozyme occurs by interaction at specific binding sites on the surface of the protein crystals. If the presence of discrete binding sites and the aggregation hypothesis is true, then it follows that the alteration of the binding site(s) should have significant effect on the measurements obtained during growth experiments. Site-directed mutagenesis allows the specific alteration of proteins by replacement, deletion or addition of specific amino acid residues. This report outlines the approach for this strategy and the progress made thus far toward that end.

Remote Internet access to advanced analytical facilities: a new approach with Web-based services.

PubMed

Sherry, N; Qin, J; Fuller, M Suominen; Xie, Y; Mola, O; Bauer, M; McIntyre, N S; Maxwell, D; Liu, D; Matias, E; Armstrong, C

2012-09-04

Over the past decade, the increasing availability of the World Wide Web has held out the possibility that the efficiency of scientific measurements could be enhanced in cases where experiments were being conducted at distant facilities. Examples of early successes have included X-ray diffraction (XRD) experimental measurements of protein crystal structures at synchrotrons and access to scanning electron microscopy (SEM) and NMR facilities by users from institutions that do not possess such advanced capabilities. Experimental control, visual contact, and receipt of results has used some form of X forwarding and/or VNC (virtual network computing) software that transfers the screen image of a server at the experimental site to that of the users' home site. A more recent development is a web services platform called Science Studio that provides teams of scientists with secure links to experiments at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens to operate, observe, and record essential parts of the experiment. As well, Science Studio provides high speed network access to computing resources to process the large data sets that are often involved in complex experiments. The simple web browser and the rapid transfer of experimental data to a processing site allow efficient use of the facility and assist decision making during the acquisition of the experimental results. The software provides users with a comprehensive overview and record of all parts of the experimental process. A prototype network is described involving X-ray beamlines at two different synchrotrons and an SEM facility. An online parallel processing facility has been developed that analyzes the data in near-real time using stream processing. Science Studio and can be expanded to include many other analytical applications, providing teams of users with rapid access to processed results along with the means for detailed discussion of their significance.

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Astrophysics Data System (ADS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-11-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Gamma-ray spectrometer experiment, Apollo 17: NaI(T1) detector crystal activation

NASA Technical Reports Server (NTRS)

Trombka, J. I.; Schmadebeck, R. L.; Bielefeld, M.; Okelley, G. D.; Eldridge, J. S.; Northcutt, K. J.; Metzger, A. E.; Schonfeld, E.; Peterson, L. E.; Arnold, J. R.

1973-01-01

An attempt was made to obtain experimental data on proton induced activity and its effect on gamma ray spectral measurements. A NaI(T1) crystal flown in Apollo 17 command module was used for the experiment.

Comparative study on ATR-FTIR calibration models for monitoring solution concentration in cooling crystallization

NASA Astrophysics Data System (ADS)

Zhang, Fangkun; Liu, Tao; Wang, Xue Z.; Liu, Jingxiang; Jiang, Xiaobin

2017-02-01

In this paper calibration model building based on using an ATR-FTIR spectroscopy is investigated for in-situ measurement of the solution concentration during a cooling crystallization process. The cooling crystallization of L-glutamic Acid (LGA) as a case is studied here. It was found that using the metastable zone (MSZ) data for model calibration can guarantee the prediction accuracy for monitoring the operating window of cooling crystallization, compared to the usage of undersaturated zone (USZ) spectra for model building as traditionally practiced. Calibration experiments were made for LGA solution under different concentrations. Four candidate calibration models were established using different zone data for comparison, by using a multivariate partial least-squares (PLS) regression algorithm for the collected spectra together with the corresponding temperature values. Experiments under different process conditions including the changes of solution concentration and operating temperature were conducted. The results indicate that using the MSZ spectra for model calibration can give more accurate prediction of the solution concentration during the crystallization process, while maintaining accuracy in changing the operating temperature. The primary reason of prediction error was clarified as spectral nonlinearity for in-situ measurement between USZ and MSZ. In addition, an LGA cooling crystallization experiment was performed to verify the sensitivity of these calibration models for monitoring the crystal growth process.

REPEAT MAMMOGRAPHY SCREENING AMONG UNMARRIED WOMEN WITH AND WITHOUT A DISABILITY

PubMed Central

Clark, Melissa A.; Rogers, Michelle L.; Wen, Xiaozhong; Wilcox, Victoria; McCarthy-Barnett, Kate; Panarace, Jeanne; Manning, Carol; Allen, Susan; Rakowski, William

2009-01-01

Objectives Unmarried women with disabilities may be a particularly vulnerable group for underutilization of repeat mammography screening. Our goal was to compare the breast cancer screening experiences of unmarried women with disabilities (WWD) versus women with no disabilities (WND), and determine whether these experiences are associated with adherence to repeat screening. Methods We conducted a matched cohort study of 93 WWD and 93 WND to compare mammography experiences by disability status, examine rates of repeat mammography by disability status, and identify factors that are associated with repeat mammography. Results WWD were less likely to be on-schedule than WND in univariable (54.8% vs. 71.0%; relative risk = 0.77, 95% CL = 0.61, 0.97), but not multivariable, analyses. In multivariable analyses, there was a significant interaction between disability status and positive experiences as the reasons for returning to the same mammography facility. Among WND, repeat screening ranged from 59% to 86%, depending on the number of positive experiences endorsed (range=1–5). In contrast, among WWD, screening rates were only 37% among those who did not report any positive experiences and increased to a maximum of 60% regardless of whether women endorsed one to four or all five positive experiences. Severity and type of disability were not associated with repeat screening. Conclusions WWD may be less likely than WND to remain on-schedule for mammography. WWD who do not report any positive experiences as reasons for returning to a mammography facility may be at particularly high risk of underutilization of screening. PMID:19775912

Filling-enforced nonsymmorphic Kondo semimetals in two dimensions

NASA Astrophysics Data System (ADS)

Pixley, J. H.; Lee, SungBin; Brandom, B.; Parameswaran, S. A.

2017-08-01

We study the competition between Kondo screening and frustrated magnetism on the nonsymmorphic Shastry-Sutherland Kondo lattice at a filling of two conduction electrons per unit cell. This model is known to host a set of gapless partially Kondo screened phases intermediate between the Kondo-destroyed paramagnet and the heavy Fermi liquid. Based on crystal symmetries, we argue that (i) both the paramagnet and the heavy Fermi liquid are semimetals protected by a glide symmetry; and (ii) partial Kondo screening breaks the symmetry, removing this protection and allowing the partially Kondo screened phase to be deformed into a Kondo insulator via a Lifshitz transition. We confirm these results using large-N mean-field theory and then use nonperturbative arguments to derive a generalized Luttinger sum rule constraining the phase structure of two-dimensional nonsymmorphic Kondo lattices beyond the mean-field limit.

One more hurdle to increasing mammography screening: pubescent, adolescent, and prior mammography screening experiences.

PubMed

Thomas, Eileen; Usher, LaToya

2009-01-01

Approximately $8.1 billion dollars is spent each year in the United States alone on the treatment of breast cancer. Survival rates are dependent on access to, and utilization of, early detection services. The primary reason for disparity in breast cancer mortality is the delay in time to diagnosis, resulting in poor prognosis. Despite ongoing research to understand barriers to mammography screening, recent studies report a decrease in mammography screening among all racial groups. A qualitative approach was used to elicit information from 36 White non- Hispanic, African-American, Hispanic, and Native American women without a history of breast cancer. Women were invited to share written or audiotape-recorded narratives about experiences pertaining to their breasts and their mammography screening experiences. Major categories identified were: teasing, family norms and values, media/societal influence, body image, and mammography screening experiences. The resulting effects of these experiences left these women with feelings of shame and "conflict" regarding their breasts. The major theme identified was breast conflict. Findings suggest that breast conflict may persist throughout the lifespan and can have a negative influence on a woman's decision to participate in mammography screening. The authors hypothesize that experiences that occur during adolescence pertaining to young girls' breasts can influence a women's body image, which in turn can later in life affect health-seeking behaviors related to mammography screening. These findings have implications for public health practice in planning for breast cancer screening, education, and interventions for women from diverse racial/ethnics groups.

Choice and maintenance of equipment for electron crystallography.

PubMed

Mills, Deryck J; Vonck, Janet

2013-01-01

The choice of equipment for an electron crystallography laboratory will ultimately be determined by the available budget; nevertheless, the ideal lab will have two electron microscopes: a dedicated 300 kV cryo-EM with a field emission gun and a smaller LaB(6) machine for screening. The high-end machine should be equipped with photographic film or a very large CCD or CMOS camera for 2D crystal data collection; the screening microscope needs a mid-size CCD for rapid evaluation of crystal samples. The microscope room installations should provide adequate space and a special environment that puts no restrictions on the collection of high-resolution data. Equipment for specimen preparation includes a carbon coater, glow discharge unit, light microscope, plunge freezer, and liquid nitrogen containers and storage dewars. When photographic film is to be used, additional requirements are a film desiccator, dark room, optical diffractometer, and a film scanner. Having the electron microscopes and ancillary equipment well maintained and always in optimum condition facilitates the production of high-quality data.

Screening Libraries of Semifluorinated Arylene Bisimides to Discover and Predict Thermodynamically Controlled Helical Crystallization.

PubMed

Ho, Ming-Shou; Partridge, Benjamin E; Sun, Hao-Jan; Sahoo, Dipankar; Leowanawat, Pawaret; Peterca, Mihai; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Ungar, Goran; Heiney, Paul A; Hsu, Chain-Shu; Percec, Virgil

2016-12-12

Synthesis, structural, and retrostructural analysis of a library containing 16 self-assembling perylene (PBI), 1,6,7,12-tetrachloroperylene (Cl 4 PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides functionalized with environmentally friendly AB 3 chiral racemic semifluorinated minidendrons at their imide groups via m = 0, 1, 2, and 3 methylene units is reported. These semifluorinated compounds melt at lower temperatures than homologous hydrogenated compounds, permitting screening of all their thermotropic phases via structural analysis to discover thermodynamically controlled helical crystallization from propeller-like, cogwheel, and tilted molecules as well as lamellar-like structures. Thermodynamically controlled helical crystallization was discovered for propeller-like PBI, Cl 4 PBI and NBI with m = 0. Unexpectedly, assemblies of twisted Cl 4 PBIs exhibit higher order than those of planar PBIs. PBI with m = 1, 2, and 3 form a thermodynamically controlled columnar hexagonal 2D lattice of tilted helical columns with intracolumnar order. PBI and Cl 4 PBI with m = 1 crystallize via a recently discovered helical cogwheel mechanism, while NBI and PMBI with m = 1 form tilted helical columns. PBI, NBI and PMBI with m = 2 generate lamellar-like structures. 3D and 2D assemblies of PBI with m = 1, 2, and 3, NBI with m = 1 and PMBI with m = 2 exhibit 3.4 Å π-π stacking. The library approach applied here and in previous work enabled the discovery of six assemblies which self-organize via thermodynamic control into 3D and 2D periodic arrays, and provides molecular principles to predict the supramolecular structure of electronically active components.

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor.

PubMed

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.

Exploration of multiple Sortase A protein conformations in virtual screening

NASA Astrophysics Data System (ADS)

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-02-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.

Exploration of multiple Sortase A protein conformations in virtual screening

PubMed Central

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-01-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds. PMID:26846342

Purification, crystallization and preliminary X-ray diffraction studies on goat (Capra hircus) hemoglobin - a low oxygen affinity species.

PubMed

Moorthy, Ponnuraj Sathya; Neelagandan, Kamariah; Balasubramanian, Moovarkumudalvan; Ponnuswamy, Mondikalipudur Nanjappa Gounder

2009-01-01

Hemoglobin is a vital protein present in almost all higher species. It is a transport protein involved in carrying oxygen from lungs to tissues and carbon dioxide back to lungs by an intrinsically coordinated manner. Even though a good amount of work has been carried out in this direction there exists scarcity of structural insight on low oxygen affinity species. Attempts are being made to unravel the structural insight of this low oxygen affinity species. Goat blood plasma was collected, treated with EDTA to avoid blood clotting and purification was accomplished using DEAE-anion chromatographic column. The goat hemoglobin was crystallized using 50mM of phosphate buffer at pH 6.7 with 1M NaCl and PEG 3350 as precipitant by hanging drop vapor diffusion method. Crystals obtained are screened and suitable crystals are taken for data collection using mar345dtb as image plate detector system. Goat hemoglobin crystal diffracted up to 2.61 A resolution. Goat hemoglobin crystallizes in orthorhombic space group P212(1)2(1) as a whole biological molecule in the asymmetric unit with cell dimensions a=53.568A, b=67.365A, c=154.183A.

Introduction to protein crystallization

PubMed Central

McPherson, Alexander; Gavira, Jose A.

2014-01-01

Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid–liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies. PMID:24419610

Introduction to protein crystallization.

PubMed

McPherson, Alexander; Gavira, Jose A

2014-01-01

Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies.

Spacelab 3 vapor crystal growth experiment

NASA Technical Reports Server (NTRS)

Schnepple, W.; Vandenberg, L.; Skinner, N.; Ortale, C.

1987-01-01

The Space Shuttle Challenger, with Spacelab 3 as its payload, was launched into orbit April 29, 1985. The mission, number 51-B, emphasized materials processing in space, although a wide variety of experiments in other disciplines were also carried onboard. One of the materials processing experiments on this flight is described, specifically the growth of single crystals of mercuric iodide by physical vapor transport.

KSC-03PD-1471

NASA Technical Reports Server (NTRS)

2003-01-01

KENNEDY SPACE CENTER, FLA. - The crystals visible in this laboratory dish were part of an experiment carried on mission STS-107. Several experiments were found during the search for Columbia debris. Included in the Commercial ITA Biomedical Experiments payload on mission STS-107 are urokinase cancer research, microencapsulation of drugs, the Growth of Bacterial Biofilm on Surfaces during Spaceflight (GOBBSS), and tin crystal formation.

Microgravity

NASA Image and Video Library

1995-09-17

Horse Serum Albumin crystals grown during the USML-1 (STS-50) mission's Protein Crystal Growth Glovebox Experiment. These crystals were grown using a vapor diffusion technique at 22 degrees C. The crystals were allowed to grow for nine days while in orbit. Crystals of 1.0 mm in length were produced. The most abundant blood serum protein, regulates blood pressure and transports ions, metabolites, and therapeutic drugs. Principal Investigator was Edward Meehan.

Angular selectivity asymmetry of holograms recorded in near infrared sensitive liquid crystal photopolymerizable materials

NASA Astrophysics Data System (ADS)

Harbour, Steven; Galstian, Tigran; Akopyan, Rafik; Galstyan, Artur

2004-08-01

We have experimentally observed and theoretically explained the angular selectivity asymmetry in polymer dispersed liquid crystal holograms. Experiments are conducted in compounds with near infrared sensitivity. The coupled-wave theory is used to describe the diffraction properties of obtained anisotropic holographic gratings. Furthermore, the comparison of theory and experiments provides information about the optical axis direction that is defined by the average molecular orientation of the liquid crystal in the polymer matrix.

Comparison of OARE Accelerometer Data with Dopant Distribution in Se-Doped GaAs Crystals Grown During USML-1

NASA Technical Reports Server (NTRS)

Moskowitz, Milton E.; Bly, Jennifer M.; Matthiesen, David H.

1997-01-01

Experiments were conducted in the crystal growth furnace (CGF) during the first United States Microgravity Laboratory (USML-1), the STS-50 flight of the Space Shuttle Columbia, to determine the segregation behavior of selenium in bulk GaAs in a microgravity environment. After the flight, the selenium-doped GaAs crystals were sectioned, polished, and analyzed to determine the free carrier concentration as a function of position, One of the two crystals initially exhibited an axial concentration profile indicative of diffusion controlled growth, but this profile then changed to that predicted for a complete mixing type growth. An analytical model, proposed by Naumann [R.J. Naumann, J. Crystal Growth 142 (1994) 253], was utilized to predict the maximum allowable microgravity disturbances transverse to the growth direction during the two different translation rates used for each of the experiments. The predicted allowable acceleration levels were 4.86 microgram for the 2.5 micrometers/s furnace translation rate and 38.9 microgram for the 5.0 micrometers/s rate. These predicted values were compared to the Orbital Acceleration Research Experiment (OARE) accelerometer data recorded during the crystal growth periods for these experiments. Based on the analysis of the OARE acceleration data and utilizing the predictions from the analytical model, it is concluded that the change in segregation behavior was not caused by any acceleration events in the microgravity environment.