High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

PubMed Central

Clifton, Matthew C.; Dranow, David M.; Leed, Alison; Fulroth, Ben; Fairman, James W.; Abendroth, Jan; Atkins, Kateri A.; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z. J.; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B.; Golub, Todd R.; Hubbard, Brian K.; Serrano-Wu, Michael H.

2015-01-01

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors. PMID:25909780

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Carboplatin binding to histidine

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

Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.

An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the brominemore » form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.« less

Shear induced structures in crystallizing cocoa butter

NASA Astrophysics Data System (ADS)

Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

2004-03-01

Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

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.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

Structural basis for antibody recognition in the receptor-binding domains of toxins A and B from Clostridium difficile.

PubMed

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N; Klassen, John S; Ng, Kenneth K S

2014-01-24

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile*

PubMed Central

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N.; Klassen, John S.; Ng, Kenneth K. S.

2014-01-01

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents. PMID:24311789

Synthesis of rhenium nitride crystals with MoS2 structure

NASA Astrophysics Data System (ADS)

Kawamura, Fumio; Yusa, Hitoshi; Taniguchi, Takashi

2012-06-01

Rhenium nitride (ReN2) crystals were synthesized from a metathesis reaction between ReCl5 and Li3N under high pressure. The reaction was well controlled by the addition of a large amount of NaCl as reaction inhibitor to prevent a violent exothermic reaction. The largest rhenium nitride crystals obtained had a millimeter-order size with a platelet shape. X-ray diffraction analysis revealed that rhenium nitride has MoS2 structure similar to hexagonal rhenium diboride (ReB2) which has recently been investigated as an ultra-hard material. The structure was different from any structures previously predicted for ReN2 by theoretical calculations.

Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

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

Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon

The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phasemore » diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.« less

Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

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

Fischmann, Thierry O.; Smith, Catherine K.; Mayhood, Todd W.

MEK1 is a member of the MAPK signal transduction pathway that responds to growth factors and cytokines. We have determined that the kinase domain spans residues 35-382 by proteolytic cleavage. The complete kinase domain has been crystallized and its X-ray crystal structure as a complex with magnesium and ATP-{gamma}S determined at 2.1 {angstrom}. Unlike crystals of a truncated kinase domain previously published, the crystals of the intact domain can be grown either as a binary complex with a nucleotide or as a ternary complex with a nucleotide and one of a multitude of allosteric inhibitors. Further, the crystals allow formore » the determination of costructures with ATP competitive inhibitors. We describe the structures of nonphosphorylated MEK1 (npMEK1) binary complexes with ADP and K252a, an ATP-competitive inhibitor (see Table 1), at 1.9 and 2.7 {angstrom} resolution, respectively. Ternary complexes have also been solved between npMEK1, a nucleotide, and an allosteric non-ATP competitive inhibitor: ATP-{gamma}S with compound 1 and ADP with either U0126 or the MEK1 clinical candidate PD325089 at 1.8, 2.0, and 2.5 {angstrom}, respectively. Compound 1 is structurally similar to PD325901. These structures illustrate fundamental differences among various mechanisms of inhibition at the molecular level. Residues 44-51 have previously been shown to play a negative regulatory role in MEK1 activity. The crystal structure of the integral kinase domain provides a structural rationale for the role of these residues. They form helix A and repress enzymatic activity by stabilizing an inactive conformation in which helix C is displaced from its active state position. Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome.« less

Dark-field transmission electron microscopy of cortical bone reveals details of extrafibrillar crystals.

PubMed

Schwarcz, Henry P; McNally, Elizabeth A; Botton, Gianluigi A

2014-12-01

In a previous study we showed that most of the mineral in bone is present in the form of "mineral structures", 5-6nm-thick, elongated plates which surround and are oriented parallel to collagen fibrils. Using dark-field transmission electron microscopy, we viewed mineral structures in ion-milled sections of cortical human bone cut parallel to the collagen fibrils. Within the mineral structures we observe single crystals of apatite averaging 5.8±2.7nm in width and 28±19nm in length, their long axes oriented parallel to the fibril axis. Some appear to be composite, co-aligned crystals as thin as 2nm. From their similarity to TEM images of crystals liberated from deproteinated bone we infer that we are viewing sections through platy crystals of apatite that are assembled together to form the mineral structures. Copyright © 2014 Elsevier Inc. All rights reserved.

Rational protein engineering in action: The first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus

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

Evdokimov, Artem G.; Mekel, Marlene; Hutchings, Kim

2008-07-08

In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog. We also explain the structure-activity relationship of several recently reported inhibitors. The native enzyme crystals were of poor quality -- they only diffracted X-rays to 3--5 {angstrom} resolution. Therefore, we have executed a rational surface mutagenesis strategy that has yielded crystals of this 2300-amino acid multidomain protein, diffracting to 2 {angstrom} or better. This methodology is discussed andmore » contrasted with the more traditional domain truncation approach.« less

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

PubMed

Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

2014-07-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

PubMed

Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

2007-03-28

Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

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

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

DOE PAGES

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.; ...

2017-09-05

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

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

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

Hematin−Hematin Self-Association States Involved in the Formation and Reactivity of the Malaria Parasite Pigment, Hemozoin

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

Klonis, Nectarios; Dilanian, Ruben; Hanssen, Eric

The malaria parasite pigment, hemozoin, is a crystal of ferriprotoporphyrin IX (FP-Fe(III)), a product of hemoglobin digestion. Hemozoin formation is essential for FP-Fe(III) detoxification in the parasite; it is the main target of quinoline antimalarials and can modulate immune and inflammation responses. To gain further insight into the likely mechanisms of crystal formation and hemozoin reactivity, we have reanalyzed the crystal structure data for {beta}-hematin and solved the crystal structure of Plasmodium falciparum hemozoin. The analysis reveals that the structures are very similar and highlights two previously unexplored modes of FP-Fe(III) self-association involving {pi}-{pi} interactions that may initiate crystal formationmore » and help to stabilize the extended structure. Hemozoin can be considered to be a crystal composed of {pi}-{pi} dimers stabilized by iron-carboxylate linkages. As a result, it is predicted that two surfaces of the crystal would consist of {pi}-{pi} dimers with Fe(III) partly exposed to solvent and capable of undergoing redox reactions. Accordingly, we demonstrate that the crystal possesses both general peroxidase activity and the ability to cause lipid oxidation.« less

Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

PubMed

Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

2017-05-05

A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product.

PubMed

Boughton, Berin A; Dobson, Renwick C J; Hutton, Craig A

2012-08-01

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures. Copyright © 2012 Wiley Periodicals, Inc.

Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

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

Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.

2014-08-01

The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an aminemore » tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.« less

The structure of XIAP BIR2: understanding the selectivity of the BIR domains

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

Lukacs, Christine, E-mail: cmlukacs230@gmail.com; Belunis, Charles; Crowther, Robert

2013-09-01

The high-resolution crystal structures of apo and peptide-bound XIAP BIR2 are presented and compared with BIR3 structures to understand their selectivity. This crystal system can be used to determine the structures of BIR2–inhibitor complexes. XIAP, a member of the inhibitor of apoptosis family of proteins, is a critical regulator of apoptosis. Inhibition of the BIR domain–caspase interaction is a promising approach towards treating cancer. Previous work has been directed towards inhibiting the BIR3–caspase-9 interaction, which blocks the intrinsic apoptotic pathway; selectively inhibiting the BIR2–caspase-3 interaction would also block the extrinsic pathway. The BIR2 domain of XIAP has successfully been crystallized;more » peptides and small-molecule inhibitors can be soaked into these crystals, which diffract to high resolution. Here, the BIR2 apo crystal structure and the structures of five BIR2–tetrapeptide complexes are described. The structural flexibility observed on comparing these structures, along with a comparison with XIAP BIR3, affords an understanding of the structural elements that drive selectivity between BIR2 and BIR3 and which can be used to design BIR2-selective inhibitors.« less

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

Bowley, S.; Okumura, N; Lord, S

'A:a' knob-hole interactions and D:D interfacial interactions are important for fibrin polymerization. Previous studies with recombinant ?N308K fibrinogen, a substitution at the D:D interface, showed impaired polymerization. We examined the molecular basis for this loss of function by solving the crystal structure of ?N308K fragment D. In contrast to previous fragment D crystals, the ?N308K crystals belonged to a tetragonal space group with an unusually long unit cell (a = b = 95 Angstroms, c = 448.3 Angstroms). Alignment of the normal and ?N308K structures showed the global structure of the variant was not changed and the knob 'A' peptidemore » GPRP was bound as usual to hole 'a'. The substitution introduced an elongated positively charged patch in the D:D region. The structure showed novel, symmetric D:D crystal contacts between ?N308K molecules, indicating the normal asymmetric D:D interface in fibrin would be unstable in this variant. We examined GPRP binding to ?N308K in solution by plasmin protection assay. The results showed weaker peptide binding, suggesting that 'A:a' interactions were altered. We examined fibrin network structures by scanning electron microscopy and found the variant fibers were thicker and more heterogeneous than normal fibers. Considered together, our structural and biochemical studies indicate both 'A:a' and D:D interactions are weaker. We conclude that stable protofibrils cannot assemble from ?N308K monomers, leading to impaired polymerization.« less

Exploiting pattern transformation to tune phononic band gaps in a two-dimensional granular crystal.

PubMed

Göncü, F; Luding, S; Bertoldi, K

2012-06-01

The band structure of a two-dimensional granular crystal composed of silicone rubber and polytetrafluoroethylene (PTFE) cylinders is investigated numerically. This system was previously shown to undergo a pattern transformation with uniaxial compression by Göncü et al. [Soft Matter 7, 2321 (2011)]. The dispersion relations of the crystal are computed at different levels of deformation to demonstrate the tunability of the band structure, which is strongly affected by the pattern transformation that induces new band gaps. Replacement of PTFE particles with rubber ones reveals that the change of the band structure is essentially governed by pattern transformation rather than particles' mechanical properties.

Crystallization of isoelectrically homogeneous cholera toxin

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

Spangler, B.D.; Westbrook, E.M.

1989-02-07

Past difficulty in growing good crystals of cholera toxin has prevented the study of the crystal structure of this important protein. The authors have determined that failure of cholera toxin to crystallize well has been due to its heterogeneity. They have now succeeded in overcoming the problem by isolating a single isoelectric variant of this oligomeric protein (one A subunit and five B subunits). Cholera toxin purified by their procedure readily forms large single crystals. The crystal form has been described previously. They have recorded data from native crystals of cholera toxin to 3.0-{angstrom} resolution with our electronic area detectors.more » With these data, they have found the orientation of a 5-fold symmetry axis within these crystals, perpendicular to the screw dyad of the crystal. They are now determining the crystal structure of cholera toxin by a combination of multiple heavy-atom isomorphous replacement and density modification techniques, making use of rotational 5-fold averaging of the B subunits.« less

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

DOE PAGES

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

2016-04-12

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. Furthermore, this observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

NASA Astrophysics Data System (ADS)

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

2016-04-01

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

PubMed

Caskey, Christopher M; Holder, Aaron; Shulda, Sarah; Christensen, Steven T; Diercks, David; Schwartz, Craig P; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S; Tumas, William; Perkins, John D; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M; Zakutayev, Andriy

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

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

Caskey, Christopher M.; Colorado School of Mines, Golden, Colorado 80401; Larix Chemical Science, Golden, Colorado 80401

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Hemispherical Laue camera

DOEpatents

Li, James C. M.; Chu, Sungnee G.

1980-01-01

A hemispherical Laue camera comprises a crystal sample mount for positioning a sample to be analyzed at the center of sphere of a hemispherical, X-radiation sensitive film cassette, a collimator, a stationary or rotating sample mount and a set of standard spherical projection spheres. X-radiation generated from an external source is directed through the collimator to impinge onto the single crystal sample on the stationary mount. The diffracted beam is recorded on the hemispherical X-radiation sensitive film mounted inside the hemispherical film cassette in either transmission or back-reflection geometry. The distances travelled by X-radiation diffracted from the crystal to the hemispherical film are the same for all crystal planes which satisfy Bragg's Law. The recorded diffraction spots or Laue spots on the film thereby preserve both the symmetry information of the crystal structure and the relative intensities which are directly related to the relative structure factors of the crystal orientations. The diffraction pattern on the exposed film is compared with the known diffraction pattern on one of the standard spherical projection spheres for a specific crystal structure to determine the orientation of the crystal sample. By replacing the stationary sample support with a rotating sample mount, the hemispherical Laue camera can be used for crystal structure determination in a manner previously provided in conventional Debye-Scherrer cameras.

Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.

2001-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study, we show that possible conformational changes induced by heating are stable and apparently non-reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for four weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 hours at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study we show that possible conformational changes induced by heating are stable and apparently non- reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for 4 weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 h at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

“Skin-Core-Skin” Structure of Polymer Crystallization Investigated by Multiscale Simulation

PubMed Central

Ruan, Chunlei

2018-01-01

“Skin-core-skin” structure is a typical crystal morphology in injection products. Previous numerical works have rarely focused on crystal evolution; rather, they have mostly been based on the prediction of temperature distribution or crystallization kinetics. The aim of this work was to achieve the “skin-core-skin” structure and investigate the role of external flow and temperature fields on crystal morphology. Therefore, the multiscale algorithm was extended to the simulation of polymer crystallization in a pipe flow. The multiscale algorithm contains two parts: a collocated finite volume method at the macroscopic level and a morphological Monte Carlo method at the microscopic level. The SIMPLE (semi-implicit method for pressure linked equations) algorithm was used to calculate the polymeric model at the macroscopic level, while the Monte Carlo method with stochastic birth-growth process of spherulites and shish-kebabs was used at the microscopic level. Results show that our algorithm is valid to predict “skin-core-skin” structure, and the initial melt temperature and the maximum velocity of melt at the inlet mainly affects the morphology of shish-kebabs. PMID:29659516

Monoclinic nanodomains in morphotropic phase boundary Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}–PbTiO{sub 3}

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

Sato, Y., E-mail: y-sato@sigma.t.u-tokyo.ac.jp; Hirayama, T.; Ikuhara, Y.

2014-02-24

Crystalline structure is a fundamental characteristic of many materials, and drastic changes in properties may accompany crystal phase transitions. A prominent example of this is the morphotropic phase boundary of (Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-PbTiO{sub 3}) single crystal, a region that exhibits a high piezoelectric effect. Although the highest piezoelectricity is often attributed to a monoclinic crystal phase, formation of ferroelectric nanodomains (NDs) complicates understanding of this crystal structure. In this Letter, we report dedicated transmission electron microscopy and electron diffraction analysis to understand the crystal structure at the ND level. Splitting of diffraction spots, caused by very small lattice distortionmore » in the NDs, is important to understanding crystal structure and has been unambiguously observed. The results can be explained by monoclinic phase NDs. Combining these results with our previous findings on ND dynamics [Sato et al. Phys. Rev. Lett. 107, 187601 (2011)], monoclinic NDs can potentially make a considerable contribution to the piezoelectricity in these materials.« less

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

Prediction of new ground-state crystal structure of T a2O5

NASA Astrophysics Data System (ADS)

Yang, Yong; Kawazoe, Yoshiyuki

2018-03-01

Tantalum pentoxide (T a2O5 ) is a wide-gap semiconductor which has important technological applications. Despite the enormous efforts from both experimental and theoretical studies, the ground-state crystal structure of T a2O5 is not yet uniquely determined. Based on first-principles calculations in combination with evolutionary algorithm, we identify a triclinic phase of T a2O5 , which is energetically much more stable than any phases or structural models reported previously. Characterization of the static and dynamical properties of the phase reveals the common features shared with previous metastable phases of T a2O5 . In particular, we show that the d spacing of ˜3.8 Å found in the x-ray diffraction patterns of many previous experimental works is actually the radius of the second Ta-Ta coordination shell as defined by radial distribution functions.

The structure of Tim50(164–361) suggests the mechanism by which Tim50 receives mitochondrial presequences

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

Li, Jingzhi; Sha, Bingdong, E-mail: bdsha@uab.edu

2015-08-25

The Tim50 crystal structure indicates that the IMS domain of Tim50 exhibits significant structural plasticity within the putative presequence-binding groove. Mitochondrial preproteins are transported through the translocase of the outer membrane (TOM) complex. Tim50 and Tim23 then transfer preproteins with N-terminal targeting presequences through the intermembrane space (IMS) across the inner membrane. The crystal structure of the IMS domain of Tim50 [Tim50(164–361)] has previously been determined to 1.83 Å resolution. Here, the crystal structure of Tim50(164–361) at 2.67 Å resolution that was crystallized using a different condition is reported. Compared with the previously determined Tim50(164–361) structure, significant conformational changes occurmore » within the protruding β-hairpin of Tim50 and the nearby helix A2. These findings indicate that the IMS domain of Tim50 exhibits significant structural plasticity within the putative presequence-binding groove, which may play important roles in the function of Tim50 as a receptor protein in the TIM complex that interacts with the presequence and multiple other proteins. More interestingly, the crystal packing indicates that helix A1 from the neighboring monomer docks into the putative presequence-binding groove of Tim50(164–361), which may mimic the scenario of Tim50 and the presequence complex. Tim50 may recognize and bind the presequence helix by utilizing the inner side of the protruding β-hairpin through hydrophobic interactions. Therefore, the protruding β-hairpin of Tim50 may play critical roles in receiving the presequence and recruiting Tim23 for subsequent protein translocations.« less

Crystal structure of new AsS{sub 2} compound

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

Bolotina, N. B., E-mail: bolotina@ns.crys.ras.ru; Brazhkin, V. V.; Dyuzheva, T. I.

2013-01-15

AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

Survey and analysis of crystal polymorphism in organic structures

PubMed Central

Kaur, Ramanpreet

2018-01-01

With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components. PMID:29765601

Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model.

PubMed

Gabriëlse, Alexander; Löwen, Hartmut; Smallenburg, Frank

2017-11-07

In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

Crystallography of waxes - an electron diffraction study of refined and natural products

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

PubMed

Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

2016-04-05

Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.

PubMed

Addy, Christine; Ohara, Masato; Kawai, Fumihiro; Kidera, Akinori; Ikeguchi, Mitsunori; Fuchigami, Sotaro; Osawa, Masanori; Shimada, Ichio; Park, Sam-Yong; Tame, Jeremy R H; Heddle, Jonathan G

2007-02-01

Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

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.

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

Transformations of the dislocation structure of nickel single crystals

NASA Astrophysics Data System (ADS)

Alfyorova, E. A.; Lychagin, D. V.; Lychagina, L. L.; Tsvetkov, N. A.

2017-12-01

A relationship between different-scale deformations of crystals has not been established yet. In order to solve this task, we investigate the development of a deformation relief and dislocation structure in nickel single crystals after deformation. The stress tensor, crystallography, and geometry of specimens affect the organization of some shear along corresponding systems of sliding. The organization of shear shows some features of self-organization. It is associated with the self-organization in the dislocation subsystem analyzed previously. The effectiveness of reducing external and internal stresses determines patterns of deformation processes at different scale levels.

Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd

PubMed Central

Yun, Mikyung; Bronner, C.Eric; Park, Cheon-Gil; Cha, Sun-Shin; Park, Hee-Won; Endow, Sharyn A.

2003-01-01

Molecular motors undergo conformational changes to produce force and move along cytoskeletal filaments. Structural changes have been detected in kinesin motors; however, further changes are expected because previous crystal structures are in the same or closely related conformations. We report here a 2.5 Å crystal structure of the minus-end kinesin, Ncd, with the coiled-coil stalk/neck and one head rotated by ∼75° relative to the other head. The two heads are asymmetrically positioned with respect to the stalk and show asymmetry of nucleotide state: one head is fully occupied, but the other is unstably bound to ADP. Unlike previous structures, our new atomic model can be fit into cryoelectron microscopy density maps of the motor attached to microtubules, where it appears to resemble a one-head-bound motor with the stalk rotated towards the minus end. Interactions between neck and motor core residues, observed in the head that moves with the stalk, are disrupted in the other head, permitting rotation of the stalk/neck. The rotation could represent a force-producing stroke that directs the motor to the minus end. PMID:14532111

Disordered Zinc in Zn4Sb3 with Phonon-Glass and Electron-Crystal Thermoelectric Properties

NASA Technical Reports Server (NTRS)

Snyder, G. Jeffrey; Christensen, Mogens; Nishibori, Eiji; Caillat, Thierry; Brummerstedt Iversen, Bo

2004-01-01

By converting waste heat into electricity, thermoelectric generators could be an important part of the solution to today's energy challenges. The compound Zn4Sb3 is one of the most efficient thermoelectric materials known. Its high efficiency results from an extraordinarily low thermal conductivity in conjunction with the electronic structure of a heavily doped semiconductor. Previous structural studies have been unable to explain this unusual combination of properties. Here, we show through a comprehensive structural analysis using single-crystal X-ray and powder-synchrotron-radiation diffraction methods, that both the electronic and thermal properties of Zn4Sb3 can be understood in terms of unique structural features that have been previously overlooked. The identification of Sb3- ions and Sb-2(4-) dimers reveals that Zn4Sb3 is a valence semiconductor with the ideal stoichiometry Zn13Sb10. In addition, the structure contains significant disorder, with zinc atoms distributed over multiple positions. The discovery of glass-like interstitial sites uncovers a highly effective mechanism for reducing thermal conductivity. Thus Zn4Sb3 is in many ways an ideal 'phonon glass, electron crystal' thermoelectric material.

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

Guo, Yiming; Fredrickson, Daniel C.

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

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

Mutation of Surface Residues to Promote Crystallization of Activated Factor XI as a Complex with Benzamidine: an Essential Step for the Iterative Structure-Based Design of Factor XI Inhibitors

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

Jin,L.; Pandey, P.; Babine, R.

Activated factor XI (FXIa) is a key enzyme in the amplification phase of the blood-coagulation cascade. Thus, a selective FXIa inhibitor may have lesser bleeding liabilities and provide a safe alternative for antithrombosis therapy to available drugs on the market. In a previous report, the crystal structures of the catalytic domain of FXIa (rhFXI370-607) in complex with various ecotin mutants have been described [Jin et al. (2005), Journal of Biological Chemistry 280, 4704-4712]. However, ecotin forms a matrix-like interaction with rhFXI370-607 and is impossible to displace with small-molecule inhibitors; ecotin crystals are therefore not suitable for iterative structure-based ligand design.more » In addition, rhFXI370-607 did not crystallize in the presence of small-molecule ligands. In order to obtain the crystal structure of rhFXI370-607 with a weak small-molecule ligand, namely benzamidine, several rounds of surface-residue mutation were implemented to promote crystal formation of rhFXI370-607. A quadruple mutant of rhFXI370-607 (rhFXI370-607-S434A, T475A, C482S, K437A) readily crystallized in the presence of benzamidine. The benzamidine in the preformed crystals was easily exchanged with other FXIa small-molecule inhibitors. These crystals have facilitated the structure-based design of small-molecule FXIa inhibitors.« less

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Crystal structures of fac-tri-chlorido-tris-(tri-methyl-phosphane-κP)rhodium(III) monohydrate and fac-tri-chlorido-tris-(tri-methyl-phosphane-κP)rhodium(III) methanol hemisolvate: rhodium structures that are isotypic with their iridium analogs.

PubMed

Merola, Joseph S; Franks, Marion A

2015-02-01

The crystal structures of two solvates of fac-tri-chlorido-tris-(tri-methyl-phosphane-κP)rhodium(III) are reported, i.e. one with water in the crystal lattice, fac-[RhCl3(Me3P)3]·H2O, and one with methanol in the crystal lattice, fac-[RhCl3(Me3P)3]·0.5CH3OH. These rhodium compounds exhibit distorted octahedral coordination spheres at the metal and are isotypic with the analogous iridium compounds previously reported by us [Merola et al. (2013 ▶). Polyhedron, 54, 67-73]. Comparison is made between the rhodium and iridium compounds, highlighting their isostructural relationships.

Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

USGS Publications Warehouse

Konnert, J.A.; Evans, H.T.

1987-01-01

The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

Structure of Bacillus halmapalus α-amylase crystallized with and without the substrate analogue acarbose and maltose

PubMed Central

Lyhne-Iversen, Louise; Hobley, Timothy J.; Kaasgaard, Svend G.; Harris, Pernille

2006-01-01

Recombinant Bacillus halmapalus α-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 Å. It was found that the crystal belonged to space group P212121, with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 Å. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES–HEPES–boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 Å. The crystal belonged to space group P212121, with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 Å. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates. PMID:16946462

Probing the Active Site of Candida Glabrata Dihydrofolate Reductase with High Resolution Crystal Structures and the Synthesis of New Inhibitors

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

Liu, J.; Bolstad, D; Smith, A

2009-01-01

Candida glabrata, a fungal strain resistant to many commonly administered antifungal agents, has become an emerging threat to human health. In previous work, we validated that the essential enzyme, dihydrofolate reductase, is a drug target in C. glabrata. Using a crystal structure of dihydrofolate reductase from C. glabrata bound to an initial lead compound, we designed a class of biphenyl antifolates that potently and selectively inhibit both the enzyme and the growth of the fungal culture. In this work, we explore the structure-activity relationships of this class of antifolates with four new high resolution crystal structures of enzyme:inhibitor complexes andmore » the synthesis of four new inhibitors. The designed inhibitors are intended to probe key hydrophobic pockets visible in the crystal structure. The crystal structures and an evaluation of the new compounds reveal that methyl groups at the meta and para positions of the distal phenyl ring achieve the greatest number of interactions with the pathogenic enzyme and the greatest degree of selectivity over the human enzyme. Additionally, antifungal activity can be tuned with substitution patterns at the propargyl and para-phenyl positions.« less

Co-crystal formation between two organic solids on the surface of Titan

NASA Astrophysics Data System (ADS)

Cable, M. L.; Vu, T. H.; Maynard-Casely, H. E.; Hodyss, R. P.

2017-12-01

Laboratory experiments of Titan molecular materials, informed by modeling, can help us to understand the complex and dynamic surface processes occurring on this moon at cryogenic temperatures. We previously demonstrated that two common organic materials on Titan, ethane and benzene, form a unique and stable co-crystalline structure at Titan surface temperatures. We have now characterized a second co-crystal that is stable on Titan, this time between two solids: acetylene and ammonia. The co-crystal forms within minutes at Titan surface temperature, as evidenced by new Raman spectral features in the lattice vibration and C-H bending regions. In addition, a red shift of the C-H stretching mode suggests that the acetylene-ammonia co-crystal is stabilized by a network of C-H···N interactions. Thermal stability studies indicate that this co-crystal remains intact to >110 K, and experiments with liquid methane and ethane reveal the co-crystal to be resistant to fluvial or pluvial exposure. Non-covalently bound structures such as these co-crystals point to far more complex surface interactions than previously believed on Titan. New physical and mechanical properties (deformation, plasticity, density, etc.), differences in storage of key species (i.e., ethane versus methane), variations in surface transport and new chemical gradients can all result in diverse surface features and chemistries of astrobiological interest.

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Finite element method analysis of band gap and transmission of two-dimensional metallic photonic crystals at terahertz frequencies.

PubMed

Degirmenci, Elif; Landais, Pascal

2013-10-20

Photonic band gap and transmission characteristics of 2D metallic photonic crystals at THz frequencies have been investigated using finite element method (FEM). Photonic crystals composed of metallic rods in air, in square and triangular lattice arrangements, are considered for transverse electric and transverse magnetic polarizations. The modes and band gap characteristics of metallic photonic crystal structure are investigated by solving the eigenvalue problem over a unit cell of the lattice using periodic boundary conditions. A photonic band gap diagram of dielectric photonic crystal in square lattice array is also considered and compared with well-known plane wave expansion results verifying our FEM approach. The photonic band gap designs for both dielectric and metallic photonic crystals are consistent with previous studies obtained by different methods. Perfect match is obtained between photonic band gap diagrams and transmission spectra of corresponding lattice structure.

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease

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

Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

2010-09-28

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

Crystal Structures of Inhibitir Complexes of Human T-Cell Leukemia Virus (HTLV-1) Protease

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

Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

2010-09-17

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

Crystal structures of tiotropium bromide and its monohydrate in view of combined solid-state nuclear magnetic resonance and gauge-including projector-augmented wave studies.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Majka, Zbigniew; Kolodziejski, Waclaw

2015-07-01

Tiotropium bromide is an anticholinergic bronchodilator used in the management of chronic obstructive pulmonary disease. The crystal structures of this compound and its monohydrate have been previously solved and published. However, in this paper, we showed that those structures contain some major errors. Our methodology based on combination of the solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum mechanical gauge-including projector-augmented wave (GIPAW) calculations of NMR shielding constants enabled us to correct those errors and obtain reliable structures of the studied compounds. It has been proved that such approach can be used not only to perform the structural analysis of a drug substance and to identify its polymorphs, but also to verify and optimize already existing crystal structures. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

(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.

Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

PubMed Central

Mandal, Kalyaneswar; Pentelute, Brad L; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A; Kent, Stephen B H

2009-01-01

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers l-plectasin and d-plectasin were prepared by total chemical synthesis; interestingly, l-plectasin showed the expected antimicrobial activity, while d-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group with one l-plectasin molecule and one d-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation. PMID:19472324

Structure and Growth Control of Organic-Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals.

PubMed

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong; Liang, Ziqi

2016-04-01

Recently, organic-inorganic halide perovskites have sparked tremendous research interest because of their ground-breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light-emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high-quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three-dimensional large sized single crystals, two-dimensional nanoplates, one-dimensional nanowires, to zero-dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high-performance (opto)electronic devices.

Physical characteristics of Medicago truncatula calcium oxalate crystals determine their effectiveness in insect defense

USDA-ARS?s Scientific Manuscript database

Plant structural traits can act as defense against herbivorous insects, causing them to avoid feeding on a given plant or tissue. Mineral crystals of calcium oxalate in leaves of Medicago truncatula Gaertn. have previously been shown to be effective deterrents of lepidopteran insect feeding. They ar...

Medicago truncatula-derived calcium oxalate crystals have a negative impact on chewing insect performance via their physical properties

USDA-ARS?s Scientific Manuscript database

Plant structural traits often act as defenses against herbivorous insects, causing them to avoid feeding on a given plant or tissue. Mineral crystals of calcium oxalate in Medicago truncatula Gaertn. (Fabaceae) leaves have previously been shown to be effective deterrents of lepidopteran insect feedi...

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

Magnetic structure and phase stability of the van der Waals bonded ferromagnet Fe 3-xGeTe 2

DOE PAGES

May, Andrew F.; Calder, Stuart A.; Cantoni, Claudia; ...

2016-01-08

The magnetic structure and phase diagram of the layered ferromagnetic compound Fe 3GeTe 2 have been investigated by a combination of synthesis, x-ray and neutron diffraction, high-resolution microscopy, and magnetization measurements. Single crystals were synthesized by self-flux reactions, and single-crystal neutron diffraction finds ferromagnetic order with moments of 1.11(5)μ B/Fe aligned along the c axis at 4 K. These flux-grown crystals have a lower Curie temperature T c ≈ 150 K than crystals previously grown by vapor transport (T c = 220 K). The difference is a reduced Fe content in the flux-grown crystals, as illustrated by the behavior observedmore » in a series of polycrystalline samples. As Fe content decreases, so do the Curie temperature, magnetic anisotropy, and net magnetization. Furthermore, Hall-effect and thermoelectric measurements on flux-grown crystals suggest that multiple carrier types contribute to electrical transport in Fe 3–xGeTe 2 and structurally similar Ni 3–xGeTe 2.« less

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.

PubMed

Oshima, Kosuke; Gao, Xuzhu; Hayashi, Seiichiro; Ueda, Toshifumi; Nakashima, Takashi; Kimura, Makoto

2018-01-01

A characteristic feature of archaeal ribonuclease P (RNase P) RNAs is that they have extended helices P12.1 and P12.2 containing kink-turn (K-turn) motifs to which the archaeal RNase P protein Rpp38, a homologue of the human RNase P protein Rpp38, specifically binds. PhoRpp38 from the hyperthermophilic archaeon Pyrococcus horikoshii is involved in the elevation of the optimum temperature of the reconstituted RNase P by binding the K-turns in P12.1 and P12.2. Previously, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was determined at 3.4 Å resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 Å resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 Å. Both structures revealed that Lys35, Asn38 and Glu39 in PhoRpp38 interact with characteristic G·A and A·G pairs in the K-turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in PhoRpp38 interact with the three-nucleotide bulge in the K-turn. Moreover, an extended stem-loop containing P10-P12.2 in complex with PhoRpp38, as well as PhoRpp21 and PhoRpp29, which are the archaeal homologues of the human proteins Rpp21 and Rpp29, respectively, was affinity-purified and crystallized. The crystals thus grown diffracted to a resolution of 6.35 Å. Structure determination of the crystals will demonstrate the previously proposed secondary structure of stem-loops including helices P12.1 and P12.2 and will also provide insight into the structural organization of the specificity domain in P. horikoshii RNase P RNA.

Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor

PubMed Central

Suzuki, Kano; Mizutani, Kenji; Maruyama, Shintaro; Shimono, Kazumi; Imai, Fabiana L.; Muneyuki, Eiro; Kakinuma, Yoshimi; Ishizuka-Katsura, Yoshiko; Shirouzu, Mikako; Yokoyama, Shigeyuki; Yamato, Ichiro; Murata, Takeshi

2016-01-01

V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model. PMID:27807367

Structural and computational study of 1,2,4-triazolin-5-thione derivative and its DMSO solvate

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Wawrzycka-Gorczyca, Irena; Struga, Marta

2017-11-01

The solid state structure of 3-(4-phenyl-5-oxo-1,2,4-triazolin-1-ylmethyl)-4-cyclohexyl-1,2,4-triazolin-5-thione (1) was characterized by FT-IR and X-ray diffraction experiment. Additionally, molecular and crystal structure of its DMSO solvate (1DMSO) has been determined by X-ray diffraction method. The influence of DMSO molecules incorporation to the crystal lattice on geometry of triazolin-5-thione derivative molecule and crystal packing was analyzed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. According to results of conformational analysis in gas, molecule of triazolin-5-thione derivative adopts the lowest energy conformation in 1DMSO crystal. The crystal structure of 1 and 1DMSO were compared with previously described structurally similar compounds, in which the cyclohexyl substituent was replaced by aromatic one (phenyl/methoxyphenyl). Very interesting differences in molecules association were found by comparing the crystal structures of 1 and 1DMSO with their, mentioned above, aromatic derivatives. Interesting properties of triazolin-5-thione derivatives are connected with their π-electron delocalization effects, thus aromaticity of heterocyclic fragments has been investigated by means of the HOMA index. Comparison of aromaticity calculations results with association tendency of molecules shows that triazolin-5-one fragments reach higher aromaticity when nitrogen atom from this moiety acts as a donor in strong Nsbnd H⋯N hydrogen bonds.

Cytotoxicity of copper(II)-complexes with some S-alkyl derivatives of thiosalicylic acid. Crystal structure of the binuclear copper(II)-complex with S-ethyl derivative of thiosalicylic acid

NASA Astrophysics Data System (ADS)

Nikolić, Miloš V.; Mijajlović, Marina Ž.; Jevtić, Verica V.; Ratković, Zoran R.; Novaković, Slađana B.; Bogdanović, Goran A.; Milovanović, Jelena; Arsenijević, Aleksandar; Stojanović, Bojana; Trifunović, Srećko R.; Radić, Gordana P.

2016-07-01

The spectroscopically predicted structure of the obtained copper(II)-complex with S-ethyl derivative of thiosalicylic acid was confirmed by X-ray structural study and compared to previously reported crystal structure of the Cu complex with S-methyl derivative. Single crystals suitable for X-ray measurements were obtained by slow crystallization from a water solution. Cytotoxic effects of S-alkyl (R = benzyl (L1), methyl (L2), ethyl (L3), propyl (L4) and butyl (L5)) derivatives of thiosalicylic acid and the corresponding binuclear copper(II)-complexes on murine colon carcinoma cell lines, CT26 and CT26.CL25 and human colon carcinoma cell line HCT-116 were reported here. The analysis of cancer cell viability showed that all the tested complexes had low cytotoxic effect on murine colon carcinoma cell lines, but several times higher cytotoxicity on normal human colon carcinoma cells.

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

DOE PAGES

Wolf, Nina M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz; ...

2018-04-03

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus . This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and ismore » probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis ( Mt FBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of Mt FBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of Mt FBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.« less

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

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

Wolf, Nina M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus . This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and ismore » probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis ( Mt FBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of Mt FBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of Mt FBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.« less

Fabrication of large area woodpile structure in polymer

NASA Astrophysics Data System (ADS)

Gupta, Jaya Prakash; Dutta, Neilanjan; Yao, Peng; Sharkawy, Ahmed S.; Prather, Dennis W.

2009-02-01

A fabrication process of three-dimensional Woodpile photonic crystals based on multilayer photolithography from commercially available photo resist SU8 have been demonstrated. A 6-layer, 2 mm × 2mm woodpile has been fabricated. Different factors that influence the spin thickness on multiple resist application have been studied. The fabrication method used removes, the problem of intermixing, and is more repeatable and robust than the multilayer fabrication techniques for three dimensional photonic crystal structures that have been previously reported. Each layer is developed before next layer photo resist spin, instead of developing the whole structure in the final step as used in multilayer process. The desired thickness for each layer is achieved by the calibration of spin speed and use of different photo resist compositions. Deep UV exposure confinement has been the defining parameter in this process. Layer uniformity for every layer is independent of the previous developed layers and depends on the photo resist planarizing capability, spin parameters and baking conditions. The intermixing problem, which results from the previous layers left uncrossed linked photo resist, is completely removed in this process as the previous layers are fully developed, avoiding any intermixing between the newly spun and previous layers. Also this process gives the freedom to redo every spin any number of times without affecting the previously made structure, which is not possible in other multilayer process where intermediate developing is not performed.

Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments.

PubMed

Hörer, Stefan; Reinert, Dirk; Ostmann, Katja; Hoevels, Yvette; Nar, Herbert

2013-06-01

Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein-ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported.

Increasing dissolution of trospium chloride by co-crystallization with urea

NASA Astrophysics Data System (ADS)

Skořepová, Eliška; Hušák, Michal; Čejka, Jan; Zámostný, Petr; Kratochvíl, Bohumil

2014-08-01

The search for various solid forms of an active pharmaceutical ingredient (API) is an important step in drug development. Our aim was to prepare co-crystals of trospium chloride, an anticholinergic drug used for the treatment of incontinence, and to investigate if they have advantageous properties for drug formulation. Phase identification was done by powder X-ray diffraction and single-crystal X-ray diffraction. The chemical composition was verified by solution NMR and the dissolution rate of the prepared phases was studied by IDR (intrinsic dissolution rate). For further analysis of phase stability and transitions, combined thermal analysis and temperature-resolved X-ray powder diffraction were used. Urea was selected as a co-crystallization partner. Trospium chloride urea (1:1) co-crystal was prepared by a solvent evaporation. From single-crystal data, the co-crystal structure was solved in a space group P21/c and compared to previously published structures of trospium chloride. Intrinsic dissolution rate revealed that the co-crystal dissolves 32% faster than pure API. However, its low thermal and pressure stability makes it a challenging choice for the final drug formulation.

Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog.

PubMed

Jaehme, Michael; Guskov, Albert; Slotboom, Dirk Jan

2014-11-01

PnuC transporters catalyze cellular uptake of the NAD+ precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3+1+3 membrane topology not previously observed in any protein. The high symmetry of PnuC with a single NR bound in the center suggests a simple alternating-access translocation mechanism.

Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

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

Pathuri, P.; Nguyen, E.T.; Svard, S.G.

2007-07-12

Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutivemore » over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower-symmetry space group with four molecules in the asymmetric unit. Vesicle-binding studies suggest that alpha-11 giardin, unlike most other annexins, does not bind to vesicles composed of acidic phospholipids in a calcium-dependent manner.« less

Binary ionic porphyrin nanosheets: electronic and light-harvesting properties regulated by crystal structure

NASA Astrophysics Data System (ADS)

Tian, Yongming; M. Beavers, Christine; Busani, Tito; Martin, Kathleen E.; Jacobsen, John L.; Mercado, Brandon Q.; Swartzentruber, Brian S.; van Swol, Frank; Medforth, Craig J.; Shelnutt, John A.

2012-02-01

Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers.Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers. Electronic supplementary information (ESI) available: Details of the crystallographic refinement, tables of refinement parameters and bond distances and NSD analysis, and figures showing SEM images of Zn/Sn nanosheets and clovers, the solid grown at different porphyrin concentrations, SEM images of nanosheets at high and low magnification, an ORTEP image showing the five crystallographically distinct porphyrin molecules and the water molecules, and a view of the crystal structure down the b axis are given in the ESI. CCDC reference number 833006. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr11826b

Some observations on rutherfordine

USGS Publications Warehouse

Clark, Joan R.; Christ, C.L.

1956-01-01

The optical properties of rutherfordine, UO2CO3, previously determined on microscopic crystals, have been redetermined on considerably larger crystals; and the relations among the indices of refraction, the morphology, and the crystal structure have been examined. Rutherfordine is orthorhombic, biaxial positive, with α = 1.715, β = 1.730, γ = 1.795, 2V = 53° (calc.); X = b, Y = c (elongation, Z = a. The crystal structure of UO2CO 3 consists of layers of carbonate groups parallel to (010) with linear (O-U-O) ions normal to the layers. The indices β and γ correspond to vibration directions parallel to layers; the unexpectedly large difference in value between β and γ is ascribed to the optical anisotropy of the uranium-oxygen bonding in the layer. Indexed X-ray powder data are given.

Studies of Nucleation, Growth, Specific Heat, and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Croat, T. K.; Gangopadhyay, A.; Holland-Moritz, D.; Hyers, Robert W.; Rathz, Thomas J.; Robinson, Michael B.; Rogers, Jan R.

2001-01-01

Undercooling experiments and thermal physical property measurements of metallic alloys on the International Space Station (ISS) are planned. This recently-funded research focuses on fundamental issues of the formation and structure of highly-ordered non-crystallographic phases (quasicrystals) and related crystal phases (crystal approximants), and the connections between the atomic structures of these phases and those of liquids and glasses. It extends studies made previously by us of the composition dependence of crystal nucleation processes in silicate and metallic glasses, to the case of nucleation from the liquid phase. Motivating results from rf-levitation and drop-tube measurements of the undercooling of Ti/Zr-based liquids that form quasicrystals and crystal approximants are discussed. Preliminary measurements by electrostatic levitation (ESL) are presented.

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.

PubMed

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-09-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=72.39, b=127.71, c=157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site.

Experimental correlation of melt structures, nucleation rates, and thermal histories of silicate melts

NASA Technical Reports Server (NTRS)

Boynton, W. V.; DRAKE; HILDEBRAND; JONES; LEWIS; TREIMAN; WARK

1987-01-01

The theory and measurement of the structure of liquids is an important aspect of modern metallurgy and igneous petrology. Liquid structure exerts strong controls on both the types of crystals that may precipitate from melts and on the chemical composition of those crystals. An interesting aspect of melt structure studies is the problem of melt memories; that is, a melt can retain a memory of previous thermal history. This memory can influence both nucleation behavior and crystal composition. This melt memory may be characterized quantitatively with techniques such as Raman, infrared and NMR spectroscopy to provide information on short-range structure. Melt structure studies at high temperature will take advantage of the microgravity conditions of the Space Station to perform containerless experiments. Melt structure determinations at high temperature (experiments that are greatly facilitated by containerless technology) will provide invaluable information for materials science, glass technology, and geochemistry. In conjunction with studies of nucleation behavior and nucleation rates, information relevant to nucleation in magma chambers in terrestrial planets will be acquired.

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

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

Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei

2012-02-21

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all ofmore » these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE PAGES

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1

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

Koenigsberg, Andrea L.; Heldwein, Ekaterina E.; Sandri-Goldin, Rozanne M.

Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here,more » we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37. IMPORTANCEThe ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires detailed navigational charts in the form of their three-dimensional structures. Here, we determined the crystal structure of the N-terminal half of a conserved tegument protein, UL37, from HSV-1. This structure, along with our previously reported structure of the UL37 homolog from PRV, provides a much needed 3-dimensional template for the dissection of both conserved and virus-specific functions of UL37 in intracellular capsid trafficking.« less

Three-dimensional Structures of Carotenoids by X-ray Crystallography

NASA Astrophysics Data System (ADS)

Helliwell, Madeleine

The number of crystal structures of carotenoid molecules and carotenoid derivatives deposited in the Cambridge Crystallographic Data Centre [1] is still relatively small, but has increased compared with the previous survey [2]. The list is summarized in Table 1.

Structure and Growth Control of Organic–Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals

PubMed Central

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong

2016-01-01

Recently, organic–inorganic halide perovskites have sparked tremendous research interest because of their ground‐breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light‐emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high‐quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three‐dimensional large sized single crystals, two‐dimensional nanoplates, one‐dimensional nanowires, to zero‐dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high‐performance (opto)electronic devices. PMID:27812463

Lattice-Matched Semiconductor Layers on Single Crystalline Sapphire Substrate

NASA Technical Reports Server (NTRS)

Choi, Sang; King, Glen; Park, Yeonjoon

2009-01-01

SiGe is an important semiconductor alloy for high-speed field effect transistors (FETs), high-temperature thermoelectric devices, photovoltaic solar cells, and photon detectors. The growth of SiGe layer is difficult because SiGe alloys have different lattice constants from those of the common Si wafers, which leads to a high density of defects, including dislocations, micro-twins, cracks, and delaminations. This innovation utilizes newly developed rhombohedral epitaxy of cubic semiconductors on trigonal substrates in order to solve the lattice mismatch problem of SiGe by using trigonal single crystals like sapphire (Al2O3) as substrate to give a unique growth-orientation to the SiGe layer, which is automatically controlled at the interface upon sapphire (0001). This technology is different from previous silicon on insulator (SOI) or SGOI (SiGe on insulator) technologies that use amorphous SiO2 as the growth plane. A cubic semiconductor crystal is a special case of a rhombohedron with the inter-planar angle, alpha = 90 deg. With a mathematical transformation, all rhombohedrons can be described by trigonal crystal lattice structures. Therefore, all cubic lattice constants and crystal planes (hkl) s can be transformed into those of trigonal crystal parameters. These unique alignments enable a new opportunity of perfect lattice matching conditions, which can eliminate misfit dislocations. Previously, these atomic alignments were thought to be impossible or very difficult. With the invention of a new x-ray diffraction measurement method here, growth of cubic semiconductors on trigonal crystals became possible. This epitaxy and lattice-matching condition can be applied not only to SiGe (111)/sapphire (0001) substrate relations, but also to other crystal structures and other materials, including similar crystal structures which have pointgroup rotational symmetries by 120 because the cubic (111) direction has 120 rotational symmetry. The use of slightly miscut (less than plus or minus 10 deg.) sapphire (0001) substrate can be used to improve epitaxial relationships better by providing attractive atomic steps in the epitaxial process.

Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase

PubMed Central

Qin, Ling; Hiser, Carrie; Mulichak, Anne; Garavito, R. Michael; Ferguson-Miller, Shelagh

2006-01-01

Well ordered reproducible crystals of cytochrome c oxidase (CcO) from Rhodobacter sphaeroides yield a previously unreported structure at 2.0 Å resolution that contains the two catalytic subunits and a number of alkyl chains of lipids and detergents. Comparison with crystal structures of other bacterial and mammalian CcOs reveals that the positions occupied by native membrane lipids and detergent substitutes are highly conserved, along with amino acid residues in their vicinity, suggesting a more prevalent and specific role of lipid in membrane protein structure than often envisioned. Well defined detergent head groups (maltose) are found associated with aromatic residues in a manner similar to phospholipid head groups, likely contributing to the success of alkyl glycoside detergents in supporting membrane protein activity and crystallizability. Other significant features of this structure include the following: finding of a previously unreported crystal contact mediated by cadmium and an engineered histidine tag; documentation of the unique His–Tyr covalent linkage close to the active site; remarkable conservation of a chain of waters in one proton pathway (D-path); and discovery of an inhibitory cadmium-binding site at the entrance to another proton path (K-path). These observations provide important insight into CcO structure and mechanism, as well as the significance of bound lipid in membrane proteins. PMID:17050688

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design

PubMed Central

Omari, Kamel EL; Bronckaers, Annelies; Liekens, Sandra; Pérez-Pérez, Maria-Jésus; Balzarini, Jan; Stammers, David K.

2006-01-01

HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end com-plex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406–415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs. PMID:16803458

PRINCEPS: A computer-based approach to the structural description and recognition of trends within structural databases, and its application to the Ce-Ni-Si System

DOE PAGES

Guo, Yiming; Fredrickson, Daniel C.

2016-04-01

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.

The transmission spectrum of sound through a phononic crystal subjected to liquid flow

NASA Astrophysics Data System (ADS)

Declercq, Nico F.; Chehami, Lynda; Moiseyenko, Rayisa P.

2018-01-01

The influence of liquid-flow up to 7 mm/s is examined on transmission spectra of phononic crystals, revealing a potential use for slow liquid-flow measurement techniques. It is known that transmission of ultrasound through a phononic crystal is determined by its periodicity and depends on the material characteristics of the crystal's constituents. Here, the crystal consists of metal rods with the space in between filled with water. Previous studies have assumed still water in the crystal, and here, we consider flowing liquid. First, the crystal bandgaps are investigated in still water, and the results of transmission experiments are compared with theoretical band structures obtained with the finite element method. Then, changes in transmission spectra are investigated for different speeds of liquid flow. Two situations are investigated: a crystal is placed with a principal symmetry axis in the flow direction ( ΓX) and then at an angle ( ΓM). The good stability of the bandgap structure of the transmission spectrum for both directions is observed, which may be of importance for the application of phononic crystals as acoustic filters in an environment of flowing liquid. Minor transmission amplitude changes on the other hand reveal a possibility for slow liquid flow measurements.

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

PubMed

Penttinen, Leena; Rutanen, Chiara; Saloheimo, Markku; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

2018-01-01

Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

Polarization-independent actively tunable colour generation on imprinted plasmonic surfaces

PubMed Central

Franklin, Daniel; Chen, Yuan; Vazquez-Guardado, Abraham; Modak, Sushrut; Boroumand, Javaneh; Xu, Daming; Wu, Shin-Tson; Chanda, Debashis

2015-01-01

Structural colour arising from nanostructured metallic surfaces offers many benefits compared to conventional pigmentation based display technologies, such as increased resolution and scalability of their optical response with structure dimensions. However, once these structures are fabricated their optical characteristics remain static, limiting their potential application. Here, by using a specially designed nanostructured plasmonic surface in conjunction with high birefringence liquid crystals, we demonstrate a tunable polarization-independent reflective surface where the colour of the surface is changed as a function of applied voltage. A large range of colour tunability is achieved over previous reports by utilizing an engineered surface which allows full liquid crystal reorientation while maximizing the overlap between plasmonic fields and liquid crystal. In combination with imprinted structures of varying periods, a full range of colours spanning the entire visible spectrum is achieved, paving the way towards dynamic pixels for reflective displays. PMID:26066375

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

PubMed

Mir, Aamir; Golden, Barbara L

2016-02-02

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

Crystal Structures of the Receiver Domain of the Response Regulator PhoP from Escherichia coli in the Absence and Presence of the Phosphoryl Analog Beryllofluoride▿

PubMed Central

Bachhawat, Priti; Stock, Ann M.

2007-01-01

The response regulator PhoP is part of the PhoQ/PhoP two-component system involved in responses to depletion of extracellular Mg2+. Here, we report the crystal structures of the receiver domain of Escherichia coli PhoP determined in the absence and presence of the phosphoryl analog beryllofluoride. In the presence of beryllofluoride, the active receiver domain forms a twofold symmetric dimer similar to that seen in structures of other regulatory domains from the OmpR/PhoB family, providing further evidence that members of this family utilize a common mode of dimerization in the active state. In the absence of activating agents, the PhoP receiver domain crystallizes with a similar structure, consistent with the previous observation that high concentrations can promote an active state of PhoP independent of phosphorylation. PMID:17545283

Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

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

Mir, Aamir; Golden, Barbara L.

2015-11-09

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the p K A of G12. Finally, on the basis ofmore » this crystal structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.« less

Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde

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

Vetting, Matthew W., E-mail: vetting@aecom.yu.edu; Hegde, Subray S.; Blanchard, John S.

2009-05-01

A method to modify proteins with glutaraldehyde under reducing conditions is presented. Treatment with glutaraldehyde and dimethylaminoborane was found to result in cyclic pentylation of free amines and facilitated the structural determination of a protein previously recalcitrant to the formation of diffraction quality crystals. The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane–dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 Å resolution;more » their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.« less

Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.

PubMed

Manjasetty, Babu A; Chance, Mark R

2006-07-07

Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 A resolution. The subunit structure of ECAI is organised into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase

PubMed Central

Jaffe, Eileen K.; Shanmugam, Dhanasekaran; Gardberg, Anna; Dieterich, Shellie; Sankaran, Banumathi; Stewart, Lance J.; Myler, Peter J.; Roos, David S.

2011-01-01

Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors. PMID:21383008

Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96

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

Ida, Koh; E-mail: idakoh@sci.kitasato-u.ac.jp; Moriguchi, Tomotaka

2005-07-29

Sarcosine oxidase from Corynebacterium sp. U-96 is a heterotetrameric enzyme. Here we report the crystal structures of the enzyme in complex with dimethylglycine and folinic acid. The {alpha} subunit is composed of two domains, contains NAD{sup +}, and binds folinic acid. The {beta} subunit contains dimethylglycine, FAD, and FMN, and these flavins are approximately 10 A apart. The {gamma} subunit is in contact with two domains of {alpha} subunit and has possibly a folate-binding structure. The {delta} subunit contains a single atom of zinc and has a Cys{sub 3}His zinc finger structure. Based on the structures determined and on themore » previous works, the structure-function relationship on the heterotetrameric sarcosine oxidase is discussed.« less

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi-Gang

2017-03-06

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2017-02-28

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

One-Dimensional Photonic Crystal Superprisms

NASA Technical Reports Server (NTRS)

Ting, David

2005-01-01

Theoretical calculations indicate that it should be possible for one-dimensional (1D) photonic crystals (see figure) to exhibit giant dispersions known as the superprism effect. Previously, three-dimensional (3D) photonic crystal superprisms have demonstrated strong wavelength dispersion - about 500 times that of conventional prisms and diffraction gratings. Unlike diffraction gratings, superprisms do not exhibit zero-order transmission or higher-order diffraction, thereby eliminating cross-talk problems. However, the fabrication of these 3D photonic crystals requires complex electron-beam substrate patterning and multilayer thin-film sputtering processes. The proposed 1D superprism is much simpler in structural complexity and, therefore, easier to design and fabricate. Like their 3D counterparts, the 1D superprisms can exhibit giant dispersions over small spectral bands that can be tailored by judicious structure design and tuned by varying incident beam direction. Potential applications include miniature gas-sensing devices.

Reply to “Structural and magnetic behavior of the cubic oxyfluoride SrFeO{sub 2}F studied by neutron diffraction”

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

Clemens, Oliver, E-mail: oliver.clemens@kit.edu; Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen; Berry, Frank J.

2015-03-15

In this article we comment on the results published by Thompson et al. (, J. Solid State Chem. 219 (2014) 173–178) on the crystal structure of SrFeO{sub 2}F, who claim the compound to crystallize in the cubic space group Pm-3m. We give a more detailed explanation of the determination of our previously reported structural model with Imma symmetry (Clemens et al., J. Solid State Chem. 206 (2013) 158–169), with addition of variable temperature XRD measurements with high counting time to provide unambiguous evidence for the Imma model being correct for our sample. - Graphical abstract: The crystal structure of SrFeO{submore » 2}F is discussed with regards to previous reports. - Highlights: • SrFeO{sub 2}F was synthesized by polymer based fluorination of SrFeO{sub 3}. • Evaluation of the diffraction data shows a pseudocubic cell metric. • Superstructure reflections at low d-spacings indicate deviation from cubic symmetry. • The phase transition temperature from orthorhombic to cubic was determined using variable temperature X-ray diffraction. • Results published by Thompson et al. are critically discussed with respect to those observations.« less

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

PubMed

Choudhury, R R; Chitra, R; Selezneva, E V; Makarova, I P

2017-10-01

The structure of the mixed crystal [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K 3 H(SO 4 ) 2 . The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K + with NH 4 + has a significant influence on the short strong hydrogen bond connecting the two SO 4 2- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 are much faster than in K 3 H(SO 4 ) 2 ; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Crystal Structure of a Phosphorylated Light Chain Domain of Scallop Smooth-Muscle Myosin

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

Kumar, V.S.; Robinson, H.; O-Neall-Hennessey, E.

2011-11-02

We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg{sup 16}, an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upon phosphorylation. This resultmore » provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.« less

Structure of the Apo Form of Bacillus stearothermophilus Phosphofructokinase

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

Mosser, Rockann; Reddy, Manchi C.M.; Bruning, John B.

2012-02-08

The crystal structure of the unliganded form of Bacillus stearothermophilus phosphofructokinase (BsPFK) was determined using molecular replacement to 2.8 {angstrom} resolution (Protein Data Bank entry 3U39). The apo BsPFK structure serves as the basis for the interpretation of any structural changes seen in the binary or ternary complexes. When the apo BsPFK structure is compared with the previously published liganded structures of BsPFK, the structural impact that the binding of the ligands produces is revealed. This comparison shows that the apo form of BsPFK resembles the substrate-bound form of BsPFK, a finding that differs from previous predictions.

Crystal structure of the human 4-1BB/4-1BBL complex.

PubMed

Gilbreth, Ryan N; Oganesyan, Vaheh Y; Amdouni, Hamza; Novarra, Shabazz; Grinberg, Luba; Barnes, Arnita; Baca, Manuel

2018-05-02

4-1BBL is a member of the TNF superfamily and is the ligand for the TNFRsuperfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells and agonists of this receptor have garnered strong attention as potentialimmunotherapy agents. Broadly speaking, the structural features of TNF superfamilymembers, their receptors and ligand/receptor complexes are similar. However, apublished crystal structure of human 4-1BBL suggests that it may be unique in thisregard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4 Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Crystal-chemical characteristics of nontronites from bottom sediments of Pacific ocean

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

Palchik, N. A., E-mail: nadezhda@igm.nsc.ru; Moroz, T. N.; Grigorieva, T. N.

A crystal-chemical analysis of the nontronite samples formed in deep-water sediments of the underwater Juan-de-Fuca ridge in the Pacific ocean has been performed using powder X-ray diffraction, IR spectroscopy, and Mössbauer spectroscopy. A comparison with the previously investigated nontronites from different regions of the Sea of Okhotsk showed that the structural features of these formations are due to the difference in the physicochemical parameters of their crystallization. The values of the basal interplanar spacing d{sub 001} (within 11–13 Å) in the samples analyzed are determined by the degree of hydration and cation filling of the interlayer space, while the differencesmore » in the IR spectra are due to isomorphic substitutions in the structure. The character of cation distribution and the nature and concentration of stacking faults in nontronite structures are determined. The differences in the composition, structure, and properties of nontronites of different origin are confirmed by theoretical calculations of their structural parameters.« less

Research on soundproof properties of cylindrical shells of generalized phononic crystals

NASA Astrophysics Data System (ADS)

Liu, Ru; Shu, Haisheng; Wang, Xingguo

2017-04-01

Based on the previous studies, the concept of generalized phononic crystals (GPCs) is further introduced into the cylindrical shell structures in this paper. And a type of cylindrical shells of generalized phononic crystals (CS-GPCs) is constructed, the structural field and acoustic-structural coupled field of the composite cylindrical shells are examined respectively. For the structural field, the transfer matrix method of mechanical state vector is adopted to build the transfer matrix of radial waves propagating from inside to outside. For the acoustic-structural coupled field, the expressions of the acoustic transmission/reflection coefficients and the sound insulation of acoustic waves with the excitation of center line sound source are set up. And the acoustic transmission coefficient and the frequency response of sound insulation in this mode were numerical calculated. Furthermore, the theoretical analysis results are verified by using the method of combining the numerical calculation and finite element simulation. Finally, the effects of inner and outer fluid parameters on the transmission/reflection coefficients of CS-GPCs are analyzed in detail.

2.4 Å resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrix.

PubMed

Sung, Nuri; Lee, Jungsoon; Kim, Ji Hyun; Chang, Changsoo; Tsai, Francis T F; Lee, Sukyeong

2016-08-01

TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1NM dimer is presented, featuring an intact N-domain and M-domain structure, bound to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.

A new pseudopolymorph of diphenic acid and 4,4‧-bipyridine co-crystal: Structural and theoretical study

NASA Astrophysics Data System (ADS)

Soleimannejad, Janet; Nazarnia, Esfandiar; Stoeckli-Evans, Helen

2014-11-01

A new pseudopolymorph (B; tetragonal, I41/acd) of the cocrystal biphenyl-2,2‧-dicarboxylic acid (diphenic acid) and 4,4‧-bipyridine was synthesized. Its solid-state structure and supramolecular synthons responsible for extending the supramolecular network have been compared with those of the previously reported polymorph (A; triclinic, P1bar). DFT calculations at the B3LYP/6-311G++ (2d,2p) level have been performed. Energies of the intermolecular hydrogen bonds in the crystal structure were calculated and their electronic aspects were investigated by NBO and AIM analysis.

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate

PubMed Central

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-01-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxy­acetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 72.39, b = 127.71, c = 157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. PMID:21904049

The Cytoplasmic Permeation Pathway of Neurotransmitter Transporters†

PubMed Central

Rudnick, Gary

2011-01-01

Ion-coupled solute transporters are responsible for transporting nutrients, ions and signaling molecules across a variety of biological membranes. Recent high-resolution crystal structures of several transporters from protein families that were previously thought to be unrelated show common structural features indicating a large structural family representing transporters from all kingdoms of life. This review describes studies that led to an understanding of the conformational changes required for solute transport in this family. The first structure in this family showed the bacterial amino acid transporter LeuT, which is homologous to neurotransmitter transporters, in an extracellularly-oriented conformation with a molecule of leucine occluded at the substrate site. Studies with the mammalian serotonin transporter identified positions, buried in the LeuT structure, that defined a potential pathway leading from the cytoplasm to the substrate binding site. Modeling studies utilized an inverted structural repeat within the LeuT crystal structure to predict the conformation of LeuT in which the cytoplasmic permeation pathway, consisting of positions identified in SERT, was open for substrate diffusion to the cytoplasm. From the difference between the model and the crystal structures, a simple “rocking bundle” mechanism was proposed, in which a 4-helix bundle changed its orientation with respect to the rest of the protein to close the extracellular pathway and open the cytoplasmic one. Subsequent crystal structures from structurally related proteins provide evidence supporting this model for transport. PMID:21774491

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774

PubMed Central

Gavel, Olga Yu.; Kladova, Anna V.; Bursakov, Sergey A.; Dias, João M.; Texeira, Susana; Shnyrov, Valery L.; Moura, José J. G.; Moura, Isabel; Romão, Maria J.; Trincão, José

2008-01-01

Native zinc/cobalt-containing ATP sulfurylase (ATPS; EC 2.7.7.4; MgATP:sulfate adenylyltransferase) from Desulfovibrio desulfuricans ATCC 27774 was purified to homogeneity and crystallized. The orthorhombic crystals diffracted to beyond 2.5 Å resolution and the X-ray data collected should allow the determination of the structure of the zinc-bound form of this ATPS. Although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the asymmetric unit. Elucidation of this structure will permit a better understanding of the role of the metal in the activity and stability of this family of enzymes. PMID:18607083

Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

PubMed Central

Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-01-01

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

Serial femtosecond crystallography: A revolution in structural biology.

PubMed

Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

2016-07-15

Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. Published by Elsevier Inc.

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Anisotropic surface physicochemical properties of spodumene and albite crystals: Implications for flotation separation

NASA Astrophysics Data System (ADS)

Xu, Longhua; Peng, Tiefeng; Tian, Jia; Lu, Zhongyuan; Hu, Yuehua; Sun, Wei

2017-12-01

Aluminosilicate minerals (e.g., spodumene, albite) have complex crystal structures and similar surface chemistries, but they have poor selectivity compared to traditional fatty acid collectors, making flotation separation difficult. Previous research has mainly considered the mineral crystal structure as a whole. In contrast, the surface characteristics at the atomic level and the effects of different crystal interfaces on the flotation behavior have rarely been investigated. This study focuses on investigating the surface anisotropy quantitatively, including the chemical bond characteristics, surface energies, and broken bond densities, using density functional theory and classical theoretical calculations. In addition, the anisotropy of the surface wettability and adsorption characteristics were examined using contact angle, zeta potential, and Fourier-transform infrared measurements. Finally, these surface anisotropies with different flotation behaviors were investigated and interpreted using molecular dynamics simulations, scanning electron microscopy, and X-ray photoelectron spectroscopy. This systematic research offers new ideas concerning the selective grinding and stage flotation of aluminosilicate minerals based on the crystal characteristics.

X-Ray Computed Tomography of Tranquility Base Moon Rock

NASA Technical Reports Server (NTRS)

Jones, Justin S.; Garvin, Jim; Viens, Mike; Kent, Ryan; Munoz, Bruno

2016-01-01

X-ray Computed Tomography (CT) was used for the first time on the Apollo 11 Lunar Sample number 10057.30, which had been previously maintained by the White House, then transferred back to NASA under the care of Goddard Space Flight Center. Results from this analysis show detailed images of the internal structure of the moon rock, including vesicles (pores), crystal needles, and crystal bundles. These crystals, possibly the common mineral ilmenite, are found in abundance and with random orientation. Future work, in particular a greater understanding of these crystals and their formation, may lead to a more in-depth understanding of the lunar surface evolution and mineral content.

Reinvestigation of L-tryptophan picrate: Establishment of the existence of the L-tryptophan L-tryptophanium dimeric cation

NASA Astrophysics Data System (ADS)

Petrosyan, A. M.; Fleck, M.; Ghazaryan, V. V.

2013-03-01

A crystal structure redetermination of the L-tryptophan picrate crystal previously studied by Ishida et al. (Chem. Pharm. Bull. 41 (1993) 433-438) showed that it comprises L-tryptophan L-tryptophanium dimeric cation, one picrate anion and picric acid. The O⋯O distance of the O-H⋯O hydrogen bond in the dimeric cation is equal to 2.470(6) Å. The infrared spectrum of the crystal was registered and analyzed. The infrared spectrum of the crystals contains a broad absorption band centered at ca. 1170 cm-1, which is assigned to the stretching vibration of the O-H bond.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

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

Morshed, Nader; Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Echols, Nathaniel, E-mail: nechols@lbl.gov

2015-05-01

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here,more » the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

1.8 Å structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells

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

Chattopadhyay, Kausik; Ramagopal, Udupi A.; Nathenson, Stanley G., E-mail: nathenso@aecom.yu.edu

2009-05-01

1.8 Å X-ray crystal structure of mouse GITRL expressed in D. melanogaster S2 cells shows an identical ‘strand-exchanged’ dimeric assembly similar to that observed previously for the E. coli-expressed protein. Glucocorticoid-induced TNF receptor ligand (GITRL), a prominent member of the TNF superfamily, activates its receptor on both effector and regulatory T cells to generate critical costimulatory signals that have been implicated in a wide range of T-cell immune functions. The crystal structures of murine and human orthologs of GITRL recombinantly expressed in Escherichia coli have previously been determined. In contrast to all classical TNF structures, including the human GITRL structure,more » murine GITRL demonstrated a unique ‘strand-exchanged’ dimeric organization. Such a novel assembly behavior indicated a dramatic impact on receptor activation as well as on the signaling mechanism associated with the murine GITRL costimulatory system. In this present work, the 1.8 Å resolution crystal structure of murine GITRL expressed in Drosophila melanogaster S2 cells is reported. The eukaryotic protein-expression system allows transport of the recombinant protein into the extracellular culture medium, thus maximizing the possibility of obtaining correctly folded material devoid of any folding/assembly artifacts that are often suspected with E. coli-expressed proteins. The S2 cell-expressed murine GITRL adopts an identical ‘strand-exchanged’ dimeric structure to that observed for the E. coli-expressed protein, thus conclusively demonstrating the novel quaternary structure assembly behavior of murine GITRL.« less

Multiple pathways of crystal nucleation in an extremely supersaturated aqueous potassium dihydrogen phosphate (KDP) solution droplet

PubMed Central

Lee, Sooheyong; Wi, Haeng Sub; Jo, Wonhyuk; Cho, Yong Chan; Lee, Hyun Hwi; Jeong, Se-Young; Kim, Yong-Il; Lee, Geun Woo

2016-01-01

Solution studies have proposed that crystal nucleation can take more complex pathways than previously expected in classical nucleation theory, such as formation of prenucleation clusters or densified amorphous/liquid phases. These findings show that it is possible to separate fluctuations in the different order parameters governing crystal nucleation, that is, density and structure. However, a direct observation of the multipathways from aqueous solutions remains a great challenge because heterogeneous nucleation sites, such as container walls, can prevent these paths. Here, we demonstrate the existence of multiple pathways of nucleation in highly supersaturated aqueous KH2PO4 (KDP) solution using the combination of a containerless device (electrostatic levitation), and in situ micro-Raman and synchrotron X-ray scattering. Specifically, we find that, at an unprecedentedly deep level of supersaturation, a high-concentration KDP solution first transforms into a metastable crystal before reaching stability at room temperature. However, a low-concentration solution, with different local structures, directly transforms into the stable crystal phase. These apparent multiple pathways of crystallization depend on the degree of supersaturation. PMID:27791068

Multiple pathways of crystal nucleation in an extremely supersaturated aqueous potassium dihydrogen phosphate (KDP) solution droplet.

PubMed

Lee, Sooheyong; Wi, Haeng Sub; Jo, Wonhyuk; Cho, Yong Chan; Lee, Hyun Hwi; Jeong, Se-Young; Kim, Yong-Il; Lee, Geun Woo

2016-11-29

Solution studies have proposed that crystal nucleation can take more complex pathways than previously expected in classical nucleation theory, such as formation of prenucleation clusters or densified amorphous/liquid phases. These findings show that it is possible to separate fluctuations in the different order parameters governing crystal nucleation, that is, density and structure. However, a direct observation of the multipathways from aqueous solutions remains a great challenge because heterogeneous nucleation sites, such as container walls, can prevent these paths. Here, we demonstrate the existence of multiple pathways of nucleation in highly supersaturated aqueous KH 2 PO 4 (KDP) solution using the combination of a containerless device (electrostatic levitation), and in situ micro-Raman and synchrotron X-ray scattering. Specifically, we find that, at an unprecedentedly deep level of supersaturation, a high-concentration KDP solution first transforms into a metastable crystal before reaching stability at room temperature. However, a low-concentration solution, with different local structures, directly transforms into the stable crystal phase. These apparent multiple pathways of crystallization depend on the degree of supersaturation.

Structure of Greyhound hemoglobin: origin of high oxygen affinity.

PubMed

Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

2011-05-01

This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

Direct observation of the ferroelectric polarization in the layered perovskite Bi{sub 4}Ti{sub 3}O{sub 12}

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

Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp; Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Nagoya 466-8555

We investigated the crystal structure and ferroelectric domains of Bi{sub 4}Ti{sub 3}O{sub 12} (BTO) by means of transmission electron microscopy (TEM) and single-crystal X-ray diffractometry. From the extinction rule, we determined that the space group in the ferroelectric phase of BTO is P1a1 rather than B2cb and B1a1 which have been proposed previously. We successfully refined the crystal structure based on the space group P1a1. The 180° and 90° ferroelectric domain structures were observed by the [001]-zone dark-field TEM imaging. In the 180° domain structure, we determined that one component of the polarization vector is parallel to the a-axis. Anmore » annular bright-field scanning transmission electron microscopy (ABF-STEM) was performed for the direct observation of the crystal structures. The ABF-STEM images displayed the contrasts with respect to every atomic position in spite of the highly distorted structure of BTO. We could evaluate the tilting and distortion of the [TiO{sub 6}] octahedra relatively. Therefore, we directly observed the ferroelectric displacements of Bi and Ti ions.« less

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.

PubMed

Johnson, Jennifer L; Entzminger, Kevin C; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P; Morales, Ivan A; Sheppard, Aly; Gumbart, James C; Maynard, Jennifer A; Lieberman, Raquel L

2015-04-01

Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.

Diamond Lattice Colloidal Crystals from Binary DNA-grafted Microspheres

NASA Astrophysics Data System (ADS)

Crocker, John; Wang, Yifan; Jenkins, Ian; McGinley, James; Sinno, Talid

Future optical materials promise to do for photonics what semiconductors did for electronics, but the challenge has long been in creating the structure they require regular, three-dimensional array of transparent microspheres arranged like the atoms in a diamond crystal. Here we demonstrate a simple approach for spontaneously growing double-diamond (or B32) crystals from a binary suspension of sub-micron polymer microspheres with synthetic DNA grafted to their surfaces. While diamond symmetry crystals have previously been grown from much smaller nanoparticles, none of those methods appear workable for the larger particles needed for photonic applications, whose size must be comparable to the wavelength of visible light. Intriguingly, matched simulations fail to nucleate or grow B32 crystals from suspension; nor have they been predicted on the basis of theoretical arguments. We conjecture that the B32 crystals may form via transformation from a precursor with a different lattice structure in the bulk or on its surface. The feasibility of converting our self-assembled crystals into diamond-symmetry photonic templates will be discussed. This finding suggests that still other unexpected microstructures may be accessible using this approach. US National Science Foundation, CBET- 1403237.

New phases of osmium carbide from evolutionary algorithm and ab initio computations

NASA Astrophysics Data System (ADS)

Fadda, Alessandro; Fadda, Giuseppe

2017-09-01

New crystal phases of osmium carbide are presented in this work. These results were found with the CA code, an evolutionary algorithm (EA) presented in a previous paper which takes full advantage of crystal symmetry by using an ad hoc search space and genetic operators. The new OsC2 and Os2C structures have a lower enthalpy than any known so far. Moreover, the layered pattern of OsC2 serves as a blueprint for building new crystals by adding or removing layers of carbon and/or osmium and generating many other Os  +  C structures like Os2C, OsC, OsC2 and OsC4. These again have a lower enthalpy than all the investigated structures, including those of the present work. The mechanical, vibrational and electronic properties are discussed as well.

Reconfigurable all-optical NOT, XOR, and NOR logic gates based on two dimensional photonic crystals

NASA Astrophysics Data System (ADS)

Parandin, Fariborz; Malmir, M. Reza; Naseri, Mosayeb; Zahedi, Abdulhamid

2018-01-01

Photonic crystals can be considered as one of the most important basis for designing optical devices. In this research, using two-dimensional photonic crystals with triangular lattices, ultra-compact logic gates are designed and simulated. The intended structure has the capability to be used as three logical gates (NOT, XOR, and NOR). The designed structures not only have characteristics of small dimensions which make them suitable for integrated optical circuits, but also exhibit very low power transfer delay which makes it possible to design high speed gates. On comparison with the previous works, our simulations show that at a wavelength of 1.55 μm , the gates indicate a time delay of about 0.1 ps and the contrast ratio for the XOR gate is about 30 dB, i.e., the proposed structures are more applicable in designing low error optical logic gates.

Molecular Assembly of Clostridium botulinum progenitor M complex of type E.

PubMed

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems

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

Zhang, Hongmin; Astrof, Nathan S.; Liu, Jin-Huan

2009-09-15

Volatile anesthetics (VAs), such as isoflurane, induce a general anesthetic state by binding to specific targets (i.e., ion channels) in the central nervous system (CNS). Simultaneously, VAs modulate immune functions, possibly via direct interaction with alternative targets on leukocytes. One such target, the integrin lymphocyte function-associated antigen-1 (LFA-1), has been shown previously to be inhibited by isoflurane. A better understanding of the mechanism by which isoflurane alters protein function requires the detailed information about the drug-protein interaction at an atomic level. Here, we describe the crystal structure of the LFA-1 ligand-binding domain (I domain) in complex with isoflurane at 1.6more » {angstrom}. We discovered that isoflurane binds to an allosteric cavity previously implicated as critical for the transition of LFA-1 from the low- to the high-affinity state. The isoflurane binding site in the I domain involves an array of amphiphilic interactions, thereby resembling a 'common anesthetic binding motif' previously predicted for authentic VA binding sites. These results suggest that the allosteric modulation of protein function by isoflurane, as demonstrated for the integrin LFA-1, might represent a unified mechanism shared by the interactions of volatile anesthetics with targets in the CNS. Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems.« less

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

PubMed

Horrell, Sam; Kekilli, Demet; Sen, Kakali; Owen, Robin L; Dworkowski, Florian S N; Antonyuk, Svetlana V; Keal, Thomas W; Yong, Chin W; Eady, Robert R; Hasnain, S Samar; Strange, Richard W; Hough, Michael A

2018-05-01

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

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

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

NMR and X-ray structural characterization and conformational aspects of fluorinated (5Z)-3-benzil-5-arylidenofuran-2(5H)-ones

NASA Astrophysics Data System (ADS)

Teixeira, R. R.; Barbosa, L. C. A.; Kabeshov, M. A.; Maltha, C. R. A.; Corrêa, R. S.; Doriguetto, A. C.

2014-10-01

Herein we describe structural insights of (5Z)-3-benzyl-5-(2-fluorobenzylidene)furan-2(5H)-one (6) and (5Z)-3-benzyl-5-(pentafluorobenzylidene)furan-2(5H)-one (7), γ-alkylidenebutenolides analogues of the natural products nostoclides. Their structures were investigated by NMR spectroscopy and X-ray crystallography. The stereochemistry of the exocyclic double bond of these fluorinated compounds was determined to be Z by NMR analysis and confirmed by X-ray data. Compounds 6 and 7 crystallized in the monoclinic crystal system P21/c group. A comparison between structural features of (6) and (7) and nostoclide derivatives previously published by us is described.

Analytical coupled-wave model for photonic crystal surface-emitting quantum cascade lasers.

PubMed

Wang, Zhixin; Liang, Yong; Yin, Xuefan; Peng, Chao; Hu, Weiwei; Faist, Jérôme

2017-05-15

An analytical coupled-wave model is developed for surface-emitting photonic-crystal quantum cascade lasers (PhC-QCLs). This model provides an accurate and efficient analysis of full three-dimensional device structure with large-area cavity size. Various laser properties of interest including the band structure, mode frequency, cavity loss, mode intensity profile, and far field pattern (FFP), as well as their dependence on PhC structures and cavity size, are investigated. Comparison with numerical simulations confirms the accuracy and validity of our model. The calculated FFP and polarization profile well explain the previously reported experimental results. In particular, we reveal the possibility of switching the lasing modes and generating single-lobed FFP by properly tuning PhC structures.

Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

PubMed

Akter, Mahfuza; Inoue, Chika; Komori, Hirofumi; Matsuda, Nana; Sakurai, Takeshi; Kataoka, Kunishige; Higuchi, Yoshiki; Shibata, Naoki

2016-10-01

Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed. Tiny crystals were obtained from the deuterated CueO initially prepared from the original construct. The X-ray crystal structure of the deuterated CueO showed that the protein contained an incompletely truncated signal sequence at the N-terminus, which resulted in the heterogeneity of the protein sample for crystallization. Here, a new CueO expression system that had an HRV3C cleavage site just after the signal sequence was constructed. Deuterated CueO from the new construct was expressed in cells cultured in deuterated algae-extract medium and the signal sequence was completely eliminated by HRV3C protease. The deuteration level of the purified protein was estimated by MALDI-TOF mass spectrometry to be at least 83.2% compared with nondeuterated protein. Nondeuterated CueO crystallized in space group P2 1 , with unit-cell parameters a = 49.51, b = 88.79, c = 53.95 Å, β = 94.24°, and deuterated CueO crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.91, b = 106.92, c = 262.89 Å. The crystallographic parameters for the crystals of the new construct were different from those previously reported for nondeuterated crystals. The nondeuterated and deuterated CueO from the new construct had similar UV-Vis spectra, enzymatic activities and overall structure and geometry of the ligands of the Cu atoms in the active site to those of previously reported CueO structures. These results indicate that the CueO protein prepared using the new construct is suitable for further neutron diffraction studies.

Method and apparatus for conducting structural health monitoring in a cryogenic, high vibration environment

NASA Technical Reports Server (NTRS)

Qing, Xinlin (Inventor); Beard, Shawn J. (Inventor); Li, Irene (Inventor)

2013-01-01

Sensors affixed to various such structures, where the sensors can withstand, remain affixed, and operate while undergoing both cryogenic temperatures and high vibrations. In particular, piezoelectric single crystal transducers are utilized, and these sensors are coupled to the structure via a low temperature, heat cured epoxy. This allows the transducers to monitor the structure while the engine is operating, even despite the harsh operating conditions. Aspects of the invention thus allow for real time monitoring and analysis of structures that operate in conditions that previously did not permit such analysis. A further aspect of the invention relates to use of piezoelectric single crystal transducers. In particular, use of such transducers allows the same elements to be used as both sensors and actuators.

Thermally induced crystallization kinetics of uncrosslinked and unfilled synthetic cis-1,4-polyisoprene rubber monitored by shear rheological tests

NASA Astrophysics Data System (ADS)

Yang, Wei; Hong, Daesun; Kim, Hyungsu; Kim, Byungsoo; Chang, Wenji V.

2016-11-01

This study demonstrates the unique capability of a shear rotational rheometer for studying the thermally induced crystallization (TIC) of uncrosslinked and unfilled cis-1,4-polyisoprene rubber (IR). At temperatures below -15°C, a crystallization phenomenon (TIC) occurred in a quasi-unstrained IR specimen. Such a distinguished phenomenon was determined from the steady and sharp changes of both tanδ and the modulus. The changing ratio of those parameters with time characterizes the crystallization rate, on which the effects of the compressive force magnitude, testing repeat, and temperature are studied. The crystallization rate was shown to depend less on the magnitude of normal force, but depended largely on the specimen's previous testing history. A specimen not fully recovered from the previous crystallized memory showed a faster rate than before. More cooling to -25°C increased the crystallization rate, but the slow crystallization helped increase the final crystallinity. The crystallization rate was further interpreted by the Avrami equation to propose the crystal structure, whose morphological feature was shown in agreement with the reported TEM and X-ray results. However, our study found a thermo-mechanically aged specimen showed a very different rheological behavior at the late stage of crystallization suggesting the crystalline metamorphosis. But this unexpected behavior turned out to be unrecoverable indicating a property failure due to material aging more plausibly. All these findings were successfully monitored by the rheometer. It is expected the well-organized rheometric measurements can sufficiently supplement some instrumental limitations of the traditional crystallization monitoring analyzers on soft materials.

Analysis of the crystal structure of an active MCM hexamer.

PubMed

Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J

2014-09-29

In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis.

Anisotropic lattice softening near the structural phase transition in the thermosalient crystal 1,2,4,5-tetrabromobenzene.

PubMed

Zakharov, Boris A; Michalchuk, Adam A L; Morrison, Carole A; Boldyreva, Elena V

2018-03-28

The thermosalient effect (crystal jumping on heating) attracts much attention as both an intriguing academic phenomenon and in relation to its potential for the development of molecular actuators but its mechanism remains unclear. 1,2,4,5-Tetrabromobenzene (TBB) is one of the most extensively studied thermosalient compounds that has been shown previously to undergo a phase transition on heating, accompanied by crystal jumping and cracking. The difference in the crystal structures and intermolecular interaction energies of the low- and high-temperature phases is, however, too small to account for the large stress that arises over the course of the transformation. The energy is released spontaneously, and crystals jump across distances that exceed the crystal size by orders of magnitude. In the present work, the anisotropy of lattice strain is followed across the phase transition by single-crystal X-ray diffraction, focusing on the structural evolution from 273 to 343 K. A pronounced lattice softening is observed close to the transition point, with the structure becoming more rigid immediately after the phase transition. The diffraction studies are further supported by theoretical analysis of pairwise intermolecular energies and zone-centre lattice vibrations. Only three modes are found to monotonically soften up to the phase transition, with complex behaviour exhibited by the remaining lattice modes. The thermosalient effect is delayed with respect to the structural transformation itself. This can originate from the martensitic mechanism of the transformation, and the accumulation of stress associated with vibrational switching across the phase transition. The finding of this study sheds more light on the nature of the thermosalient effect in 1,2,4,5-tetrabromobenzene and can be applicable also to other thermosalient compounds.

First- and second-order Raman scattering from MoTe2 single crystal

NASA Astrophysics Data System (ADS)

Caramazza, Simone; Collina, Arianna; Stellino, Elena; Ripanti, Francesca; Dore, Paolo; Postorino, Paolo

2018-02-01

We report on Raman experiments performed on a MoTe2 single crystal. The system belongs to the wide family of transition metal dichalcogenides which includes several of the most interesting two-dimensional materials for both basic and applied physics. Measurements were performed in the standard basal plane configuration, by placing the ab plane of the crystal perpendicular to the wave vector k i of the incident beam to explore the in-plane vibrational modes, and in the edge plane configuration with k i perpendicular to the crystal c axis, thus mainly exciting out-of-plane modes. For both configurations we performed a polarization-dependent study of the first-order Raman components and detailed computation of the corresponding selection rules. We were thus able to provide a complete assignment of the observed first-order Raman peaks, in agreement with previous literature results. A thorough analysis of the second-order Raman bands, as observed in both basal and edge plane configurations, provides new information and allows a precise assignment of these spectral structures. In particular, we have observed and assigned Raman active modes of the M point of the Brillouin zone previously predicted by ab initio calculations but never previously measured.

High pressure ices.

PubMed

Hermann, Andreas; Ashcroft, N W; Hoffmann, Roald

2012-01-17

H(2)O will be more resistant to metallization than previously thought. From computational evolutionary structure searches, we find a sequence of new stable and meta-stable structures for the ground state of ice in the 1-5 TPa (10 to 50 Mbar) regime, in the static approximation. The previously proposed Pbcm structure is superseded by a Pmc2(1) phase at p = 930 GPa, followed by a predicted transition to a P2(1) crystal structure at p = 1.3 TPa. This phase, featuring higher coordination at O and H, is stable over a wide pressure range, reaching 4.8 TPa. We analyze carefully the geometrical changes in the calculated structures, especially the buckling at the H in O-H-O motifs. All structures are insulating--chemistry burns a deep and (with pressure increase) lasting hole in the density of states near the highest occupied electronic levels of what might be component metallic lattices. Metallization of ice in our calculations occurs only near 4.8 TPa, where the metallic C2/m phase becomes most stable. In this regime, zero-point energies much larger than typical enthalpy differences suggest possible melting of the H sublattice, or even the entire crystal.

ROY Revisited, Again: The Eighth Solved Structure

DOE PAGES

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai; ...

2018-01-01

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

ROY Revisited, Again: The Eighth Solved Structure

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

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.

PubMed

Zhang, Di; Wlodawer, Alexander; Lubkowski, Jacek

2016-11-20

The crystal structure of a construct consisting of the FERM and SH2-like domains of the human Janus kinase 1 (JAK1) bound to a fragment of the intracellular domain of the interferon-λ receptor 1 (IFNLR1) has been determined at the nominal resolution of 2.1Å. In this structure, the receptor peptide forms an 85-Å-long extended chain, in which both the previously identified box1 and box2 regions bind simultaneously to the FERM and SH2-like domains of JAK1. Both domains of JAK1 are generally well ordered, with regions not seen in the crystal structure limited to loops located away from the receptor-binding regions. The structure provides a much more complete and accurate picture of the interactions between JAK1 and IFNLR1 than those given in earlier reports, illuminating the molecular basis of the JAK-cytokine receptor association. A glutamate residue adjacent to the box2 region in IFNLR1 mimics the mode of binding of a phosphotyrosine in classical SH2 domains. It was shown here that a deletion of residues within the box1 region of the receptor abolishes stable interactions with JAK1, although it was previously shown that box2 alone is sufficient to stabilize a similar complex of the interferon-α receptor and TYK2. Published by Elsevier Ltd.

Structure of catalase determined by MicroED

PubMed Central

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

A crystal-chemical classification of borate structures with emphasis on hydrated borates

USGS Publications Warehouse

Christ, C.L.; Clark, J.R.

1977-01-01

The rules governing formation of hydrated borate polyanions that were proposed by C.L. Christ in 1960 are critically reviewed and new rules added on the basis of recent crystal structure determinations. Principles and classifications previously published by others are also critically reviewed briefly. The fundamental building blocks from which borate polyanions can be constructed are defined on the basis of the number n of boron atoms, and the fully hydrated polyanions are illustrated. Known structures are grouped accordingly, and a shorthand notation using n and symbols ?? = triangle, T = tetrahedron is introduced so that the polyanions can be easily characterized. For example, 3:??+2T describes [B3O3(OH)5]2-. Correct structural formulas are assigned borates with known structures whereas borates of unknown structure are grouped separately. ?? 1977 Springer-Verlag.

Preparation, characterization and crystal structures of three salts of the quaterpyridine ligand

NASA Astrophysics Data System (ADS)

Ciesielski, Artur; Stefankiewicz, Artur R.; Patroniak, Violetta; Kubicki, Maciej

2009-07-01

As a result of a reaction between 6,6'''-dimethyl-2,2':6',2'':6'',2'''-quaterpyridine C 22H 18N 4 and lanthanide(III) salts, compounds, [C 22H 20N 4] 2+·2(CF 3SO 3) - ( 1) and [C 22H 20N 4] 2+·2(ClO 4) - ( 2), have been obtained. They were characterized by spectroscopic techniques (ESI-MS, NMR, IR), elemental analysis, and their formulae were confirmed on the basis of X-ray crystallography. It turned out that the perchlorate crystallizes as two solvates: with acetonitrile and disordered water molecules. These are the first structural characterization of a 6,6'″-dimethyl-2,2':6',2″:6″,2'″-quaterpyridinium dication. Due to the intramolecular hydrogen bond it adopts the previously unobserved cis/trans/cis conformation. In all three crystals the dications have C i symmetry, they occupy the special positions in their respective space groups. In the crystal structures the π-π stacking and weak hydrogen bonds add directionality to the dominating electrostatic interactions between cations and anions.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Crystal Structure of the Passenger Domain of the Escherichia coli Autotransporter EspP

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

Khan, Shekeb; Mian, Hira S.; Sandercock, Linda E.

2013-03-07

Autotransporters represent a large superfamily of known and putative virulence factors produced by Gram-negative bacteria. They consist of an N-terminal 'passenger domain' responsible for the specific effector functions of the molecule and a C-terminal '{beta}-domain' responsible for translocation of the passenger across the bacterial outer membrane. Here, we present the 2.5-{angstrom} crystal structure of the passenger domain of the extracellular serine protease EspP, produced by the pathogen Escherichia coli O157:H7 and a member of the serine protease autotransporters of Enterobacteriaceae (SPATEs). Like the previously structurally characterized SPATE passenger domains, the EspP passenger domain contains an extended right-handed parallel {beta}-helix precededmore » by an N-terminal globular domain housing the catalytic function of the protease. Of note, however, is the absence of a second globular domain protruding from this {beta}-helix. We describe the structure of the EspP passenger domain in the context of previous results and provide an alternative hypothesis for the function of the {beta}-helix within SPATEs.« less

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility

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

McMahon, Roisin M., E-mail: r.mcmahon1@uq.edu.au; Coinçon, Mathieu; Tay, Stephanie

The crystal structure of a P. aeruginosa DsbA1 variant is more suitable for fragment-based lead discovery efforts to identify inhibitors of this antimicrobial drug target. In the reported structures the active site of the protein can simultaneously bind multiple ligands introduced in the crystallization solution or via soaking. Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discoverymore » approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface.« less

Terahertz birefringence of potassium niobate crystals

NASA Astrophysics Data System (ADS)

Antsygin, V. D.; Mamrashev, A. A.; Nikolaev, N. A.

2018-03-01

We present terahertz optical properties (refractive indices and absorption coefficients) of potassium niobate crystals measured by time-domain spectroscopy in the range of 0.2-2.0 THz. We observe average refractive indices nx = 5.25, ny = 4.8, nz = 5.9 for corresponding optical axes X, Y, Z with the large birefringence of Δn = nz - ny = 1.1. We report rising absorption coefficient at higher frequencies (α ∼ 50 cm-1 at 1 THz for all three axes) while the dichroism is not pronounced. Somewhat higher absorption compared to the previous results could be attributed to some polydomain structure remaining in the crystal.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

2.4 Å resolution crystal structure of human TRAP1 NM , the Hsp90 paralog in the mitochondrial matrix

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

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun

2016-07-13

TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1 NMdimer is presented, featuring an intact N-domain and M-domain structure, boundmore » to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.« less

Structure of Arabidopsis thaliana Rubisco activase.

PubMed

Hasse, Dirk; Larsson, Anna M; Andersson, Inger

2015-04-01

The CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is inactivated by the formation of dead-end complexes with inhibitory sugar phosphates. In plants and green algae, the ATP-dependent motor protein Rubisco activase restores catalytic competence by facilitating conformational changes in Rubisco that promote the release of the inhibitory compounds from the active site. Here, the crystal structure of Rubisco activase from Arabidopsis thaliana is presented at 2.9 Å resolution. The structure reveals an AAA+ two-domain structure. More than 100 residues in the protein were not visible in the electron-density map owing to conformational disorder, but were verified to be present in the crystal by mass spectrometry. Two sulfate ions were found in the structure. One was bound in the loop formed by the Walker A motif at the interface of the domains. A second sulfate ion was bound at the N-terminal end of the first helix of the C-terminal domain. The protein packs in a helical fashion in the crystal, as observed previously for Rubisco activase, but differences in the helical pitch indicate flexibility in the packing of the protein.

Protein crystal growth and the International Space Station

NASA Technical Reports Server (NTRS)

DeLucas, L. J.; Moore, K. M.; Long, M. M.

1999-01-01

Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration.

PubMed

Awad, Wael; Svensson Birkedal, Gabriel; Thunnissen, Marjolein M G M; Mani, Katrin; Logan, Derek T

2013-12-01

The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1. Crystals were subjected to controlled dehydration using the HC1 device. The optimal protocol for dehydration was developed by careful investigation of the following parameters: dehydration rate, final relative humidity and total incubation time Tinc. Of these, the most important was shown to be Tinc. After dehydration using the optimal protocol the crystals showed significantly reduced anisotropy and improved electron density, allowing the building of previously disordered parts of the structure.

Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

PubMed Central

Tsurumura, Toshiharu; Tsumori, Yayoi; Qiu, Hao; Oda, Masataka; Sakurai, Jun; Nagahama, Masahiro; Tsuge, Hideaki

2013-01-01

Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD+ analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD+-bound form (NAD+-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD+-Ia-actin complex. Here we report high-resolution structures of NAD+-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD+ under different conditions. The structures of NAD+-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases. PMID:23382240

Monoclinic Tungsten Oxide with {100} Facet Orientation and Tuned Electronic Band Structure for Enhanced Photocatalytic Oxidations.

PubMed

Zhang, Ning; Chen, Chen; Mei, Zongwei; Liu, Xiaohe; Qu, Xiaolei; Li, Yunxiang; Li, Siqi; Qi, Weihong; Zhang, Yuanjian; Ye, Jinhua; Roy, Vellaisamy A L; Ma, Renzhi

2016-04-27

Exploring surface-exposed highly active crystal facets for photocatalytic oxidations is promising in utilizing monoclinic WO3 semiconductor. However, the previously reported highly active facets for monoclinic WO3 were mainly toward enhancing photocatalytic reductions. Here we report that the WO3 with {100} facet orientation and tuned surface electronic band structure can effectively enhance photocatalytic oxidation properties. The {100} faceted WO3 single crystals are synthesized via a facile hydrothermal method. The UV-visible diffuse reflectance, X-ray photoelectron spectroscopy valence band spectra, and photoelectrochemical measurements suggest that the {100} faceted WO3 has a much higher energy level of valence band maximum compared with the normal WO3 crystals without preferred orientation of the crystal face. The density functional theory calculations reveal that the shift of O 2p and W 5d states in {100} face induce a unique band structure. In comparison with the normal WO3, the {100} faceted WO3 exhibits an O2 evolution rate about 5.1 times in water splitting, and also shows an acetone evolution rate of 4.2 times as well as CO2 evolution rate of 3.8 times in gaseous degradation of 2-propanol. This study demonstrates an efficient crystal face engineering route to tune the surface electronic band structure for enhanced photocatalytic oxidations.

Pressure induced Ag 2Te polymorphs in conjunction with topological non trivial to metal transition

DOE PAGES

Zhu, J.; Oganov, A. R.; Feng, W. X.; ...

2016-08-01

Silver telluride (Ag 2Te) is well known as superionic conductor and topologica insulator with polymorphs. Pressure induced three phase transitions in Ag 2Te hav been reported in previous. Here, we experimentally identified high pressure phas above 13 GPa of Ag 2Te by using high pressure synchrotron x ray diffraction metho in combination with evolutionary crystal structure prediction, showing it crystallize into a monoclinic structure of space group C2/m with lattice parameters a = 6.081Å b = 5.744Å, c = 6.797 Å, β = 105.53°. The electronic properties measurements of Ag 2Te reveal that the topologically non-trivial semiconducting phase I andmore » semimetalli phase II previously predicated by theory transformed into bulk metals fo high pressure phases in consistent with the first principles calculations« less

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Melt Flow before Crystal Seeding in Cz Si Growth with Transversal MF

NASA Astrophysics Data System (ADS)

Iizuka, Masaya; Mukaiyama, Yuji; Demina, S. E.; Kalaev, V. V.

2017-06-01

Industrial Cz growth of Si crystal of 300 mm and higher diameter usually requires DC magnetic fields (MFs) to suppress turbulence in the melt. We present 3D unsteady analysis of melt turbulent convection in an industrial Cz system coupled with the effect of the transversal MF for different argon gas flow rates for the stage before crystal seeding. We have performed detailed 2D axisymmetric modeling of global heat transfer in the whole Cz furnace. Radiative heat fluxes obtained in 2D modeling have been used in detailed 3D steady and unsteady modeling of crystallization zone. LES method is applied as a predictive approach for modeling of turbulent flow of silicon melt. We have obtained flow structure and temperature distribution in the melt, which were different from previously reported data. We have observed a well-fixed dark spike which includes low temperature melt area on the melt free surface in MF cases. These results indicates that MF and argon flow rate conditions are important to achieve stable positioning of the dark spike on the melt free surface for optimized crystal seeding without uncontrollable meltdown and single crystal structure loss.

Evaluation of structural vacancies for 1/1-Al-Re-Si approximant crystals by positron annihilation spectroscopy

NASA Astrophysics Data System (ADS)

Yamada, K.; Suzuki, H.; Kitahata, H.; Matsushita, Y.; Nozawa, K.; Komori, F.; Yu, R. S.; Kobayashi, Y.; Ohdaira, T.; Oshima, N.; Suzuki, R.; Takagiwa, Y.; Kimura, K.; Kanazawa, I.

2018-01-01

The size of structural vacancies and structural vacancy density of 1/1-Al-Re-Si approximant crystals with different Re compositions were evaluated by positron annihilation lifetime and Doppler broadening measurements. Incident positrons were found to be trapped at the monovacancy-size open space surrounded by Al atoms. From a previous analysis using the maximum entropy method and Rietveld method, such an open space is shown to correspond to the centre of Al icosahedral clusters, which locates at the vertex and body centre. The structural vacancy density of non-metallic Al73Re17Si10 was larger than that of metallic Al73Re15Si12. The observed difference in the structural vacancy density reflects that in bonding nature and may explain that in the physical properties of the two samples.

Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

PubMed

Hu, Xiao-Qian; Guo, Peng-Chao; Ma, Jin-Di; Li, Wei-Fang

2013-11-01

The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

Two types of amorphous protein particles facilitate crystal nucleation.

PubMed

Yamazaki, Tomoya; Kimura, Yuki; Vekilov, Peter G; Furukawa, Erika; Shirai, Manabu; Matsumoto, Hiroaki; Van Driessche, Alexander E S; Tsukamoto, Katsuo

2017-02-28

Nucleation, the primary step in crystallization, dictates the number of crystals, the distribution of their sizes, the polymorph selection, and other crucial properties of the crystal population. We used time-resolved liquid-cell transmission electron microscopy (TEM) to perform an in situ examination of the nucleation of lysozyme crystals. Our TEM images revealed that mesoscopic clusters, which are similar to those previously assumed to consist of a dense liquid and serve as nucleation precursors, are actually amorphous solid particles (ASPs) and act only as heterogeneous nucleation sites. Crystalline phases never form inside them. We demonstrate that a crystal appears within a noncrystalline particle assembling lysozyme on an ASP or a container wall, highlighting the role of heterogeneous nucleation. These findings represent a significant departure from the existing formulation of the two-step nucleation mechanism while reaffirming the role of noncrystalline particles. The insights gained may have significant implications in areas that rely on the production of protein crystals, such as structural biology, pharmacy, and biophysics, and for the fundamental understanding of crystallization mechanisms.

Structure elucidation of 3-[1-(6-methoxy-2-naphtyl)ethyl]-6-(2,4-dichlorophenyl)-7H-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazine, C 23H 18Cl 2N 4OS from synchrotron X-ray powder diffraction

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

Gündoğdu, Gülsüm; Aytaç, Sevim Peri; Müller, Melanie

The 3-[1-(6-methoxy-2-naphtyl)ethyl]-6-(2,4-dichlorophenyl)-7H-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazine, C 23H 18Cl 2N 4OS compound was synthesized, as a member of the family of novel potential anticancer agents. The structure of the title compound was characterized by IR, 1H-NMR, mass spectroscopy, and elemental analysis, previously. In this study, the crystal structure of this compound has been determined from synchrotron X-ray powder diffraction data. The crystal structure was solved by simulated annealing and the final structure was achieved by Rietveld refinement method using soft restrains on all interatomic bond lengths and angles. This compound crystallizes in space groupP21,Z= 2, with the unit-cell parametersa= 15.55645(11) Å,b= 8.61693(6) Å,c= 8.56702(6)more » Å,β= 104.3270(4)°, andV= 1112.68(1) Å 3. In the crystal structure, strong C-H∙∙∙πand weak intermolecular hydrogen-bonding interactions link the molecules into a three-dimensional network. The molecules are in a head-to-head arrangement in the unit cell.« less

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

PubMed

Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

2018-04-10

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

Magnetic and crystal structures of the honeycomb lattice Na2IrO3 and single layer Sr2IrO4

NASA Astrophysics Data System (ADS)

Ye, Feng

2013-03-01

5 d based iridates have recently attracted great attention due to the large spin-orbit coupling (SOC). It is now recognized that the SOC that competes with other relevant energies, particularly the on-site Coulomb interaction U, and have driven novel electronic and magnetic phases. Combining single crystal neutron and x-ray diffractions, we have investigated the magnetic and crystal structures of the honeycomb lattice Na2IrO3. The system orders magnetically below 18.1 K with Ir4+ ions forming zigzag spin chains within the layered honeycomb network with ordered moment of 0.22 μB /Ir site. Such a configuration sharply contrasts the Neel or stripe states proposed in the Kitaev-Heisenberg model. The structure refinement reveals that the Ir atoms form nearly ideal 2D honeycomb lattice while the IrO6 octahedra experience a trigonal distortion that is critical to the ground state. The results of this study provide much-needed experimental insights into the magnetic and crystal structure crucial to the understanding of the exotic magnetic order and possible topological characteristics in the 5 d-electron based honeycomb lattice. Neutron diffraction experiments are also performed to investigate the magnetic and crystal structure of the single layer iridate Sr2IrO4, where new structural information and spin order are obtained that is not available from previous neutron powder diffraction measurement. This work was sponsored in part by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy.

Crystal Structure of the Escherichia coli 23S rRNA: m{5}C Methyltransferase RlmI (YccW) Reveals Evolutionary Links Between RNA Modification Enzymes

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

Sunita, S.; Tkaczuk, K; Purta, E

2008-01-01

Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 {angstrom} to a final R-factor of 0.194 (R{sub free} = 0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously foundmore » in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a {Beta}-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.« less

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

Montemayor, Eric J.; Didychuk, Allison L.; Liao, Honghong

U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayoret al.(2014),Nature Struct. Mol. Biol.21, 544–551]. The structure revealedmore » a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein–RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.« less

Mathematical modeling and statistical analysis of SPE-OCDMA systems utilizing second harmonic generation effect in thick crystal receivers

NASA Astrophysics Data System (ADS)

Matinfar, Mehdi D.; Salehi, Jawad A.

2009-11-01

In this paper we analytically study and evaluate the performance of a Spectral-Phase-Encoded Optical CDMA system for different parameters such as the user's code length and the number of users in the network. In this system an advanced receiver structure in which the Second Harmonic Generation effect imposed in a thick crystal is employed as the nonlinear pre-processor prior to the conventional low speed photodetector. We consider ASE noise of the optical amplifiers, effective in low power conditions, besides the multiple access interference (MAI) noise which is the dominant source of noise in any OCDMA communications system. We use the results of the previous work which we analyzed the statistical behavior of the thick crystals in an optically amplified digital lightwave communication system to evaluate the performance of the SPE-OCDMA system with thick crystals receiver structure. The error probability is evaluated using Saddle-Point approximation and the approximation is verified by Monte-Carlo simulation.

Band structure of an electron in a kind of periodic potentials with singularities

NASA Astrophysics Data System (ADS)

Hai, Kuo; Yu, Ning; Jia, Jiangping

2018-06-01

Noninteracting electrons in some crystals may experience periodic potentials with singularities and the governing Schrödinger equation cannot be defined at the singular points. The band structure of a single electron in such a one-dimensional crystal has been calculated by using an equivalent integral form of the Schrödinger equation. Both the perturbed and exact solutions are constructed respectively for the cases of a general singular weak-periodic system and its an exactly solvable version, Kronig-Penney model. Any one of them leads to a special band structure of the energy-dependent parameter, which results in an effective correction to the previous energy-band structure and gives a new explanation for forming the band structure. The used method and obtained results could be a valuable aid in the study of energy bands in solid-state physics, and the new explanation may trigger investigation to different physical mechanism of electron band structures.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

Understanding how the electronic structure of energetic materials change under compression is important to elucidating mechanisms of shock-induced reactions and detonation. In this presentation, the electronic structure of prototypical energetic crystals are examined under high degrees of compression using ab initio quantum chemical calculations. The effects of compression on and interactions between the constituent molecules are examined in particular. The insights these results provide into previous experimental observations and theoretical predictions of energetic materials under high pressure are discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Fusion Partner Toolchest for the Stabilization and Crystallization of G Protein-Coupled Receptors

PubMed Central

Chun, Eugene; Thompson, Aaron A.; Liu, Wei; Roth, Christopher B.; Griffith, Mark T.; Katritch, Vsevolod; Kunken, Joshua; Xu, Fei; Cherezov, Vadim; Hanson, Michael A.; Stevens, Raymond C.

2012-01-01

SUMMARY Structural studies of human G protein-coupled receptors (GPCRs) have recently been accelerated through the use of the T4 lysozyme fusion partner that was inserted into the third intracellular loop. Using chimeras of the human β2-adrenergic and human A2A adenosine receptors, we present the methodology and data for the selection of five new fusion partners for crystallizing GPCRs. In particular, the use of the thermostabilized apocytochrome b562RIL as a fusion partner displays certain advantages over the previously utilized T4 lysozyme, resulting in a significant improvement in stability and structure in GPCR-fusion constructs. PMID:22681902

Foreword

NASA Astrophysics Data System (ADS)

Benisty, Henri; Kawakami, Shojiro; Norris, David J.; Soukoulis, Costas M.

2004-10-01

The Fifth International Symposium on Photonic and Electromagnetic Crystal Structures (PECS-V) was held in Kyoto, Japan (2004). The Symposium followed the format of previous international meetings held at Laguna Beach, USA (1999), Sendai, Japan (2000), St. Andrews, UK (2001) and Los Angeles, USA (2002).

Crystal growth and magnetic characterization of a tetragonal polymorph of NiNb2O6

NASA Astrophysics Data System (ADS)

Munsie, T. J. S.; Millington, A.; Dube, P. A.; Dabkowska, H. A.; Britten, J.; Luke, G. M.; Greedan, J. E.

2016-04-01

A previously unidentified polymorph of nickel niobate, NiNb2O6, was grown and stabilized in single crystalline form using an optical floating zone furnace. Key parameters of the growth procedure involved use of a slight excess of NiO (1.2% by mol), an O2 atmosphere and a growth rate of 25 mm/h. The resulting boule consisted of a polycrystalline exterior shell of the columbite structure - columbite is the thermodynamically stable form of NiNb2O6 under ambient conditions - and a core region consisting of transparent yellow-green single crystals up to 5 mm×2 mm×1 mm in dimension of the previously unidentified phase. The crystal structure, solved from single crystal x-ray diffraction data, is described in the P42/n space group. Interestingly, this is not a subgroup of P42/mnm, the rutile space group. The Ni2+ ions form layers which are displaced such that interlayer magnetic frustration is anticipated. Magnetic susceptibility data shows a broad maximum at approximately 22 K and evidence for long range antiferromagnetic order at approximately 14 K, obtained by Fisher heat capacity analysis as well as heat capacity measurements. The susceptibility data for T > 25 K are well fit by a square lattice S = 1 model, consistent with the Ni sublattice topology.

Modeling local structure using crystal field and spin Hamiltonian parameters: the tetragonal FeK3+-OI2- defect center in KTaO3 crystal

NASA Astrophysics Data System (ADS)

Gnutek, P.; Y Yang, Z.; Rudowicz, C.

2009-11-01

The local structure and the spin Hamiltonian (SH) parameters, including the zero-field-splitting (ZFS) parameters D and (a+2F/3), and the Zeeman g factors g_{\\parallel } and g_{\\perp } , are theoretically investigated for the FeK3+-OI2- center in KTaO3 crystal. The microscopic SH (MSH) parameters are modeled within the framework of the crystal field (CF) theory employing the CF analysis (CFA) package, which also incorporates the MSH modules. Our approach takes into account the spin-orbit interaction as well as the spin-spin and spin-other-orbit interactions omitted in previous studies. The superposition model (SPM) calculations are carried out to provide input CF parameters for the CFA/MSH package. The combined SPM-CFA/MSH approach is used to consider various structural models for the FeK3+-OI2- defect center in KTaO3. This modeling reveals that the off-center displacement of the Fe3+ ions, Δ1(Fe3+), combined with an inward relaxation of the nearest oxygen ligands, Δ2(O2-), and the existence of the interstitial oxygen OI2- give rise to a strong tetragonal crystal field. This finding may explain the large ZFS experimentally observed for the FeK3+-OI2- center in KTaO3. Matching the theoretical MSH predictions with the available structural data as well as electron magnetic resonance (EMR) and optical spectroscopy data enables predicting reasonable ranges of values of Δ1(Fe3+) and Δ2(O2-) as well as the possible location of OI2- ligands around Fe3+ ions in KTaO3. The defect structure model obtained using the SPM-CFA/MSH approach reproduces very well the ranges of the experimental SH parameters D, g_{\\parallel } and g_{\\perp } and importantly yields not only the correct magnitude of D but also the sign, unlike previous studies. More reliable predictions may be achieved when experimental data on (a+2F/3) and/or crystal field energy levels become available. Comparison of our results with those arising from alternative models existing in the literature indicates considerable advantages of our method and presumably higher reliability of our predictions.

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

PubMed

Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

2015-10-01

Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues in the N-terminus of a symmetry-related molecule and the complementary DNA strand facing away from the active site were also observed which seem to stabilize the enzyme-DNA complex. However, the significance of this observation remains to be investigated. The results provide new insights into the current knowledge about DNA damage recognition and repair by uracil-DNA glycosylases.

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

2D photonic crystal complete band gap search using a cyclic cellular automaton refination

NASA Astrophysics Data System (ADS)

González-García, R.; Castañón, G.; Hernández-Figueroa, H. E.

2014-11-01

We present a refination method based on a cyclic cellular automaton (CCA) that simulates a crystallization-like process, aided with a heuristic evolutionary method called differential evolution (DE) used to perform an ordered search of full photonic band gaps (FPBGs) in a 2D photonic crystal (PC). The solution is proposed as a combinatorial optimization of the elements in a binary array. These elements represent the existence or absence of a dielectric material surrounded by air, thus representing a general geometry whose search space is defined by the number of elements in such array. A block-iterative frequency-domain method was used to compute the FPBGs on a PC, when present. DE has proved to be useful in combinatorial problems and we also present an implementation feature that takes advantage of the periodic nature of PCs to enhance the convergence of this algorithm. Finally, we used this methodology to find a PC structure with a 19% bandgap-to-midgap ratio without requiring previous information of suboptimal configurations and we made a statistical study of how it is affected by disorder in the borders of the structure compared with a previous work that uses a genetic algorithm.

Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A

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

Gandhi, Prafull S.; Page, Michael J.; Chen, Zhiwei

2009-09-15

The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its drastically reduced activity toward substrate. Whether this collapsed conformation is genuine, rather than the result of crystal packing or the mutation introduced in the critical 215-217 {beta}-strand, and whether binding of thrombomodulin to exosite I can allosterically shift the E* form to the active E form to restore activity toward protein C are issues of considerable mechanistic importance to improve themore » design of an anticoagulant thrombin mutant for therapeutic applications. Here we present four crystal structures of WE in the human and murine forms that confirm the collapsed conformation reported previously under different experimental conditions and crystal packing. We also present structures of human and murine WE bound to exosite I with a fragment of the platelet receptor PAR1, which is unable to shift WE to the E form. These structural findings, along with kinetic and calorimetry data, indicate that WE is strongly stabilized in the E* form and explain why binding of ligands to exosite I has only a modest effect on the E*-E equilibrium for this mutant. The E* {yields} E transition requires the combined binding of thrombomodulin and protein C and restores activity of the mutant WE in the anticoagulant pathway.« less

Structure and Bonding Investigation of Plutonium Peroxocarbonate Complexes Using Cerium Surrogates and Electronic Structure Modeling.

PubMed

Sweet, Lucas E; Corbey, Jordan F; Gendron, Frédéric; Autschbach, Jochen; McNamara, Bruce K; Ziegelgruber, Kate L; Arrigo, Leah M; Peper, Shane M; Schwantes, Jon M

2017-01-17

Herein, we report the synthesis and structural characterization of K 8 [(CO 3 ) 3 Pu] 2 (μ-η 2 -η 2 -O 2 ) 2 ·12H 2 O. This is the second Pu-containing addition to the previously studied alkali-metal peroxocarbonate series M 8 [(CO 3 ) 3 A] 2 (μ-η 2 -η 2 -O 2 ) 2 ·xH 2 O (M = alkali metal; A = Ce or Pu; x = 8, 10, 12, or 18), for which only the M = Na analogue has been previously reported when A = Pu. The previously reported crystal structure for Na 8 [(CO 3 ) 3 Pu] 2 (μ-η 2 -η 2 -O 2 ) 2 ·12H 2 O is not isomorphous with its known Ce analogue. However, a new synthetic route to these M 8 [(CO 3 ) 3 A] 2 (μ-η 2 -η 2 -O 2 ) 2 ·12H 2 O complexes, described below, has produced crystals of Na 8 [(CO 3 ) 3 Ce] 2 (μ-η 2 -η 2 -O 2 ) 2 ·12H 2 O that are isomorphous with the previously reported Pu analogue. Via this synthetic method, the M = Na, K, Rb, and Cs salts of M 8 [(CO 3 ) 3 Ce] 2 (μ-η 2 -η 2 -O 2 ) 2 ·xH 2 O have also been synthesized for a systematic structural comparison with each other and the available Pu analogues using single-crystal X-ray diffraction, Raman spectroscopy, and density functional theory calculations. The Ce salts, in particular, demonstrate subtle differences in the peroxide bond lengths, which correlate with Raman shifts for the peroxide O p -O p stretch (O p = O atoms of the peroxide bridges) with each of the cations studied: Na + [1.492(3) Å/847 cm -1 ], Rb + [1.471(1) Å/854 cm -1 ], Cs + [1.474(1) Å/859 cm -1 ], and K + [1.468(6) Å/870 cm -1 ]. The trends observed in the O p -O p bond distances appear to relate to supermolecular interactions between the neighboring cations.

Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

NASA Astrophysics Data System (ADS)

Strzelczyk, Paweł; Bujacz, Grzegorz

2016-04-01

Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

Molecular assembly of Clostridium botulinum progenitor M complex of type E

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

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. Furthermore, the similarity of the general architecture betweenmore » the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.« less

Electrical, Thermal, and Magnetic Properties of Single Crystal CaMn2O4 Marokite

NASA Astrophysics Data System (ADS)

White, B. D.; Neumeier, J. J.; Souza, J. A.; Chiorescu, C.; Cohn, J. L.

2008-03-01

CaMn2O4 was first described [1] in 1963 as a natural mineral called Marokite. Since its discovery, it has been studied as a minor structural impurity phase in CMR- related CaMnO3 and for its structural similarities to high-pressure phases of spinel-oxide compounds. However, little attention has previously been paid to physical properties beyond its temperature-dependent magnetization. We will present a detailed physical properties study of CaMn2O4 single crystals grown by the optical floating zone method. [2] These measurements, several of which display anisotropy as a result of an orthorhombic crystal structure, include electrical transport, thermal transport, thermal expansion, heat capacity, and magnetization. [1] C. Gaudefroy, G. Jouravsky, F. Permingeat, Bull. Soc. Franc. Min'er. Crist. 86 (1963) 359. [2] B. D. White, C. A. M. dos Santos, J. A. Souza, K. J. McClellan, J. J. Neumeier submitted to J. Cryst. Growth.

Crystallographic studies of the Anthrax lethal toxin. Annual report

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

Frederick, C.A.

1996-07-01

The lethal form of Anthrax results from the inhalation of anthrax spores. Death is primarily due to the effects of the lethal toxin (Protective Antigen (PA) + Lethal Factor) from the causative agent, Bacillus anthracis. All the Anthrax vaccines currently in use or under development contain or produce PA, the major antigenic component of anthrax toxin, and there is a clear need for an improved vaccine for human use. In the previous report we described the first atomic resolution structure of PA, revealing that the molecule is composed largely of beta-sheets organized into four domains. This information can be usedmore » in the design. of recombinant PA vaccines. In this report we describe additional features of the full-length PA molecule derived from further crystallographic refinement and careful examination of the structure. We compare two crystal forms of PA grown at different pH values and discuss the functional implications. A complete definition of the function of each domain must await the crystal structure of the PA63 heptamer. We have grown crystals of the heptamer under both detergent and detergent-free conditions, and made substantial progress towards the crystal structure. The mechanism of anthrax intoxication in the light of our results is reviewed.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

PubMed Central

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

2016-01-01

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

First Protein Crystallization Experiments on The International Space Station: Sweet Success in Space With Thaumatin

NASA Technical Reports Server (NTRS)

Kundrot, Craig E.; Barnes, Cindy L.; Snell, Eddie H.; Achari, Aniruddha; Whitaker, Ann F. (Technical Monitor)

2001-01-01

We determined the room temperature 1.2 A structure of thaumatin using a crystal grown in the first protein crystallization experiment conducted aboard the International Space Station (ISS). The crystals were grown in the Enhanced Gaseous Nitrogen Dewar (EGN) developed by Alexander McPherson and co-workers. EGN transports frozen solutions contained in tygon tubing in a liquid nitrogen Dewar to ISS where the tubes then thaw. Batch, free interface diffusion (FID), or vapor diffusion crystallization occurs after thawing. EGN was flown to the ISS on STS-106 on September 8, 2000. This was a "risk mitigation" flight that tested EGN performance and the process of conducting experiments on ISS. We focused on how to map a hanging drop crystallization recipe to the EGN FID method. Thaumatin was chosen as the test system. Three series of crystallization recipes were set-up. Each series tested different volume ratios of protein-rich solution to precipitant-rich solution. The series differed from each other by fixing either the protein concentration or the amount of protein in the solutions. Upon return of the samples to Earth on October 24 by STS-92, bubbles that spanned the diameter of the tubing were observed in all tubes. Such bubbles interrupt liquid-liquid diffusion and force vapor diffusion equilibration to occur instead. Nonetheless, crystals grew in 9 of 30 tubes. Many large crystals were grown, the largest being 2.0 x 1.1 x 1.0 cubic mm. The largest crystal was used to collect data at room temperature on beamline 7-1 of the Stanford Synchrotron Radiation Source to a maximum resolution of 1.2 A. The structure was refined anisotropically using SHELX with a data to parameter ratio of 4.5 to give an R(sub factor) of 15.8% (R(sub free) = 18.2%) for ail reflections without generated hydrogens. This refinement is proceeding. Comparisons of this 1.2 A microgravity structure to previous reports of the thaumatin structure at 1.75 A and to ground control crystals will be presented.

Crystal structure of Au25(SePh)18 nanoclusters and insights into their electronic, optical and catalytic properties

NASA Astrophysics Data System (ADS)

Song, Yongbo; Zhong, Juan; Yang, Sha; Wang, Shuxin; Cao, Tiantian; Zhang, Jun; Li, Peng; Hu, Daqiao; Pei, Yong; Zhu, Manzhou

2014-10-01

The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster.The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04631e

Accessing protein conformational ensembles using room-temperature X-ray crystallography

PubMed Central

Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

2011-01-01

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

Average and local crystal structures of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles

DOE PAGES

Feygenson, Mikhail; Neuefeind, Joerg C.; Tyson, Trevor A.; ...

2015-11-06

We report the comprehensive study of the crystal structure of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles by means of neutron and synchrotron x-ray scattering. In our study we used four different types of (Ga 1–xZn x)(N 1–xO x) nanoparticles, with diameters of 10–27 nm and x = 0.075–0.51, which show the narrow energy-band gaps from 2.21 to 2.61 eV. The Rietveld analysis of the neutron diffraction data revealed that the average crystal structure is the hexagonal wurtzite (space group P6 3mc), in agreement with previous reports on similar bulk materials. The pair-distribution function (PDF) analysis of the samemore » data found that the local structure is more disordered than the average one. It is best described by the model with a lower symmetry space group P1, where atoms are quasirandomly distorted from their nominal positions in the hexagonal wurtzite lattice.« less

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance.

PubMed

Morales, Yalemi; Olsen, Keith J; Bulcher, Jacqueline M; Johnson, Sean J

2018-01-01

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH results in an ATP binding site that is undisturbed by crystal contacts and adopts a conformation consistent with nucleotide binding and hydrolysis. Strikingly, this new FRH structure adopts an arch domain conformation that is dramatically altered from previous structures. Comparison of the existing FRH structures reveals conserved hinge points that appear to facilitate arch motion. Regions in the arch have been previously shown to mediate a variety of protein-protein interactions critical for RNA surveillance and circadian clock functions. The conformational changes highlighted in the FRH structures provide a platform for investigating the relationship between arch dynamics and Mtr4/FRH function.

Structural characterization of metal binding to a cold-adapted frataxin.

PubMed

Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2015-06-01

Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

DOE PAGES

Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

2015-04-25

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

Crystal structures of the ionic conductors Bi{sub 46}M{sub 8}O{sub 89} (M=P, V) related to the fluorite-type structure

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

Darriet, J.; Launay, J.C.; Zuniga, F.J.

2005-06-15

The crystal structures of the two oxides Bi{sub 46}M{sub 8}O{sub 89} (M=P, V) have been solved from single crystals X-ray data at room temperature. Bi{sub 46}P{sub 8}O{sub 89} crystallizes in the monoclinic symmetry (space group C2/m) with the cell parameters a=19.6073(4)A, b=11.4181(4)A, c=21.1119(4)A and {beta}=112.14(3){sup o}. The symmetry of Bi{sub 46}V{sub 8}O{sub 89} is also monoclinic but the space group is P2{sub 1}/c with the unit-cell parameters: a=20.0100(4)A, b=11.6445(4)A, c=20.4136(4)A and {beta}=107.27(3){sup o}. Both structures derive from an oxygen deficient fluorite-type structure where the Bi and M cations (M=P, V) are ordered in the framework. The structures are characterised bymore » isolated MO{sub 4} tetrahedra (M=P, V) which contradicts the previous results. The difference between the two structures is only due to a different order of the M atoms (M=P, V) in the fluorite-type superstructure. It will be shown that some oxygen sites are partially occupied in both structures which can explain the ion conduction properties of these phases. A structural building principle will be proposed that can explain the large domain of solid solution related to the fluorite-type observed in both systems.« less

Statistical foundations of liquid-crystal theory: II: Macroscopic balance laws.

PubMed

Seguin, Brian; Fried, Eliot

2013-01-01

Working on a state space determined by considering a discrete system of rigid rods, we use nonequilibrium statistical mechanics to derive macroscopic balance laws for liquid crystals. A probability function that satisfies the Liouville equation serves as the starting point for deriving each macroscopic balance. The terms appearing in the derived balances are interpreted as expected values and explicit formulas for these terms are obtained. Among the list of derived balances appear two, the tensor moment of inertia balance and the mesofluctuation balance, that are not standard in previously proposed macroscopic theories for liquid crystals but which have precedents in other theories for structured media.

Statistical foundations of liquid-crystal theory

PubMed Central

Seguin, Brian; Fried, Eliot

2013-01-01

Working on a state space determined by considering a discrete system of rigid rods, we use nonequilibrium statistical mechanics to derive macroscopic balance laws for liquid crystals. A probability function that satisfies the Liouville equation serves as the starting point for deriving each macroscopic balance. The terms appearing in the derived balances are interpreted as expected values and explicit formulas for these terms are obtained. Among the list of derived balances appear two, the tensor moment of inertia balance and the mesofluctuation balance, that are not standard in previously proposed macroscopic theories for liquid crystals but which have precedents in other theories for structured media. PMID:23554513

Laser-induced ferroelectric domain engineering in LiNbO3 crystals using an amorphous silicon overlayer

NASA Astrophysics Data System (ADS)

Zisis, G.; Martinez-Jimenez, G.; Franz, Y.; Healy, N.; Masaud, T. M.; Chong, H. M. H.; Soergel, E.; Peacock, A. C.; Mailis, S.

2017-08-01

We report laser-induced poling inhibition and direct poling in lithium niobate crystals (LiNbO3), covered with an amorphous silicon (a-Si) light-absorbing layer, using a visible (488 nm) continuous wave laser source. Our results show that the use of the a-Si overlayer produces deeper poling inhibited domains with minimum surface damage, as compared to previously reported UV laser writing experiments on uncoated crystals, thus increasing the applicability of this method in the production of ferroelectric domain engineered structures for nonlinear optical applications. The characteristics of the poling inhibited domains were investigated using differential etching and piezoresponse force microscopy.

Conserved Binding Mode of Human [beta subscript 2] Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

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

Wacker, Daniel; Fenalti, Gustavo; Brown, Monica A.

2010-11-15

G protein-coupled receptors (GPCRs) represent a large fraction of current pharmaceutical targets, and of the GPCRs, the {beta}{sub 2} adrenergic receptor ({beta}{sub 2}AR) is one of the most extensively studied. Previously, the X-ray crystal structure of {beta}{sub 2}AR has been determined in complex with two partial inverse agonists, but the global impact of additional ligands on the structure or local impacts on the binding site are not well-understood. To assess the extent of such ligand-induced conformational differences, we determined the crystal structures of a previously described engineered {beta}{sub 2}AR construct in complex with two inverse agonists: ICI 118,551 (2.8 {angstrom}),more » a recently described compound (2.8 {angstrom}) (Kolb et al, 2009), and the antagonist alprenolol (3.1 {angstrom}). The structures show the same overall fold observed for the previous {beta}{sub 2}AR structures and demonstrate that the ligand binding site can accommodate compounds of different chemical and pharmacological properties with only minor local structural rearrangements. All three compounds contain a hydroxy-amine motif that establishes a conserved hydrogen bond network with the receptor and chemically diverse aromatic moieties that form distinct interactions with {beta}{sub 2}AR. Furthermore, receptor ligand cross-docking experiments revealed that a single {beta}{sub 2}AR complex can be suitable for docking of a range of antagonists and inverse agonists but also indicate that additional ligand-receptor structures may be useful to further improve performance for in-silico docking or lead-optimization in drug design.« less

Beating the Heat - Fast Scanning Melts Silk Beta Sheet Crystals

NASA Astrophysics Data System (ADS)

Cebe, Peggy; Hu, Xiao; Kaplan, David L.; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniela; Schick, Christoph

2013-01-01

Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk, or proteins forming plaques as in Alzheimer's disease. Previous thinking, and the accepted paradigm, was that beta-pleated-sheet crystals in the dry solid state were so stable they would not melt upon input of heat energy alone. Here we overturn that assumption and demonstrate that beta-pleated-sheet crystals melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. Significance for controlling beta-pleated-sheet content during thermal processing of biomaterials, as well as towards disease therapies, is envisioned based on these new findings.

The crystal structures of two salivary cystatins from the tick Ixodes scapularis and the effect of these inhibitors on the establishment of Borrelia burgdorferi infection in a murine model

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

Kotsyfakis, Michalis; Horka, Helena; Salat, Jiri

2010-11-17

We have previously demonstrated that two salivary cysteine protease inhibitors from the Borrelia burgdorferi (Lyme disease) vector Ixodes scapularis - namely sialostatins L and L2 - play an important role in tick biology, as demonstrated by the fact that silencing of both sialostatins in tandem results in severe feeding defects. Here we show that sialostatin L2 - but not sialostatin L - facilitates the growth of B. burgdorferi in murine skin. To examine the structural basis underlying these differential effects of the two sialostatins, we have determined the crystal structures of both sialostatin L and L2. This is the firstmore » structural analysis of cystatins from an invertebrate source. Sialostatin L2 crystallizes as a monomer with an 'unusual' conformation of the N-terminus, while sialostatin L crystallizes as a domain-swapped dimer with an N-terminal conformation similar to other cystatins. Deletion of the 'unusual' N-terminal five residues of sialostatin L2 results in marked changes in its selectivity, suggesting that this region is a particularly important determinant of the biochemical activity of sialostatin L2. Collectively, our results reveal the structure of two tick salivary components that facilitate vector blood feeding and that one of them also supports pathogen transmission to the vertebrate host.« less

Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

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

Stogios, Peter J.; Cuesta-Seijo, Jose Antonio; Chen, Lu

2010-09-22

The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel {beta}-sheet with a strand from the other chain. We have solved the crystal structures of the BTB domains from Fanconi anemia zinc finger (FAZF) and Miz1 (Myc-interacting zinc finger 1) to resolutions of 2.0 {angstrom} and 2.6 {angstrom}, respectively. Unlike previous examples of BTB domain structures, the FAZF BTB domain is a nonswapped dimer, with each N-terminalmore » {beta}-strand associated with its own chain. As a result, the dimerization interface in the FAZF BTB domain is about half as large as in the domain-swapped dimers. The Miz1 BTB domain resembles a typical swapped BTB dimer, although it has a shorter N-terminus that is not able to form the interchain sheet. Using cysteine cross-linking, we confirmed that the promyelocytic leukemia zinc finger (PLZF) BTB dimer is strand exchanged in solution, while the FAZF BTB dimer is not. A phylogenic tree of the BTB fold based on both sequence and structural features shows that the common ancestor of the BTB domain in BTB-ZF (bric a brac, tramtrack, broad-complex zinc finger) proteins was a domain-swapped dimer. The differences in the N-termini seen in the FAZF and Miz1 BTB domains appear to be more recent developments in the structural evolution of the domain.« less

A Crystal Structure of the Dengue Virus Non-structural Protein 5 (NS5) Polymerase Delineates Interdomain Amino Acid Residues That Enhance Its Thermostability and de Novo Initiation Activities*

PubMed Central

Lim, Siew Pheng; Koh, Jolene Hong Kiew; Seh, Cheah Chen; Liew, Chong Wai; Davidson, Andrew D.; Chua, Leng Shiew; Chandrasekaran, Ramya; Cornvik, Tobias C.; Shi, Pei-Yong; Lescar, Julien

2013-01-01

The dengue virus (DENV) non-structural protein 5 (NS5) comprises an N-terminal methyltransferase and a C-terminal RNA-dependent RNA polymerase (RdRp) domain. Both enzymatic activities form attractive targets for antiviral development. Available crystal structures of NS5 fragments indicate that residues 263–271 (using the DENV serotype 3 numbering) located between the two globular domains of NS5 could be flexible. We observed that the addition of linker residues to the N-terminal end of the DENV RdRp core domain stabilizes DENV1–4 proteins and improves their de novo polymerase initiation activities by enhancing the turnover of the RNA and NTP substrates. Mutation studies of linker residues also indicate their importance for viral replication. We report the structure at 2.6-Å resolution of an RdRp fragment from DENV3 spanning residues 265–900 that has enhanced catalytic properties compared with the RdRp fragment (residues 272–900) reported previously. This new orthorhombic crystal form (space group P21212) comprises two polymerases molecules arranged as a dimer around a non-crystallographic dyad. The enzyme adopts a closed “preinitiation” conformation similar to the one that was captured previously in space group C2221 with one molecule per asymmetric unit. The structure reveals that residues 269–271 interact with the RdRp domain and suggests that residues 263–268 of the NS5 protein from DENV3 are the major contributors to the flexibility between its methyltransferase and RdRp domains. Together, these results should inform the screening and development of antiviral inhibitors directed against the DENV RdRp. PMID:24025331

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

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

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

Diaz, Z.; Xavier, K; Miller, S

2009-01-01

Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (??)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology withmore » aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.« less

Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase.

PubMed

Boucher, Lauren E; Bosch, Jürgen

2014-09-01

The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolase has been crystallized in space group P22121, with the biologically relevant tetramer in the asymmetric unit, and the structure has been determined via molecular replacement to a resolution of 2.0 Å. An analysis of the quality of the model and of the differences between the four chains in the asymmetric unit and a comparison between the T. gondii and P. falciparum aldolase structures is presented.

3D lattice distortions and defect structures in ion-implanted nano-crystals

DOE PAGES

Hofmann, Felix; Robinson, Ian K.; Tarleton, Edmund; ...

2017-04-06

The ability of Focused Ion Beam (FIB) techniques to cut solid matter at the nano-scale revolutionized the study of material structure across the life-, earth- and material sciences. But a detailed understanding of the damage caused by the ion beam and its effect on material properties remains elusive. We examine this damage in 3D using coherent X-ray diffraction to measure the full lattice strain tensor in FIB-milled gold nano-crystals. We also found that even very low ion doses, previously thought to be negligible, cause substantial lattice distortions. At higher doses, extended self-organized defect structures appear. Combined with detailed numerical calculations,more » these observations allow fundamental insight into the nature of the damage created and the structural instabilities that lead to a surprisingly inhomogeneous morphology.« less

A structural analysis of small vapor-deposited 'multiply twinned' gold particles

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Heinemann, K.; Yacaman, M. J.; Poppa, H.

1979-01-01

High resolution selected zone dark field, Bragg reflection imaging and weak beam dark field techniques of transmission electron microscopy were used to determine the structure of small gold particles vapor deposited on NaCl substrates. Attention was focused on the analysis of those particles in the 50-150 A range that have pentagonal or hexagonal bright field profiles. These particles have been previously described as multiply twinned crystallites composed of face-centered cubic tetrahedra. The experimental evidence of the present studies can be interpreted on the assumption that the particle structure is a regular icosahedron or decahedron for the hexagonal or the pentagonal particles respectively. The icosahedron is a multiply twinned rhombohedral crystal and the decahedron is a multiply twinned body-centered orthorhombic crystal, each of which constitutes a slight distortion from the face-centered cubic structure.

A study of tantalum pentoxide Ta 2O 5 structures up to 28 GPa

DOE PAGES

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; ...

2017-05-02

In this study, tantalum pentoxide Ta 2O 5 with the orthorhombic L-Ta 2O 5 structure has been experimentally studied up to 28.3 GPa (at ambient temperature) using synchrotron angle-dispersive powder X-ray diffraction (XRD). The ambient pressure phase remains stable up to 25 GPa where with increased pressure a crystalline to amorphous phase transition occurs. A detailed equation of state (EOS), including pressure dependent lattice parameters, is reported. The results of this study were compared with a previous high-pressure XRD study by Li et al. A clear discrepancy between the ambient-pressure crystal structures and, consequently, the reported EOSs between the twomore » studies was revealed. Finally, he origin of this discrepancy is attributed to two different crystal structures used to index the XRD patterns.« less

Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.

PubMed Central

Spink, N; Brown, D G; Skelly, J V; Neidle, S

1994-01-01

The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width. Images PMID:7515488

3D lattice distortions and defect structures in ion-implanted nano-crystals

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

Hofmann, Felix; Robinson, Ian K.; Tarleton, Edmund

The ability of Focused Ion Beam (FIB) techniques to cut solid matter at the nano-scale revolutionized the study of material structure across the life-, earth- and material sciences. But a detailed understanding of the damage caused by the ion beam and its effect on material properties remains elusive. We examine this damage in 3D using coherent X-ray diffraction to measure the full lattice strain tensor in FIB-milled gold nano-crystals. We also found that even very low ion doses, previously thought to be negligible, cause substantial lattice distortions. At higher doses, extended self-organized defect structures appear. Combined with detailed numerical calculations,more » these observations allow fundamental insight into the nature of the damage created and the structural instabilities that lead to a surprisingly inhomogeneous morphology.« less

Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

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

Wubben, T.; Mesecar, A.D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observedmore » in the MtPPAT-CoA complex.« less

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

Wurzburg, Beth A.; Tarchevskaya, Svetlana S.; Jardetzky, Theodore S.

CD23, the low-affinity receptor for IgE (Fc{var_epsilon}RII), regulates IgE synthesis and also mediates IgE-dependent antigen transport and processing. CD23 is a unique Fc receptor belonging to the C-type lectin-like domain superfamily and binds IgE in an unusual, non-lectin-like manner, requiring calcium but not carbohydrate. We have solved the high-resolution crystal structures of the human CD23 lectin domain in the presence and absence of Ca{sup 2+}. The crystal structures differ significantly from a previously determined NMR structure and show that calcium binding occurs at the principal binding site, but not at an auxiliary site that appears to be absent in humanmore » CD23. Conformational differences between the apo and Ca{sup 2+} bound structures suggest how IgE-Fc binding can be both calcium-dependent and carbohydrate-independent.« less

Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.

PubMed

Di Pisa, Flavio; Landi, Giacomo; Dello Iacono, Lucia; Pozzi, Cecilia; Borsari, Chiara; Ferrari, Stefania; Santucci, Matteo; Santarem, Nuno; Cordeiro-da-Silva, Anabela; Moraes, Carolina B; Alcantara, Laura M; Fontana, Vanessa; Freitas-Junior, Lucio H; Gul, Sheraz; Kuzikov, Maria; Behrens, Birte; Pöhner, Ina; Wade, Rebecca C; Costi, Maria Paola; Mangani, Stefano

2017-03-08

Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues ( 1 - 3 ) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes ( Trypanosoma brucei PTR1- Tb PTR1 and Leishmania major-Lm PTR1) and parasites ( Trypanosoma brucei and Leishmania infantum ). A crystal structure of Tb PTR1 in complex with compound 1 and the first crystal structures of Lm PTR1-flavanone complexes (compounds 1 and 3 ) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.

Effects of rotation on crystal settling in a terrestrial magma ocean: Spherical shell model

NASA Astrophysics Data System (ADS)

Maas, C.; Hansen, U.

2015-12-01

Like Moon or Mars, Earth experienced one or several deep magma ocean periods of globalextent in a later stage of its accretion. The crystallization of these magma oceans is of keyimportance for the chemical structure of Earth, the mantle evolution and the onset of platetectonics. Due to the fast rotation of early Earth and the small magma viscosity, rotationprobably had a profound effect on differentiation processes. For example, Matyska et al.[1994] propose that the distribution of heterogeneities like the two large low shear velocityprovinces (LLSVP) at the core mantle boundary is influenced by rotational dynamicsof early Earth. Further Garnero and McNamara [2008] suggest that the LLSVPs arevery long-living anomalies, probably reaching back to the time of differentiation andsolidification of Earth. However, nearly all previous studies neglect the effects of rotation.In our previous work using a Cartesian model, a strong influence of rotation as well asof latitude on the differentiation processes in an early magma ocean was revealed. Weshowed that crystal settling in an early stage of magma ocean crystallization cruciallydepends on latitude as well as on rotational strength and crystal density.In order to overcome the restrictions as to the geometry of the Cartesian model, we arecurrently developing a spherical model to simulate crystal settling in a rotating sphericalshell. This model will allow us not only to investigate crystal settling at the poles andthe equator, but also at latitudes in-between these regions, as well as the migration ofcrystals between poles and equator. ReferencesE. J. Garnero and A. K. McNamara. Structure and dynamics of earth's lower mantle.Science, 320(5876):626-628, 2008.C. Matyska, J. Moser, and D. A. Yuen. The potential influence of radiative heat transferon the formation of megaplumes in the lower mantle. Earth and Planetary ScienceLetters, 125(1):255-266, 1994.

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Conversion of scFv peptide-binding specificity for crystal chaperone development

PubMed Central

Pai, Jennifer C.; Culver, Jeffrey A.; Drury, Jason E.; Motani, Rakesh S.; Lieberman, Raquel L.; Maynard, Jennifer A.

2011-01-01

In spite of advances in protein expression and purification over the last decade, many proteins remain recalcitrant to structure determination by X-ray crystallography. One emerging tactic to obtain high-quality protein crystals for structure determination, particularly in the case of membrane proteins, involves co-crystallization with a protein-specific antibody fragment. Here, we report the development of new recombinant single-chain antibody fragments (scFv) capable of binding a specific epitope that can be introduced into internal loops of client proteins. The previously crystallized hexa-histidine-specific 3D5 scFv antibody was modified in the complementary determining region and by random mutagenesis, in conjunction with phage display, to yield scFvs with new biochemical characteristics and binding specificity. Selected variants include those specific for the hexa-histidine peptide with increased expression, solubility (up to 16.6 mg/ml) and sub-micromolar affinity, and those with new specificity for the EE hexa-peptide (EYMPME) and nanomolar affinity. Complexes of one such chaperone with model proteins harboring either an internal or a terminal EE tag were isolated by gel filtration. The 3.1 Å resolution structure of this chaperone reveals a binding surface complementary to the EE peptide and a ∼52 Å channel in the crystal lattice. Notably, in spite of 85% sequence identity, and nearly identical crystallization conditions, the engineered scFv crystallizes in a different space group than the parent 3D5 scFv, and utilizes two new crystal contacts. These engineered scFvs represent a new class of chaperones that may eliminate the need for de novo identification of candidate chaperones from large antibody libraries. PMID:21217145

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of the toxic core of α-synuclein from invisible crystals

DOE PAGES

Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.; ...

2015-09-09

We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

Structure of N-acetyl-[beta]-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

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

Langley, David B.; Harty, Derek W.S.; Jacques, Nicholas A.

2008-09-17

The crystal structure of GcnA, an N-acetyl-{beta}-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal {alpha}-helical domain has not been observed previously and forms a large dimerization interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical ({beta}/{alpha}){sub 8} TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a familymore » 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-{beta}-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.« less

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

PubMed Central

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.; Louro, Ricardo O.; Moe, Elin

2016-01-01

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing. PMID:27599855

Robust Level Coincidences in the Subband Structure of Quasi 2D Systems

NASA Astrophysics Data System (ADS)

Winkler, R.; Wang, L. Y.; Lin, Y. H.; Chu, C. S.

2011-03-01

Recently, level crossings in the energy bands of crystals have been identified as a key signature for topological phase transitions. In general, three independent parameters must be tuned appropriately to bring two quantum levels into degeneracy. Using realistic models we show that for Bloch electrons in a crystal the parameter space controlling the occurrence of level coincidences has a much richer structure than anticipated previously. In particular, we identify cases where level coincidences depend on only two independent parameters thus making the level coincidences robust, i.e., they cannot be removed by a small perturbation of the Hamiltonian compatible with the crystal symmetry. We consider HgTe/CdTe quantum wells as a specific example. (See arXiv:1011.xxxx) Work supported by Taiwan NSC (Contract No. 99-2112-M-009-006) and a MOE-ATU grant. Work at Argonne supported by DOE BES under Contract No. DE-AC02-06CH11357.

Classification of octet AB-type binary compounds using dynamical charges: A materials informatics perspective

DOE PAGES

Pilania, G.; Gubernatis, J. E.; Lookman, T.

2015-12-03

The role of dynamical (or Born effective) charges in classification of octet AB-type binary compounds between four-fold (zincblende/wurtzite crystal structures) and six-fold (rocksalt crystal structure) coordinated systems is discussed. We show that the difference in the dynamical charges of the fourfold and sixfold coordinated structures, in combination with Harrison’s polarity, serves as an excellent feature to classify the coordination of 82 sp–bonded binary octet compounds. We use a support vector machine classifier to estimate the average classification accuracy and the associated variance in our model where a decision boundary is learned in a supervised manner. Lastly, we compare the out-of-samplemore » classification accuracy achieved by our feature pair with those reported previously.« less

Pt-Bi Antibonding Interaction: The Key Factor for Superconductivity in Monoclinic BaPt2Bi2.

PubMed

Gui, Xin; Xing, Lingyi; Wang, Xiaoxiong; Bian, Guang; Jin, Rongying; Xie, Weiwei

2018-02-19

In the search for superconductivity in a BaAu 2 Sb 2 -type monoclinic structure, we have successfully synthesized the new compound BaPt 2 Bi 2 , which crystallizes in the space group P2 1 /m (No. 11; Pearson symbol mP10) according to a combination of powder and single-crystal X-ray diffraction and scanning electron microscopy. A sharp electrical resistivity drop and large diamagnetic magnetization below 2.0 K indicates it owns superconducting ground state. This makes BaPt 2 Bi 2 the first reported superconductor in a monoclinic BaAu 2 Sb 2 -type structure, a previously unappreciated structure for superconductivity. First-principles calculations considering spin-orbit coupling indicate that Pt-Bi antibonding interaction plays a critical role in inducing superconductivity.

XTALOPT version r11: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Avery, Patrick; Falls, Zackary; Zurek, Eva

2018-01-01

Version 11 of XTALOPT, an evolutionary algorithm for crystal structure prediction, has now been made available for download from the CPC library or the XTALOPT website, http://xtalopt.github.io. Whereas the previous versions of XTALOPT were published under the Gnu Public License (GPL), the current version is made available under the 3-Clause BSD License, which is an open source license that is recognized by the Open Source Initiative. Importantly, the new version can be executed via a command line interface (i.e., it does not require the use of a Graphical User Interface). Moreover, the new version is written as a stand-alone program, rather than an extension to AVOGADRO.

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

Huang, Xin; Chen, Hao; Shaffer, Paul L.

Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABA ARs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08more » Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABA ARs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.« less

Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1

PubMed Central

Hong, Zebin; De Meulemeester, Laura; Jacobi, Annemarie; Pedersen, Jan Skov; Morth, J. Preben; Andreasen, Peter A.; Jensen, Jan K.

2016-01-01

Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhibitor of several serine proteases, including hepatocyte growth factor activator and matriptase. The protein is essential for development as knock-out mice die in utero due to placental defects caused by misregulated extracellular proteolysis. HAI-1 contains two Kunitz-type inhibitor domains (Kunitz), which are generally thought of as a functionally self-contained protease inhibitor unit. This is not the case for HAI-1, where our results reveal how interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. Here we present an x-ray crystal structure of an HAI-1 fragment covering the internal domain and Kunitz-1. The structure reveals not only that the previously uncharacterized internal domain is a member of the polycystic kidney disease domain family but also how the two domains engage in interdomain interactions. Supported by solution small angle x-ray scattering and a combination of site-directed mutagenesis and functional assays, we show that interdomain interactions not only stabilize the fold of the internal domain but also stimulate the inhibitory activity of Kunitz-1. By completing our structural characterization of the previously unknown N-terminal region of HAI-1, we provide new insight into the interplay between tertiary structure and the inhibitory activity of a multidomain protease inhibitor. We propose a previously unseen mechanism by which the association of an auxiliary domain stimulates the inhibitory activity of a Kunitz-type inhibitor (i.e. the first structure of an intramolecular interaction between a Kunitz and another domain). PMID:27189939

Protein-directed self-assembly of a fullerene crystal.

PubMed

Kim, Kook-Han; Ko, Dong-Kyun; Kim, Yong-Tae; Kim, Nam Hyeong; Paul, Jaydeep; Zhang, Shao-Qing; Murray, Christopher B; Acharya, Rudresh; DeGrado, William F; Kim, Yong Ho; Grigoryan, Gevorg

2016-04-26

Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.

Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima

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

Lyashenko, Andrey V.; Zhukhlistova, Nadegda E.; Gabdoulkhakov, Azat G.

2006-10-01

The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccasemore » structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R{sub free} = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO{sub 2} substituents.« less

The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids

NASA Astrophysics Data System (ADS)

Beckmann, Peter A.; Paty, Carol; Allocco, Elizabeth; Herd, Maria; Kuranz, Carolyn; Rheingold, Arnold L.

2004-03-01

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.

Phosphoryl transfer reaction snapshots in crystals: Insights into the mechanism of protein kinase a catalytic subunit

DOE PAGES

Das, Amit; Gerlits, Oksana O.; Heller, William T.; ...

2015-06-19

To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca 2+ ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex,more » the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca 2+ cations with Mg 2+ ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. As a result, the present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.« less

Deglycosylated Filovirus Glycoproteins as Effective Vaccine Immunogens

DTIC Science & Technology

2015-11-01

pre-fusion 119 EBOV GP1,2 ΔTM structure ( PDB ID: 3CSY) that lacks the MLD was performed as previously 120 described (22, 23). Briefly, the published... structure lacks four NGS in GP1 due to disordered 121 regions missing from the structure (N204 and N296) or mutations that promoted crystallization...122 (N40 and N228) (20, 21). The EBOV GP sequence was submitted to the PHYRE2 protein fold 123 recognition server (16), which provided a structure

Detergent-Mediated Formation of β-Hematin: Heme Crystallization Promoted by Detergents Implicates Nanostructure Formation for Use as a Biological Mimic

PubMed Central

2016-01-01

Hemozoin is a unique biomineral that results from the sequestration of toxic free heme liberated as a consequence of hemoglobin degradation in the malaria parasite. Synthetic neutral lipid droplets (SNLDs) and phospholipids were previously shown to support the rapid formation of β-hematin, abiological hemozoin, under physiologically relevant pH and temperature, though the mechanism by which heme crystallization occurs remains unclear. Detergents are particularly interesting as a template because they are amphiphilic molecules that spontaneously organize into nanostructures and have been previously shown to mediate β-hematin formation. Here, 11 detergents were investigated to elucidate the physicochemical properties that best recapitulate crystal formation in the parasite. A strong correlation between the detergent’s molecular structure and the corresponding kinetics of β-hematin formation was observed, where higher molecular weight polar chains promoted faster reactions. The larger hydrophilic chains correlated to the detergent’s ability to rapidly sequester heme into the lipophilic core, allowing for crystal nucleation to occur. The data presented here suggest that detergent nanostructures promote β-hematin formation in a similar manner to SNLDs and phospholipids. Through understanding mediator properties that promote optimal crystal formation, we are able to establish an in vitro assay to probe this drug target pathway. PMID:27175104

Second-order many-body perturbation study of ice Ih

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

He, Xiao; Sode, Olaseni; Xantheas, Sotiris S.

2012-11-28

Ice Ih is arguably the most important molecular crystal in nature, yet our understanding of its structural and dynamical properties is still incomplete. To explain the origin of two peaks in the hydrogen-bond-stretching region of the inelastic neutron scattering (INS) spectra, the existence of two types of hydrogen bonds with strengths differing by a factor of two was previously hypothesized. We present first-principles calculations based on diagrammatic many-body perturbation theory of the structures and vibrational spectra of ice Ih, which suggest that the observed spectral features arise from the directionality or anisotropy of the hydrogen-bond stretching vibrations rather than theirmore » vastly different force constants, disproving the previous hypothesis. Our calculations also reproduce the infrared and Raman spectra, the variation of INS spectra with deuterium concentration, and the anomaly of heat capacities at low temperatures, together rendering our calculations a paradigm for "crystals from first principles" as envisioned by Maddox.« less

High Photon-to-Current Conversion in Solar Cells Based on Light-Absorbing Silver Bismuth Iodide.

PubMed

Zhu, Huimin; Pan, Mingao; Johansson, Malin B; Johansson, Erik M J

2017-06-22

Here, a lead-free silver bismuth iodide (AgI/BiI 3 ) with a crystal structure with space group R3‾ m is investigated for use in solar cells. Devices based on the silver bismuth iodide deposited from solution on top of TiO 2 and the conducting polymer poly(3-hexylthiophene-2,5-diyl) (P3HT) as a hole-transport layer are prepared and the photovoltaic performance is very promising with a power conversion efficiency over 2 %, which is higher than the performance of previously reported bismuth-halide materials for solar cells. Photocurrent generation is observed between 350 and 700 nm, and the maximum external quantum efficiency is around 45 %. The results are compared to solar cells based on the previously reported material AgBi 2 I 7 , and we observe a clearly higher performance for the devices with the new silver and bismuth iodides composition and different crystal structure. The X-ray diffraction spectrum of the most efficient silver bismuth iodide material shows a hexagonal crystal structure with space group R3‾ m, and from the light absorption spectrum we obtain an indirect band gap energy of 1.62 eV and a direct band gap energy of 1.85 eV. This report shows the possibility for finding new structures of metal-halides efficient in solar cells and points out new directions for further exploration of lead-free metal-halide solar cells. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Structural basis of redox-dependent substrate binding of protein disulfide isomerase

PubMed Central

Yagi-Utsumi, Maho; Satoh, Tadashi; Kato, Koichi

2015-01-01

Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b′ and a′ domains provide substrate binding sites and undergo an open–closed domain rearrangement depending on the redox states of the a′ domain. Despite the long research history of this enzyme, three-dimensional structural data remain unavailable for its ligand-binding mode. Here we characterize PDI substrate recognition using α-synuclein (αSN) as the model ligand. Our nuclear magnetic resonance (NMR) data revealed that the substrate-binding domains of PDI captured the αSN segment Val37–Val40 only in the oxidized form. Furthermore, we determined the crystal structure of an oxidized form of the b′–a′ domains in complex with an undecapeptide corresponding to this segment. The peptide-binding mode observed in the crystal structure with NMR validation, was characterized by hydrophobic interactions on the b′ domain in an open conformation. Comparison with the previously reported crystal structure indicates that the a′ domain partially masks the binding surface of the b′ domain, causing steric hindrance against the peptide in the reduced form of the b′–a′ domains that exhibits a closed conformation. These findings provide a structural basis for the mechanism underlying the redox-dependent substrate binding of PDI. PMID:26350503

Crystal Structure of a Four-Layer Aggregate of Engineered TMV CP Implies the Importance of Terminal Residues for Oligomer Assembly

PubMed Central

Li, Xiangyang; Song, Baoan; Chen, Xi; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Hu, Deyu; Chen, Zhuo; Jin, Linhong; Yang, Song; Yang, Caiguang; Chen, Baoen

2013-01-01

Background Crystal structures of the tobacco mosaic virus (TMV) coat protein (CP) in its helical and disk conformations have previously been determined at the atomic level. For the helical structure, interactions of proteins and nucleic acids in the main chains were clearly observed; however, the conformation of residues at the C-terminus was flexible and disordered. For the four-layer aggregate disk structure, interactions of the main chain residues could only be observed through water–mediated hydrogen bonding with protein residues. In this study, the effects of the C-terminal peptides on the interactions of TMV CP were investigated by crystal structure determination. Methodology/Principal Findings The crystal structure of a genetically engineered TMV CP was resolved at 3.06 Å. For the genetically engineered TMV CP, a six-histidine (His) tag was introduced at the N-terminus, and the C-terminal residues 155 to 158 were truncated (N-His-TMV CP19). Overall, N-His-TMV CP19 protein self-assembled into the four-layer aggregate form. The conformations of residues Gln36, Thr59, Asp115 and Arg134 were carefully analyzed in the high radius and low radius regions of N-His-TMV CP19, which were found to be significantly different from those observed previously for the helical and four-layer aggregate forms. In addition, the aggregation of the N-His-TMV CP19 layers was found to primarily be mediated through direct hydrogen-bonding. Notably, this engineered protein also can package RNA effectively and assemble into an infectious virus particle. Conclusion The terminal sequence of amino acids influences the conformation and interactions of the four-layer aggregate. Direct protein–protein interactions are observed in the major overlap region when residues Gly155 to Thr158 at the C-terminus are truncated. This engineered TMV CP is reassembled by direct protein–protein interaction and maintains the normal function of the four-layer aggregate of TMV CP in the presence of RNA. PMID:24223721

Demonstration of lipofuscin and Nissl bodies in crystal violet stained sections using a fluorescence technique or pyronin Y stain.

PubMed

Terr, L I

1986-09-01

This paper presents two simple, reliable methods for identification of lipofuscin and Nissl bodies in the same section. One method shows that lipofuscin stained with crystal violet retains its ability to fluoresce and can be observed under the fluorescence microscope after the stain has faded. Fading is accompanied by a gradual increase in the intensity of the fluorescence and is complete in about 5 min. Exciting illumination from this part of the spectrum also substantially fades staining of other autofluorescing tissue elements, such as lipids. Nonfluorescing structures, such as Nissl bodies, remain stained. By changing from transillumination with tungsten light to epifluorescent illumination and vice versa, both types of structures--Nissl bodies and lipofuscin--can be identified in the same section. The second technique uses pyronin Y for staining Nissl bodies in preparations previously stained with crystal violet. Nissl bodies are stained pink but lipofuscin remains violet. Lipofuscin in these sections also remains autofluorescent after the crystal violet stain has faded under violet or near-UV light.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

Redetermination of 2-methyl-4-nitro­pyridine N-oxide

PubMed Central

Peukert, Max; Seichter, Wilhelm; Weber, Edwin

2014-01-01

An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the ortho­rhom­bic space group Pca21 and refined to R = 0.067, has been solved in the ortho­rhom­bic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The mol­ecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of mol­ecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers. PMID:24826136

Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1.

PubMed

Zandarashvili, Levani; White, Mark A; Esadze, Alexandre; Iwahara, Junji

2015-07-08

The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation. We have determined, at a 1.4-Å resolution, the crystal structure of the Egr-1 zinc-finger complex with completely methylated target DNA. Structural comparison of the three different methylation states reveals why Egr-1 can recognize the target sequences regardless of CpG methylation. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

The FapF amyloid secretion transporter possesses an atypical asymmetric coiled coil.

PubMed

Rouse, Sarah L; Stylianou, Fisentzos; Grace Wu, H Y; Berry, Jamie-Lee; Sewell, Lee; Morgan, R Marc L; Sauerwein, Andrea C; Matthews, Steve

2018-06-07

Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits, the fibres of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialised outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8 Å resolution. This domain forms a novel asymmetric trimeric coiled-coil that possesses a single buried tyrosine residue as well as a extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail. Copyright © 2018. Published by Elsevier Ltd.

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

DOE PAGES

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.; ...

2017-05-17

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

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

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Hydrogen bonding intermolecular effect on electro-optical response of doped 6PCH nematic liquid crystal with some azo dyes

NASA Astrophysics Data System (ADS)

Kiani, S.; Zakerhamidi, M. S.; Tajalli, H.

2016-05-01

Previous studies on the electro-optical responses of dye-doped liquid crystal have shown that dopant material have a considerable effect on their electro-optical responses. Despite the studies carried out on electro-optical properties of dye-doped liquid crystal, no attention has been paid to study of the interaction and structural effects in this procedure. In this paper, linear dyes and with similar structure were selected as dopants. The only difference in used dyes is the functional groups in their tails. So, doping of these dyes into liquid crystals determines the influence of interaction type on electro-optical behaviours of the doped systems. Therefore, in this work, two aminoazobenzene (;A-dye;: hydrogen bond donor) and dimethyl-aminoazobenzene (;B-dye;) dyes with different compositional percentages in liquid crystal host were used. Electro-optical Kerr behaviour, the pre-transition temperature and third order nonlinear susceptibility were investigated. The obtained results effectively revealed that type of interactions between the dye and liquid crystal is determinative of behavioral difference of doped system, compared to pure liquid crystal. Also, pre-transitional behaviour and thereupon Kerr electro-optical responses were affected by formed interactions into doped systems. In other words, it will be shown that addition of any dopants in liquid crystal, regardless of the nature of interactions, cannot cause appropriate electro-optical responses. In fact, type of dye, nature of interactions between dopant and liquid crystalline host as well as concentration of dye are the key factors in selecting the appropriate liquid crystal and dopant dye.

Monoclinic crystal structure of α - RuCl 3 and the zigzag antiferromagnetic ground state

DOE PAGES

Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

2015-12-10

We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition around 8 T for in-plane fields followed by a gradual, asymptotic approach to magnetization saturation, as characteristic of strongly anisotropic exchange interactions.« less

Murine Leukemia Virus Reverse Transcriptase: Structural Comparison with HIV-1 Reverse Transcriptase

PubMed Central

Coté, Marie L.; Roth, Monica J.

2008-01-01

Recent X-ray crystal structure determinations of Moloney murine leukemia virus reverse transcriptase (MoMLV RT) have allowed for more accurate structure/function comparisons to HIV-1 RT than were formerly possible. Previous biochemical studies of MoMLV RT in conjunction with knowledge of sequence homologies to HIV-1 RT and overall fold similarities to RTs in general, provided a foundation upon which to build. In addition, numerous crystal structures of the MoMLV RT fingers/palm subdomain had also shed light on one of the critical functions of the enzyme, specifically polymerization. Now in the advent of new structural information, more intricate examination of MoMLV RT in its entirety can be realized, and thus the comparisons with HIV-1 RT may be more critically elucidated. Here, we will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information. PMID:18294720

Crystal structure of diaphorin methanol monosolvate isolated from Diaphorina citri Kuwayama, the insect vector of citrus greening disease.

PubMed

Szebenyi, D Marian; Kriksunov, Irina; Howe, Kevin J; Ramsey, John S; Hall, David G; Heck, Michelle L; Krasnoff, Stuart B

2018-04-01

The title compound C 22 H 39 NO 9 ·CH 3 OH [systematic name: ( S )- N -(( S )-{(2 S ,4 R ,6 R )-6-[( S )-2,3-di-hydroxy-prop-yl]-4-hy-droxy-5,5-di-methyl-tetra-hydro-2 H -pyran-2-yl}(hy-droxy)meth-yl)-2-hy-droxy-2-[(2 R ,5 R ,6 R )-2-meth-oxy-5,6-dimeth-yl-4-methyl-ene-tetra-hydro-2 H -pyran-2-yl]acetamide methanol monosolvate], was isolated from the Asian citrus psyllid, Diaphorina citri Kuwayama, and crystallizes in the space group P 2 1 . ' Candidatus Profftella armatura' a bacterial endosymbiont of D. citri , biosynthesizes diaphorin, which is a hybrid polyketide-nonribosomal peptide comprising two highly substituted tetra-hydro-pyran rings joined by an N -acyl aminal bridge [Nakabachi et al. (2013 ▸). Curr. Biol. 23 , 1478-1484]. The crystal structure of the title compound establishes the complete relative configuration of diaphorin, which agrees at all nine chiral centers with the structure of the methanol monosolvate of the di- p -bromo-benzoate derivative of pederin, a biogenically related compound whose crystal structure was reported previously [Furusaki et al. (1968 ▸). Tetra-hedron Lett. 9 , 6301-6304]. Thus, the absolute configuration of diaphorin is proposed by analogy to that of pederin.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

DOE PAGES

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; ...

2016-09-19

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstaclemore » is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined.We showwith four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

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

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstaclemore » is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined.We showwith four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.« less

Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A.

PubMed

Kita, Shunsuke; Matsubara, Haruki; Kasai, Yoshiyuki; Tamaoki, Takaharu; Okabe, Yuki; Fukuhara, Hideo; Kamishikiryo, Jun; Krayukhina, Elena; Uchiyama, Susumu; Ose, Toyoyuki; Kuroki, Kimiko; Maenaka, Katsumi

2015-06-01

Emerging evidence has revealed the pivotal roles of C-type lectin-like receptors (CTLRs) in the regulation of a wide range of immune responses. Human natural killer cell receptor-P1A (NKRP1A) is one of the CTLRs and recognizes another CTLR, lectin-like transcript 1 (LLT1) on target cells to control NK, NKT and Th17 cells. The structural basis for the NKRP1A-LLT1 interaction was limitedly understood. Here, we report the crystal structure of the ectodomain of LLT1. The plausible receptor-binding face of the C-type lectin-like domain is flat, and forms an extended β-sheet. The residues of this face are relatively conserved with another CTLR, keratinocyte-associated C-type lectin, which binds to the CTLR member, NKp65. A LLT1-NKRP1A complex model, prepared using the crystal structures of LLT1 and the keratinocyte-associated C-type lectin-NKp65 complex, reasonably satisfies the charge consistency and the conformational complementarity to explain a previous mutagenesis study. Furthermore, crystal packing and analytical ultracentrifugation revealed dimer formation, which supports a complex model. Our results provide structural insights for understanding the binding modes and signal transduction mechanisms, which are likely to be conserved in the CTLR family, and for further rational drug design towards regulating the LLT1 function. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystallisation and crystal forms of carbohydrate derivatives

NASA Astrophysics Data System (ADS)

Lennon, Lorna

This thesis is focused on the synthesis and solid state analysis of carbohydrate derivatives, including many novel compounds. Although the synthetic chemistry surrounding carbohydrates is well established in the literature, the crystal chemistry of carbohydrates is less well studied. Therefore this research aims to improve understanding of the solid state properties of carbohydrate derivatives through gaining more information on their supramolecular bonding. Chapter One focuses on an introduction to the solid state of organic compounds, with a background to crystallisation, including issues that can arise during crystal growth. Chapter Two is based on glucopyranuronate derivatives which are understudied in terms of their solid state forms. This chapter reports on the formation of novel glucuronamides and utilising the functionality of the amide bond for crystallisation. TEMPO oxidation was completed to form glucopyranuronates by oxidation of the primary alcohol groups of glucosides to the carboxylic acid derivatives, to increase functionality for enhanced crystal growth. Chapter Three reports on the synthesis of glucopyranoside derivatives by O-glycosylation reactions and displays crystal structures, including a number of previously unsolved acetate protected and deprotected crystal structures. More complex glycoside derivatives were also researched in an aim to study the resultant supramolecular motifs. Chapter Four contains the synthesis of aryl cellobioside derivatives including the novel crystal structures that were solved for the acetate protected and deprotected compounds. Research was carried out to determine if 1-deoxycellodextrins could act as putative isostructures for cellulose. Our research displays the presence of isostructural references with 1-deoxycellotriose shown to be similar to cellulose III11, 1-deoxycellotetraose correlates with cellulose IV11 and 1-deoxycellopentose shows isostructurality similar to that of cellulose II. Chapter Five contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project and relevant crystallographic information.

Magnetic field role on the structure and optical response of photonic crystals based on ferrofluids containing Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} nanoparticles

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

López, J., E-mail: javier.lopez@correounivalle.edu.co; González, Luz E.; Quiñonez, M. F.

2014-05-21

Ferrofluids based on magnetic Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} ferrite nanoparticles were prepared by co-precipitation method from aqueous salt solutions of Co (II), ZnSO{sub 4}, and Fe (III) in an alkaline medium. Ferrofluids placed in an external magnetic field show properties that make them interesting as magneto-controllable soft photonic crystals. Morphological and structural characterizations of the samples were obtained from Scanning Electron Microscopy and Transmission Electron Microscopy studies. Magnetic properties were investigated with the aid of a vibrating sample magnetometer at room temperature. Herein, the Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} samples showed superparamagnetic behavior, according to hysteresis loop results. Takingmore » in mind that the Co-Zn ferrite hysteresis loop is very small, our magnetic nanoparticles can be considered soft magnetic material with interesting technological applications. In addition, by using the plane-wave expansion method, we studied the photonic band structure of 2D photonic crystals made of ferrofluids with the same nanoparticles. Previous experimental results show that a magnetic field applied perpendicular to the ferrofluid plane agglomerates the magnetic nanoparticles in parallel rods to form a hexagonal 2D photonic crystal. We calculated the photonic band structure of photonic crystals by means of the effective refractive index of the magnetic fluid, basing the study on the Maxwell-Garnett theory, finding that the photonic band structure does not present any band gaps under the action of applied magnetic field strengths used in our experimental conditions.« less

Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

PubMed Central

Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Arthur; Kristensen, Ole; Kastrup, Jette Sandholm; Berezin, Vladimir; Bock, Elisabeth; Gajhede, Michael

2007-01-01

Fibroblast growth factors (FGFs) constitute a family of 22 structurally related heparin-binding polypeptides that are involved in the regulation of cell growth, survival, differentiation and migration. Here, a 1.4 Å resolution X-ray structure of rat FGF1 is presented. Two molecules are present in the asymmetric unit of the crystal and they coordinate a total of five sulfate ions. The structures of human, bovine and newt FGF1 have been published previously. Human and rat FGF1 are found to have very similar structures. PMID:17277441

Spectroscopic study of the inhibition of calcium oxalate calculi by Larrea tridentata

NASA Astrophysics Data System (ADS)

Pinales, Luis Alonso

The causes of urolithiasis include such influences as diet, metabolic disorders, and genetic factors which have been documented as sources that aggravate urinary calculi depositions and aggregations, and, implicitly, as causes of urolithiasis. This study endeavors to detail the scientific mechanisms involved in calcium oxalate calculi formation, and, more importantly, their inhibition under growth conditions imposed by the traditional medicinal approach using the herbal extract, Larrea tridentata. The calculi were synthesized without and with Larrea tridentata infusion by employing the single diffusion gel technique. A visible decrease in calcium oxalate crystal growth with increasing amounts of Larrea tridentata herbal infusion was observed in photomicrographs, as well as a color change from white-transparent for pure crystals to light orange-brown for crystals with inhibitor. Analysis of the samples, which includes Raman, infrared absorption, scanning electron microscopy (SEM), and X-ray powder diffraction (XRD) techniques, demonstrate an overall transition in morphology of the crystals from monohydrate without herbal extract to dihydrate with inhibitor. Furthermore, the resulting data from Raman and infrared absorption support the possibilities of the influences, in this complex process, of NDGA and its derivative compounds from Larrea tridentata, and of the bonding of the magnesium of the inhibitor with the oxalate ion on the surface of the calculi crystals. This assumption corroborates well with the micrographs obtained under higher magnification, which show that the separated small crystallites consist of darker brownish cores, which we attribute to the dominance of growth inhibition by NDGA, surrounded by light transparent thin shells, which possibly correspond to passivation of the crystals by magnesium oxalate. The SEM results reveal the transformation from the dominant monoclinic structure of the calcium oxalate crystals grown alone to the tetragonal dipyramidal crystal structure of the calcium oxalate crystals grown with Larrea tridentata. Comparison between XRD experimental and simulated data, besides corroborating with our previous results, show that each sample is a combination of different structures.

Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases.

PubMed

Kim, Chang-Yub; Webster, Cecelia; Roberts, Justin K M; Moon, Jin Ho; Alipio Lyon, Emily Z; Kim, Heungbok; Yu, Minmin; Hung, Li-Wei; Terwilliger, Thomas C

2009-12-01

We show that Cibacron Blue F3GA dye resin chromatography can be used to identify ligands that specifically interact with proteins from Mycobacterium tuberculosis, and that the identification of these ligands can facilitate structure determination by enhancing the quality of crystals. Four native Mtb proteins of the aldehyde dehydrogenase (ALDH) family were previously shown to be specifically eluted from a Cibacron Blue F3GA dye resin with nucleosides. In this study we characterized the nucleoside-binding specificity of one of these ALDH isozymes (recombinant Mtb Rv0223c) and compared these biochemical results with co-crystallization experiments with different Rv0223c-nucleoside pairings. We found that the strongly interacting ligands (NAD and NADH) aided formation of high-quality crystals, permitting solution of the first Mtb ALDH (Rv0223c) structure. Other nucleoside ligands (AMP, FAD, adenosine, GTP and NADP) exhibited weaker binding to Rv0223c, and produced co-crystals diffracting to lower resolution. Difference electron density maps based on crystals of Rv0223c with various nucleoside ligands show most share the binding site where the natural ligand NAD binds. From the high degree of similarity of sequence and structure compared to human mitochondrial ALDH-2 (BLAST Z-score = 53.5 and RMSD = 1.5 A), Rv0223c appears to belong to the ALDH-2 class. An altered oligomerization domain in the Rv0223c structure seems to keep this protein as monomer whereas native human ALDH-2 is a multimer.

Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex.

PubMed

Schiering, N; Casale, E; Caccia, P; Giordano, P; Battistini, C

2000-11-07

Src homology 2 (SH2) domains are key modules in intracellular signal transduction. They link activated cell surface receptors to downstream targets by binding to phosphotyrosine-containing sequence motifs. The crystal structure of a Grb2-SH2 domain-phosphopeptide complex was determined at 2.4 A resolution. The asymmetric unit contains four polypeptide chains. There is an unexpected domain swap so that individual chains do not adopt a closed SH2 fold. Instead, reorganization of the EF loop leads to an open, nonglobular fold, which associates with an equivalent partner to generate an intertwined dimer. As in previously reported crystal structures of canonical Grb2-SH2 domain-peptide complexes, each of the four hybrid SH2 domains in the two domain-swapped dimers binds the phosphopeptide in a type I beta-turn conformation. This report is the first to describe domain swapping for an SH2 domain. While in vivo evidence of dimerization of Grb2 exists, our SH2 dimer is metastable and a physiological role of this new form of dimer formation remains to be demonstrated.

Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

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

Zhou, Dongwen; Chung, Suhman; Miller, Maria

2012-06-19

The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intactmore » RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.« less

Non-3D domain swapped crystal structure of truncated zebrafish alphaA crystallin

PubMed Central

Laganowsky, A; Eisenberg, D

2010-01-01

In previous work on truncated alpha crystallins (Laganowsky et al., Protein Sci 2010; 19:1031–1043), we determined crystal structures of the alpha crystallin core, a seven beta-stranded immunoglobulin-like domain, with its conserved C-terminal extension. These extensions swap into neighboring cores forming oligomeric assemblies. The extension is palindromic in sequence, binding in either of two directions. Here, we report the crystal structure of a truncated alphaA crystallin (AAC) from zebrafish (Danio rerio) revealing C-terminal extensions in a non three-dimensional (3D) domain swapped, “closed” state. The extension is quasi-palindromic, bound within its own zebrafish core domain, lying in the opposite direction to that of bovine AAC, which is bound within an adjacent core domain (Laganowsky et al., Protein Sci 2010; 19:1031–1043). Our findings establish that the C-terminal extension of alpha crystallin proteins can be either 3D domain swapped or non-3D domain swapped. This duality provides another molecular mechanism for alpha crystallin proteins to maintain the polydispersity that is crucial for eye lens transparency. PMID:20669149

Crystal Structure of the Neuropilin-1 MAM Domain: Completing the Neuropilin-1 Ectodomain Picture.

PubMed

Yelland, Tamas; Djordjevic, Snezana

2016-11-01

Neuropilins (NRPs) are single-pass transmembrane receptors involved in several signaling pathways that regulate key physiological processes such as vascular morphogenesis and axon guidance. The MAM domain of NRP, which has previously been implicated in receptor multimerization, was the only portion of the ectopic domain of the NRPs for which the structure, until now, has been elusive. Using site-directed mutagenesis in the linker region preceding the MAM domain we generated a protein construct amenable to crystallization. Here we present the crystal structure of the MAM domain of human NRP1 at 2.24 Å resolution. The protein exhibits a jellyroll topology, with Ca 2+ ions bound at the inter-strand space enhancing the thermostability of the domain. We show that the MAM domain of NRP1 is monomeric in solution and insufficient to drive receptor dimerization, which leads us to propose a different role for this domain in the context of NRP membrane assembly and signaling. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Influence of the liquid crystal behaviour on the Langmuir and Langmuir-Blodgett film supramolecular architecture of an ionic liquid crystal.

PubMed

Pérez-Gregorio, Víctor; Giner, Ignacio; López, M Carmen; Gascón, Ignacio; Cavero, Emma; Giménez, Raquel

2012-06-01

A new luminescent ionic liquid crystal, called Ipz-2, has been synthesised and its mesophase behaviour and also at the air-liquid interface has been studied and compared with Ipz, another ionic pyrazole derivative, with a similar molecular structure, previously studied. The X-ray diffraction pattern shows that Ipz-2 exhibits hexagonal columnar mesomorphism, while Ipz adopts lamellar mesophases. Langmuir films of both compounds are flat and homogeneous at large areas per molecule, but create different supramolecular structures under further compression. Ipz-2 Langmuir films have been transferred onto solid substrates, and Atomic Force Microscopy (AFM) images of the Langmuir-Blodgett films have shown that large columnar structures hundreds of nm in diameter are formed on top of the initial monolayer, in contrast with well-defined trilayer LB films obtained for Ipz. Our results show that Ipz-2 has a tendency to stack in columnar arrangements both in liquid crystalline bulk and in Langmuir and Langmuir-Blodgett films. Copyright © 2012 Elsevier Inc. All rights reserved.

Eu2P7X and Ba2As7X (X = Br, I): Chiral double-Zintl salts containing heptapnictotricyclane clusters

NASA Astrophysics Data System (ADS)

Dolyniuk, Juli-Anna; Lee, Shannon; Tran, Nhon; Wang, Jian; Wang, Lin-Lin; Kovnir, Kirill

2018-07-01

Chiral double Zintl salts present tunable crystal structures with enhanced structural flexibilities and potential for applications requiring chiral control and enantioselectivity. To accompany the chiral Sr2P7I and Sr2P7Br double Zintl salts reported by us previously, six new chiral Zintl salts of the form Ba2-ySryAs7I (y = 0, 0.23, 2), Eu2P7I, Eu2P7Br, and Eu1.3Ba0.7P7Br have been synthesized and characterized by single crystal X-ray diffraction and SEM-EDS analyses. All new compounds crystallize in the Sohncke space group P213 (No. 198) with variations of P73- (heptaphosphanortricyclane) or As73- (heptaarsanortricyclane) clusters surrounded by alkaline-earth or Eu cations and halogen anions. Band structure calculations predict semiconducting properties for all synthesized compounds. Diffuse reflectance UV-vis spectroscopy indicates that Eu2P7I is a direct bandgap semiconductor with Eg of 1.7 eV.

Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

PubMed Central

Inoguchi, Noriko; Mizuno, Nobuhiro; Baba, Seiki; Kumasaka, Takashi; Natarajan, Chandrasekhar; Storz, Jay F.

2017-01-01

Background Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. Results Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetrameric hemoglobin molecules. Conclusions The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites. PMID:28362841

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer–Villiger monooxygenase

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

Isupov, Michail N.; Schröder, Ewald; Gibson, Robert P.

The first crystal structure of a type II Baeyer–Villiger monooxygenase reveals a different ring orientation of its FMN cofactor compared with other related bacterial luciferase-family enzymes. The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer–Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model.more » The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.« less

Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

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

Inoguchi, Noriko; Mizuno, Nobuhiro; Baba, Seiki

2017-03-31

Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetramericmore » hemoglobin molecules. The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites.« less

Crystallization and initial X-ray diffraction studies of scaffolding protein (gp7) of bacteriophage ϕ29

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

Badasso, Mohammed O., E-mail: badas001@umn.edu; Anderson, Dwight L.; Department of Oral Science, University of Minnesota, Minneapolis, MN 55455

2005-04-01

ϕ29 bacteriophage scaffolding protein (gp7) has been overproduced in E. coli, purified, crystallized and characterized by X-ray diffraction. Two distinct crystal forms were obtained and a diffraction data set was collected to 1.8 Å resolution. The Bacillus subtilis bacteriophage ϕ29 scaffolding protein (gp7) has been crystallized by the hanging-drop vapour-diffusion method at 293 K. Two new distinct crystal forms that both differed from a previously crystallized and solved scaffolding protein were grown under the same conditions. Form I belongs to the primitive tetragonal space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 77.13, c = 37.12 Å.more » Form II crystals exhibit an orthorhombic crystal form, with space group C222 and unit-cell parameters a = 107.50, b = 107. 80, c = 37.34 Å. Complete data sets have been collected to 1.78 and 1.80 Å for forms I and II, respectively, at 100 K using Cu Kα X-rays from a rotating-anode generator. Calculation of a V{sub M} value of 2.46 Å{sup 3} Da{sup −1} for form I suggests the presence of one molecule in the asymmetric unit, corresponding to a solvent content of 50.90%, whereas form II has a V{sub M} of 4.80 Å{sup 3} Da{sup −1} with a solvent content of 48.76% and two molecules in the asymmetric unit. The structures of both crystal forms are being determined by the molecular-replacement method using the coordinates of the published crystal structure of gp7.« less

Synthesis, crystal structure, and protonation behaviour in solution of the recently-discovered drug metabolite, N1,N10-diacetyltriethylenetetramine

NASA Astrophysics Data System (ADS)

Wichmann, Kathrin A.; Söhnel, Tilo; Cooper, Garth J. S.

2012-03-01

N1,N10-diacetyltriethylenetetramine (DAT) is a recently-discovered major in vivo metabolite of triethylenetetramine (TETA), a highly-selective CuII chelator currently under clinical development as a novel first-in-class therapeutic for the cardiovascular, renal and retinal complications of diabetes mellitus. Characterisation of DAT is an integral aspect of the pharmacological work-up required to support this clinical development programme and, to our knowledge, no previous synthesis for it has been published. Here we report the synthesis of DAT dihydrochloride (DAT·2 HCl); its crystal structure as determined by X-ray single-crystal (XRD) and powder diffraction (XRPD); and protonation constants and species distribution in aqueous solution, which represents the different protonation states of DAT at different pH values. The crystal structure of DAT·2 HCl reveals 3D-assemblies of alternating 2D-layers comprising di-protonated DAT strands and anionic species, which form an extensive hydrogen-bond network between amine groups, acetyl groups, and chloride anions. Potentiometric titrations show that HDAT+ is the physiologically relevant state of DAT in solution. These findings contribute to the understanding of TETA's pharmacology and to its development for the experimental therapeutics of the diabetic complications.

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

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

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.

The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition. Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI-RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this proteinmore » are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.« less

Structure and magnetic properties of Ce₃(Ni/Al/Ga)₁₁—A new phase with the La₃Al₁₁ structure type

DOE PAGES

Janka, Oliver; Shang, Tian; Baumbach, Ryan E.; ...

2015-03-01

Single crystals of Ce₃(Ni/Al/Ga)₁₁ were obtained from an Al flux reaction. Single crystals of the title compound crystallizing in the orthorhombic space group Immm (No. 71, Z = 2) with a = 436.38(14), b = 1004.5(3) and c = 1293.4(4) pm. This is a standardized unit cell of the previously published La₃Al₁₁ structure type. Wavelength dispersive microprobe provides the composition of Ce₃.₁₁₍₁₎Ni₀.₀₃₍₁₎Al₈.₉₅₍₁₎Ga₁.₉₀₍₁₎. Single crystal refinement provides the composition Ce₃Ni₀.₀₈Al₉.₁₃Ga₁.₇₈ with substitution of the Ni and Ga on the Al1 and Al4 sites with the Al2 and Al3 solely occupied by Al. Magnetic susceptibility measurements reveal antiferromagnetic ordering with T Nmore » = 4.8 K and there is no evidence for a ferromagnetic ordering that has been reported for Ce₃Al₁₁. The effective magnetic moment was found to be μ eff = 1.9μB/Ce, which is lower than the expected value for trivalent Ce (2.54μB/Ce).« less

Effect of crystal orientation on the phase diagrams, dielectric and piezoelectric properties of epitaxial BaTiO{sub 3} thin films

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

Wu, Huaping, E-mail: wuhuaping@gmail.com, E-mail: hpwu@zjut.edu.cn; State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024; Ma, Xuefu

2016-01-15

The influence of crystal orientations on the phase diagrams, dielectric and piezoelectric properties of epitaxial BaTiO{sub 3} thin films has been investigated using an expanded nonlinear thermodynamic theory. The calculations reveal that crystal orientation has significant influence on the phase stability and phase transitions in the misfit strain-temperature phase diagrams. In particular, the (110) orientation leads to a lower symmetry and more complicated phase transition than the (111) orientation in BaTiO{sub 3} films. The increase of compressive strain will dramatically enhance the Curie temperature T{sub C} of (110)-oriented BaTiO{sub 3} films, which matches well with previous experimental data. The polarizationmore » components experience a great change across the boundaries of different phases at room temperature in both (110)- and (111)-oriented films, which leads to the huge dielectric and piezoelectric responses. A good agreement is found between the present thermodynamics calculation and previous first-principles calculations. Our work provides an insight into how to use crystal orientation, epitaxial strain and temperature to tune the structure and properties of ferroelectrics.« less

The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK)

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

Davies, Christopher W.; Chaney, Joseph; Korbel, Gregory

2012-07-25

UCHL1 is a 223 amino acid member of the UCH family of deubiquitinating enzymes (DUBs), found abundantly and exclusively expressed in neurons and the testis in normal tissues. Two naturally occurring variants of UCHL1 are directly involved in Parkinson's disease (PD). Not only has UCHL1 been linked to PD, but it has oncogenic properties, having been found abnormally expressed in lung, pancreatic, and colorectal cancers. Although inhibitors of UCHL1 have been described previously the co-crystal structure of the enzyme bound to any inhibitor has not been reported. Herein, we report the X-ray structure of UCHL1 co-crystallized with a peptide-based fluoromethylketonemore » inhibitor, Z-VAE(OMe)-FMK (VAEFMK) at 2.35 {angstrom} resolution. The co-crystal structure reveals that the inhibitor binds in the active-site cleft, irreversibly modifying the active-site cysteine; however, the catalytic histidine is still misaligned as seen in the native structure, suggesting that the inhibitor binds to an inactive form of the enzyme. Our structure also reveals that the inhibitor approaches the active-site cleft from the opposite side of the crossover loop as compared to the direction of approach of ubiquitin's C-terminal tail, thereby occupying the P1{prime} (leaving group) site, a binding site perhaps used by the unknown C-terminal extension of ubiquitin in the actual in vivo substrate(s) of UCHL1. This structure provides a view of molecular contacts at the active-site cleft between the inhibitor and the enzyme as well as furnishing structural information needed to facilitate further design of inhibitors targeted to UCHL1 with high selectivity and potency.« less

Crystallography of Magnetite Plaquettes and their Significance as Asymmetric Catalysts for the Synthesis of Chiral Organics in Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Chan, Q. H. S.; Zolensky, M. E.

2015-01-01

We have previously observed the magnetite plaquettes in carbonaceous chondrites using scanning electron microscope (SEM) imaging, examined the crystal orientation of the polished surfaces of magnetite plaquettes in CI Orgueil using electron backscattered diffraction (EBSD) analysis, and concluded that these magnetite plaquettes are likely naturally asymmetric materials. In this study, we expanded our EBSD observation to other magnetite plaquettes in Orgueil, and further examined the internal structure of these remarkable crystals with the use of X-ray computed microtomography.

Quantum and isotope effects in lithium metal

NASA Astrophysics Data System (ADS)

Ackland, Graeme J.; Dunuwille, Mihindra; Martinez-Canales, Miguel; Loa, Ingo; Zhang, Rong; Sinogeikin, Stanislav; Cai, Weizhao; Deemyad, Shanti

2017-06-01

The crystal structure of elements at zero pressure and temperature is the most fundamental information in condensed matter physics. For decades it has been believed that lithium, the simplest metallic element, has a complicated ground-state crystal structure. Using synchrotron x-ray diffraction in diamond anvil cells and multiscale simulations with density functional theory and molecular dynamics, we show that the previously accepted martensitic ground state is metastable. The actual ground state is face-centered cubic (fcc). We find that isotopes of lithium, under similar thermal paths, exhibit a considerable difference in martensitic transition temperature. Lithium exhibits nuclear quantum mechanical effects, serving as a metallic intermediate between helium, with its quantum effect-dominated structures, and the higher-mass elements. By disentangling the quantum kinetic complexities, we prove that fcc lithium is the ground state, and we synthesize it by decompression.

X-ray diffraction of solid tin to 1.2 TPa

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

Lazicki, A.; Rygg, J. R.; Coppari, F.

2015-08-12

In this study, we report direct in situ measurements of the crystal structure of tin between 0.12 and 1.2 TPa, the highest stress at which a crystal structure has ever been observed. Using angle-dispersive powder x-ray diffraction, we find that dynamically compressed Sn transforms to the body-centered-cubic (bcc) structure previously identified by ambient-temperature quasistatic-compression studies and by zero-kelvin density-functional theory predictions between 0.06 and 0.16 TPa. However, we observe no evidence for the hexagonal close-packed (hcp) phase found by those studies to be stable above 0.16 TPa. Instead, our results are consistent with bcc up to 1.2 TPa. We conjecturemore » that at high temperature bcc is stabilized relative to hcp due to differences in vibrational free energy.« less

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

PubMed Central

Nogly, Przemyslaw; James, Daniel; Wang, Dingjie; White, Thomas A.; Zatsepin, Nadia; Shilova, Anastasya; Nelson, Garrett; Liu, Haiguang; Johansson, Linda; Heymann, Michael; Jaeger, Kathrin; Metz, Markus; Wickstrand, Cecilia; Wu, Wenting; Båth, Petra; Berntsen, Peter; Oberthuer, Dominik; Panneels, Valerie; Cherezov, Vadim; Chapman, Henry; Schertler, Gebhard; Neutze, Richard; Spence, John; Moraes, Isabel; Burghammer, Manfred; Standfuss, Joerg; Weierstall, Uwe

2015-01-01

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway. PMID:25866654

Inhibition of Fatty Acid Synthase in Prostate Cancer by Olristat, a Novel Therapeutic

DTIC Science & Technology

2006-11-01

previous crystallography studies by solving the crystal structure of FAS bound to a cleaved orlistat . These data will provide valuable insight into...timeline of XBP-1 15 processing following orlistat treatment (Figure 3A). Previous studies have demonstrated that inhibition of protein translation with...future drug discovery and design within the FAS pathway. In total, we have made great strides toward understanding the anti-tumor effects of orlistat

Structure of Mesorhizobium loti arylamine N-acetyltransferase 1

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

Holton, Simon J.; Dairou, Julien; Sandy, James

2005-01-01

The crystal structure of a M. loti arylamine N-acetyltransferase 1 has been determined at 2.0 Å resolution. The arylamine N-acetyltransferase (NAT) enzymes have been found in a broad range of both eukaryotic and prokaryotic organisms. The NAT enzymes catalyse the transfer of an acetyl group from acetyl Co-enzyme A onto the terminal nitrogen of a range of arylamine, hydrazine and arylhydrazine compounds. Recently, several NAT structures have been reported from different prokaryotic sources including Salmonella typhimurium, Mycobacterium smegmatis and Pseudomonas aeruginosa. Bioinformatics analysis of the Mesorhizobium loti genome revealed two NAT paralogues, the first example of multiple NAT isoenzymes inmore » a eubacterial organism. The M. loti NAT 1 enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme was crystallized in 0.5 M Ca(OAc){sub 2}, 16% PEG 3350, 0.1 M Tris–HCl pH 8.5 using the sitting-drop vapour-diffusion method. A data set diffracting to 2.0 Å was collected from a single crystal at 100 K. The crystal belongs to the orthorhombic spacegroup P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 53.2, b = 97.3, c = 114.3 Å. The structure was refined to a final free-R factor of 24.8%. The structure reveals that despite low sequence homology, M. loti NAT1 shares the common fold as reported in previous NAT structures and exhibits the same catalytic triad of residues (Cys-His-Asp) in the active site.« less

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, Kap; Ho, Joseph X.; Keeling, Kim; Gilliland, Gary L.; Ji, Xinhua; Rueker, Florian; Carter, Daniel C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2017-05-01

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum

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

Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen

2011-09-06

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1 {angstrom}, respectively. The apoenzyme crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with twomore » molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4{sub 3} with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.« less

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

Rashin, Alexander A., E-mail: alexander-rashin@hotmail.com; Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020; Domagalski, Marcin J.

Conformational differences between myoglobin structures are studied. Most structural differences in whale myoglobin beyond the uncertainty threshold can be correlated with a few specific structural factors. There are always exceptions and a search for additional factors is needed. The results might have serious implications for biological insights from conformational differences. Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horsemore » and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific ‘unusual’ ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be ‘functionally important’ but rather artifacts caused by the binding of ‘unusual’ substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.« less

Alternative expression of the Bloch wave group velocity in loss-less periodic media using the electromagnetic field energy

NASA Astrophysics Data System (ADS)

Deparis, Olivier; Lambin, Philippe

2018-01-01

In periodic optical media, the group velocity is defined as the gradient with respect to wave-vector of the corresponding Bloch mode frequency dispersion curve, forming the photonic band structure. Instead of deducing it from the numerically computed photonic crystal band structure, the group velocity can be calculated directly from the integral of the Poynting vector over the crystal unit cell, the physical meaning of which is immediately perceivable. The related formula, which can be regarded as the application of Hellmann-Feynman theorem to electromagnetism, has been reported previously though without proof. We provide hereafter a full derivation of that formula starting from Maxwell's equations and we discuss its usefulness in photonics.

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2003-01-22

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.

Temperature-driven Phase Transformation in Y3Co: Neutron Scattering and DFT Studies

NASA Astrophysics Data System (ADS)

Podlesnyak, A.; Ehlers, G.; Cao, H.; Matsuda, M.; Frontzek, M.; Zaharko, O.; Kazantsev, V. A.; Gubkin, A. F.; Baranov, N. V.

2013-03-01

The effects of a crystal structure deformation due to subtle atomic displacements have attracted much attention because they can result in colossal changes of the electronic and magnetic properties of solids. The R3Co binary intermetallic systems exhibit a number of complicated phenomena, including field-induced magnetic phase transitions (R=Er, Ho, Tb), giant magnetoresistance (R=Dy), a substantial magnetocaloric effect (R=Gd) and superconductivity (R=La). Contrary to previous studies that defined the ground state crystal structure of the entire R3Co series as orthorhombic Pnma, we find that Y3Co undergoes a structural phase transition upon cooling around Tc 160K. Density functional theory calculations reveal a dynamical instability of the Pnma structure of Y3Co. Employing inelastic neutron scattering measurements we find a strong damping of the (00 ξ) acoustic phonon mode below the critical temperature Tc. We suggest that some other members of the R3Co series (or even all of them) have ground state crystal symmetry lower than reported Pnma. This raises a question about the true magnetic structures and hence the influence of magnetic properties of the entire R3Co series. The research at ORNL was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy.

Crystal structure and theoretical studies of derivative of imidazo-1,2,4-triazine

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Sztanke, Krzysztof

2016-09-01

In this study, we present the result of X-ray structure analysis of methyl [8-(3-chlorophenyl)-4-oxo-2,3,4,6,7,8-heksahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetate (1). The molecule conformation is flat, with a chlorophenyl substituent and the ester moiety lying in the plain of the heterobicyclic scaffold. Its conformation is stabilized by an intramolecular Nsbnd H…O hydrogen bond. Within the crystalline structure of 1, molecules associate with one another by weak Csbnd H…O, Csbnd H…Cl and Csbnd H…π bonds. The molecular and crystal structure of 1 was compared with the previously described structurally similar compound possessing the same bicyclic rigid core and similar chemical nature of the functional ester moiety. Very interesting differences in molecules geometry and association were observed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. Moreover, the quantum chemical calculation for 1 in the gas phase were carried out. The DFT calculation methods was used to optimize of molecule geometry and obtain molecular energy profiles with respect to selected torsion angles. The quantum chemical conformational analysis that was carried out for compound 1 in the gas phase suggests that in the solid state the molecules adopt the minimum energy conformation.

Diffusion paths formation for Cu + ions in superionic Cu 6PS 5I single crystals studied in terms of structural phase transition

NASA Astrophysics Data System (ADS)

Gągor, A.; Pietraszko, A.; Kaynts, D.

2005-11-01

In order to understand the structural transformations leading to high ionic conductivity of Cu + ions in Cu 6PS 5I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T=(144-169) K Cu 6PS 5I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above Tc delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43 c ( a'=19.528 Å, z=32). Finally, above T1=274 K increasing disordering of the Cu + ions heightens the symmetry to F-43 m ( a=9.794 Å, z=4). In this work, the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions ( R1=0.0397 for F-43 c phase, and 0.0245 for F-43 m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.

EPR hyperfine structure of the Mo-related defect in CdWO4

NASA Astrophysics Data System (ADS)

Elsts, E.; Rogulis, U.

2005-01-01

The hyperfine structure (hf) of the electron paramagnetic resonance (EPR) spectrum of Mo-related impurity defects in CdWO4 crystals observed previously (U. Rogulis, Radiat. Meas. 29, 287 (1998) [1]) is reconsidered taking into account interactions with two different groups of neighbouring Cd nuclei. The best fit calculated EPR spectrum to the experimental is obtained considering 2 groups of 3 and 2 equivalent Cd nuclei, respectively.

The incommensurately modulated(1 - x)Ta 2O 5· xWO 3, 0 ≤ x ≤ 0.267 solid solution

NASA Astrophysics Data System (ADS)

Schmid, Siegbert; Withers, Ray L.; Thompson, John G.

1992-08-01

The phase(1 - x)Ta 2O 5 · WO 3, 0 ≤ x ≤ 0.267 has been studied by X-ray powder diffraction and transmission electron microscopy. It was previously described as an infinite series of anion-deficient, α-UO 3-type "line phases," with compositions resulting from intergrowths of different blocks made up by small numbers of α-UO 3-type cells. More correctly(1 - x)Ta 2O 5· xWO 3, 0 ≤ x ≤ 0.267 is described as an incommensurately modulated structure with a linearly composition-dependent primary modulation wave-vector qprim. = qb*. The underlying orthorhombically distorted α-UO 3-type parent structure has space group symmetry Cmmm ( a ≈ 6.20-6.14, b ≈ 3.66, c ≈ 3.89-3.85Å). Characteristic extinction conditions imply a superspace group symmetry of P : Cmmmm : s, -1,1. The four previously reported crystal structures in the solid solution field are examined by means of apparent valence calculations. Crystal chemical reasons are proposed for the width of the composition range,0 ≤ x ≤ 0.267, observed for the title phase.

Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.

Aggregation Properties and Liquid Crystal Phase of a Dye Based on Naphthalenetetracarboxylic Acid

NASA Astrophysics Data System (ADS)

Tomasik, Michelle; Collings, Peter

2007-03-01

R003 is a dye produced for thin film optical components by Optiva, Inc.^1 made from the sulfonation of the dibenzimidazole derivative of naphthalenetetracarboxylic acid. Its molecular structure is very different from the aggregating food dye previously investigated in our laboratory^2 and R003 forms a liquid crystal phase at significantly lower concentrations. We have performed polarizing microscopy, absorption spectroscopy, and x-ray diffraction experiments in order to determine the phase diagram and aggregate structure. In addition, we have included both translational and orientational entropy in the theoretical analysis of the aggregation process, and have used a more realistic lineshape in analyzing the absorption data. Our results indicate that the ``bond energy'' for molecules in an aggregate is even larger than for the previously studied dye and that the aggregate structure has a cross-sectional area equal to two or three molecular areas rather than one.^1Lazarev, P., N. Ovchinnikova, M. Paukshto, SID Int. Symp. Digest of Tech. Papers, San Jose, California, June XXXII, 571 (2001).^2V. R. Horowitz, L. A. Janowitz, A. L. Modic, P. A. Heiney, and P. J. Collings, Phys. Rev. E 72, 041710 (2005).

Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1: FUNCTIONAL INTERACTIONS BETWEEN THE KUNITZ-TYPE INHIBITOR DOMAIN-1 AND THE NEIGHBORING POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN.

PubMed

Hong, Zebin; De Meulemeester, Laura; Jacobi, Annemarie; Pedersen, Jan Skov; Morth, J Preben; Andreasen, Peter A; Jensen, Jan K

2016-07-01

Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhibitor of several serine proteases, including hepatocyte growth factor activator and matriptase. The protein is essential for development as knock-out mice die in utero due to placental defects caused by misregulated extracellular proteolysis. HAI-1 contains two Kunitz-type inhibitor domains (Kunitz), which are generally thought of as a functionally self-contained protease inhibitor unit. This is not the case for HAI-1, where our results reveal how interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. Here we present an x-ray crystal structure of an HAI-1 fragment covering the internal domain and Kunitz-1. The structure reveals not only that the previously uncharacterized internal domain is a member of the polycystic kidney disease domain family but also how the two domains engage in interdomain interactions. Supported by solution small angle x-ray scattering and a combination of site-directed mutagenesis and functional assays, we show that interdomain interactions not only stabilize the fold of the internal domain but also stimulate the inhibitory activity of Kunitz-1. By completing our structural characterization of the previously unknown N-terminal region of HAI-1, we provide new insight into the interplay between tertiary structure and the inhibitory activity of a multidomain protease inhibitor. We propose a previously unseen mechanism by which the association of an auxiliary domain stimulates the inhibitory activity of a Kunitz-type inhibitor (i.e. the first structure of an intramolecular interaction between a Kunitz and another domain). © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

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

Le Bail, A.; Cranswick, L; Adil, K

2009-01-01

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solvingmore » a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.« less

The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin.

PubMed

Sun, Y J; Chou, C C; Chen, W S; Wu, R T; Meng, M; Hsiao, C D

1999-05-11

Phosphoglucose isomerase (PGI) plays a central role in both the glycolysis and the gluconeogenesis pathways. We present here the complete crystal structure of PGI from Bacillus stearothermophilus at 2.3-A resolution. We show that PGI has cell-motility-stimulating activity on mouse colon cancer cells similar to that of endogenous autocrine motility factor (AMF). PGI can also enhance neurite outgrowth on neuronal progenitor cells similar to that observed for neuroleukin. The results confirm that PGI is neuroleukin and AMF. PGI has an open twisted alpha/beta structural motif consisting of two globular domains and two protruding parts. Based on this substrate-free structure, together with the previously published biological, biochemical, and modeling results, we postulate a possible substrate-binding site that is located within the domains' interface for PGI and AMF. In addition, the structure provides evidence suggesting that the top part of the large domain together with one of the protruding loops might participate in inducing the neurotrophic activity.

Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.

Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

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

Jacques, David A.; Streamer, Margaret; Rowland, Susan L.

2009-09-02

The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomericmore » or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations.« less

Beating the Heat: Fast Scanning Melts Beta Sheet Crystals

NASA Astrophysics Data System (ADS)

Cebe, Peggy; Hu, Xiao; Kaplan, David; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniella; Schick, Christoph

2014-03-01

Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk. Previous thinking was that beta-pleated-sheet crystals in the dry solid state would not melt upon input of heat energy alone. Indeed, at conventional heating rates (~1-50 °C/min), silk exhibits its glass transition (~175 °C), followed by cold crystallization, and then by immediate thermal degradation beginning at about 225 °C. Here we demonstrate that beta-pleated-sheet crystals can melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s to avoid thermal degradation, and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. The authors acknowledge support from the National Science Foundation and German Academic Exchange Service DAAD; EZ acknowledges a European Union funded Marie Curie EST fellowship (ADVATEC); XH and DK acknowledge NIH P41 Tissue Engineering Resource Center.

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

Chen, Hui; Mustafi, Sourajit M.; LeMaster, David M.

Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences formore » this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.« less

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.

PubMed

Dharmaiah, Srisathiyanarayanan; Bindu, Lakshman; Tran, Timothy H; Gillette, William K; Frank, Peter H; Ghirlando, Rodolfo; Nissley, Dwight V; Esposito, Dominic; McCormick, Frank; Stephen, Andrew G; Simanshu, Dhirendra K

2016-11-01

Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated-methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated-methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated-methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated-methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein-protein interaction interface in KRAS4b-PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.

Characterization of the scintillation anisotropy in crystalline stilbene scintillator detectors

DOE PAGES

Schuster, P.; Brubaker, E.

2016-11-23

This study reports a series of measurements that characterize the directional dependence of the scintillation response of crystalline melt-grown and solution-grown trans-stilbene to incident DT and DD neutrons. These measurements give the amplitude and pulse shape dependence on the proton recoil direction over one hemisphere of the crystal, confirming and extending previous results in the literature for melt-grown stilbene and providing the first measurements for solution-grown stilbene. In similar measurements of liquid and plastic detectors, no directional dependence was observed, confirming the hypothesis that the anisotropy in stilbene and other organic crystal scintillators is a result of internal effects duemore » to the molecular or crystal structure and not an external effect on the measurement system.« less

Multiscale real-space quantum-mechanical tight-binding calculations of electronic structure in crystals with defects using perfectly matched layers

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

Pourmatin, Hossein, E-mail: mpourmat@andrew.cmu.edu; Dayal, Kaushik, E-mail: kaushik@cmu.edu

2016-10-15

Graphical abstract: - Abstract: We consider the scattering of incident plane-wave electrons from a defect in a crystal modeled by the time-harmonic Schrödinger equation. While the defect potential is localized, the far-field potential is periodic, unlike standard free-space scattering problems. Previous work on the Schrödinger equation has been almost entirely in free-space conditions; a few works on crystals have been in one-dimension. We construct absorbing boundary conditions for this problem using perfectly matched layers in a tight-binding formulation. Using the example of a point defect in graphene, we examine the efficiency and convergence of the proposed absorbing boundary condition.

Neutron and X-ray investigations of the Jahn–Teller switch in partially deuterated ammonium copper Tutton salt, (NH 4 ) 2 [Cu(H 2 O) 6 ](SO 4 ) 2

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

Jørgensen, Mads R. V.; Piccoli, Paula M. B.; Hathwar, Venkatesha R.

2017-01-31

The structural phase transition accompanied by a Jahn–Teller switch has been studied over a range of H/D ratios in (NH 4) 2[Cu(H 2O) 6](SO 4) 2(ACTS). In particular, single-crystal neutron diffraction investigations of crystals with deuteration in the range 50 to 82% are shown to be consistent with previous electron paramagnetic resonance (EPR) experiments exhibiting a phase boundary at 50% deuteration under ambient pressure. Polycrystalline samples show that the two phases can co-exist. In addition, single-crystal neutron and polycrystalline X-ray diffraction pressure experiments show a shift to lower pressure at 60% deuterationversusprevious measurements at 100% deuteration.

The uteroglobin fold.

PubMed

Callebaut, I; Poupon, A; Bally, R; Demaret, J P; Housset, D; Delettré, J; Hossenlopp, P; Mornon, J P

2000-01-01

Uteroglobin (UTG) forms a fascinating homodimeric structure that binds small- to medium-sized ligands through an internal hydrophobic cavity, located at the interface between the two monomers. Previous studies have shown that UTG fold is not limited to the UTG/CC10 family, whose sequence/structure relationships are highlighted here, but can be extended to the cap domain of Xanthobacter autotrophicus haloalkane dehalogenase. We show here that UTG fold is adopted by several other cap domains within the alpha/beta hydrolase family, making it a well-suited "geode" structure allowing it to sequester various hydrophobic molecules. Additionally, some data about a new crystal form of oxidized rabbit UTG are presented, completing previous structural studies, as well as results from molecular dynamics, suggesting an alternative way for the ligand to reach the internal cavity.

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

DOE PAGES

Zheng, Tao; Yang, Zaixing; Gui, Daxiang; ...

2017-05-30

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. We overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. Furthermore, these compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest voidmore » volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism.« less

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

PubMed Central

Zheng, Tao; Yang, Zaixing; Gui, Daxiang; Liu, Zhiyong; Wang, Xiangxiang; Dai, Xing; Liu, Shengtang; Zhang, Linjuan; Gao, Yang; Chen, Lanhua; Sheng, Daopeng; Wang, Yanlong; Diwu, Juan; Wang, Jianqiang; Zhou, Ruhong; Chai, Zhifang; Albrecht-Schmitt, Thomas E.; Wang, Shuao

2017-01-01

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. Herein, we overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. These compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest void volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism. PMID:28555656

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

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

Zheng, Tao; Yang, Zaixing; Gui, Daxiang

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. We overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. Furthermore, these compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest voidmore » volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism.« less

Tip-induced domain growth on the non-polar cuts of lithium niobate single-crystals

DOE PAGES

Alikin, Denis O.; Ievlev, Anton; Turigin, Anton P.; ...

2015-05-05

Currently ferroelectric materials with designed domain structures are considered as a perspective material for new generation of photonic, data storage and data processing devices. Application of external electric field is the most convenient way of the domain structure formation. Lots of papers are devoted to investigation of the domain kinetics on polar surface of crystals while the forward growth remains one of the most mysterious stages due to lack of experimental methods allowing to study it. Here we performed tip-induced polarization reversal on X- and Y-non-polar cuts in single-crystal of congruent lithium niobate allows us to study the forward growthmore » with high spatial resolution. The revealed difference in the shape and length of domains induced on X- and Y-cuts is beyond previously developed theoretical approaches used for the theoretical consideration of the domains growth at non-polar ferroelectric surfaces. Lastly, to explain experimental results we used kinetic approach with anisotropy of screening efficiency along different crystallographic directions.« less

A low-temperature polymorph of m-quinquephenyl.

PubMed

Gomes, Ligia R; Howie, R Alan; Low, John Nicolson; Rodrigues, Ana S M C; Santos, Luís M N B F

2012-12-01

A low-temperature polymorph of 1,1':3',1'':3'',1''':3''',1''''-quinquephenyl (m-quinquephenyl), C(30)H(22), crystallizes in the space group P2(1)/c with two molecules in the asymmetric unit. The crystal is a three-component nonmerohedral twin. A previously reported room-temperature polymorph [Rabideau, Sygula, Dhar & Fronczek (1993). Chem. Commun. pp. 1795-1797] also crystallizes with two molecules in the asymmetric unit in the space group P-1. The unit-cell volume for the low-temperature polymorph is 4120.5 (4) Å(3), almost twice that of the room-temperature polymorph which is 2102.3 (6) Å(3). The molecules in both structures adopt a U-shaped conformation with similar geometric parameters. The structural packing is similar in both compounds, with the molecules lying in layers which stack perpendicular to the longest unit-cell axis. The molecules pack alternately in the layers and in the stacked columns. In both polymorphs, the only interactions between the molecules which can stabilize the packing are very weak C-H...π interactions.

Phase transitions in orthopyroxene (En 90) to 49GPa from single-crystal X-ray diffraction

DOE PAGES

Finkelstein, Gregory J.; Dera, Przemyslaw K.; Duffy, Thomas S.

2014-10-29

Synchrotron-based high-pressure single-crystal X-ray diffraction experiments were conducted on ~Mg 0.9Fe 0.1SiO 3 (En 90) orthopyroxene crystals at room temperature to a maximum pressure of 48.5 GPa. The sample was compressed in a diamond anvil cell with a neon pressure medium and a gold pressure calibrant. In addition to the previously described orthopyroxene to β-opx transition (designated HPCEN2 in previous studies), we observe two further phase transitions at 29.9 GPa and 40.3 GPa. However, we do not observe the γ-opx phase recently described in an Fe-rich orthopyroxene composition. The structures of both of the new phases were solved in spacemore » group Pca21. While their Mg-O layers remain pyroxene-like, their Si-O layers transform in a stepwise fashion to akimotoite-like sheets, with sites in 4-, 5-, or 6-fold coordination, depending on the specific structure and layer. Due to the increased Si-O coordination number, we designate the new structures α- and β-post-orthopyroxene (α-popx and β-popx). α-popx has one Si-O layer that is entirely tetrahedral, and one layer that contains both tetrahedra and 5-coordinated Si in distorted square pyramids. β-popx retains the mixed 4- and 5-coordinated Si layer found in α-popx, while the other Si layer adopts fully octahedral coordination. The α- and β-popx structures show a progressive transformation towards the arrangement of Si layers found in akimotoite, a potentially important phase in the earth’s transition zone. Metastable transformations in pyroxenes are of interest for understanding possible metastability in geological environments such as subducting slabs and meteorite impacts« less

Phase transitions in orthopyroxene (En 90) to 49GPa from single-crystal X-ray diffraction

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

Finkelstein, Gregory J.; Dera, Przemyslaw K.; Duffy, Thomas S.

Synchrotron-based high-pressure single-crystal X-ray diffraction experiments were conducted on ~Mg 0.9Fe 0.1SiO 3 (En 90) orthopyroxene crystals at room temperature to a maximum pressure of 48.5 GPa. The sample was compressed in a diamond anvil cell with a neon pressure medium and a gold pressure calibrant. In addition to the previously described orthopyroxene to β-opx transition (designated HPCEN2 in previous studies), we observe two further phase transitions at 29.9 GPa and 40.3 GPa. However, we do not observe the γ-opx phase recently described in an Fe-rich orthopyroxene composition. The structures of both of the new phases were solved in spacemore » group Pca21. While their Mg-O layers remain pyroxene-like, their Si-O layers transform in a stepwise fashion to akimotoite-like sheets, with sites in 4-, 5-, or 6-fold coordination, depending on the specific structure and layer. Due to the increased Si-O coordination number, we designate the new structures α- and β-post-orthopyroxene (α-popx and β-popx). α-popx has one Si-O layer that is entirely tetrahedral, and one layer that contains both tetrahedra and 5-coordinated Si in distorted square pyramids. β-popx retains the mixed 4- and 5-coordinated Si layer found in α-popx, while the other Si layer adopts fully octahedral coordination. The α- and β-popx structures show a progressive transformation towards the arrangement of Si layers found in akimotoite, a potentially important phase in the earth’s transition zone. Metastable transformations in pyroxenes are of interest for understanding possible metastability in geological environments such as subducting slabs and meteorite impacts« less

Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

NASA Astrophysics Data System (ADS)

Gonzalez Lazo, Eduardo; Cruz Inclán, Carlos M.; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

2017-09-01

A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modeling.

PubMed

Engelsen, Søren Balling; Madsen, Anders Østergaard; Blennow, Andreas; Motawia, Mohammed Saddik; Møller, Birger Lindberg; Larsen, Sine

2003-04-24

The only known in planta substitution of starch is phosphorylation. Whereas the function of starch phosphorylation is poorly understood, phosphorylated starch possesses improved functionality in vitro. Molecular models of native crystalline starch are currently being developed and the starch phosphorylating enzyme has recently been discovered. Accordingly, it is desirable to obtain a more exact description of the molecular structures of phosphorylated starch. We have determined the crystal structure of methyl alpha-D-glucopyranoside 6-O-phosphate as its potassium salt which is thought to be the starch phosphate counterion in vivo. From this structure and previously known glucophosphate structures we describe the possible 6-O-phosphate geometries and through modeling extrapolate the results to the double helical structure of the crystalline part of amylopectin. The geometries of the existing crystal structures of 6-O-phosphate groups were found to belong to two main adiabatic valleys. One of these conformations could be fitted into the double helical amylopectin part without perturbing the double helical amylopectin structure and without creating steric problems for the hexagonal chain-chain packing.

Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase

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

Boucher, Lauren E.; Bosch, Jürgen, E-mail: jbosch@jhu.edu; Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205

The structure of T. gondii fructose-1,6-bisphosphate aldolase, a glycolytic enzyme and structural component of the invasion machinery, was determined to a resolution of 2.0 Å. The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-@@bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolasemore » has been crystallized in space group P22{sub 1}2{sub 1}, with the biologically relevant tetramer in the asymmetric unit, and the structure has been determined via molecular replacement to a resolution of 2.0 Å. An analysis of the quality of the model and of the differences between the four chains in the asymmetric unit and a comparison between the T. gondii and P. falciparum aldolase structures is presented.« less

Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit.

PubMed

Campbell, Zachary T; Weichsel, Andrzej; Montfort, William R; Baldwin, Thomas O

2009-07-07

Bacterial luciferase from Vibrio harveyi is a heterodimer composed of a catalytic alpha subunit and a homologous but noncatalytic beta subunit. Despite decades of enzymological investigation, structural evidence defining the active center has been elusive. We report here the crystal structure of V. harveyi luciferase bound to flavin mononucleotide (FMN) at 2.3 A. The isoalloxazine ring is coordinated by an unusual cis-Ala-Ala peptide bond. The reactive sulfhydryl group of Cys106 projects toward position C-4a, the site of flavin oxygenation. This structure also provides the first data specifying the conformations of a mobile loop that is crystallographically disordered in both prior crystal structures [(1995) Biochemistry 34, 6581-6586; (1996) J. Biol. Chem. 271, 21956 21968]. This loop appears to be a boundary between solvent and the active center. Within this portion of the protein, a single contact was observed between Phe272 of the alpha subunit, not seen in the previous structures, and Tyr151 of the beta subunit. Substitutions at position 151 on the beta subunit caused reductions in activity and total quantum yield. Several of these mutants were found to have decreased affinity for reduced flavin mononucleotide (FMNH(2)). These findings partially address the long-standing question of how the beta subunit stabilizes the active conformation of the alpha subunit, thereby participating in the catalytic mechanism.

DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein

PubMed Central

Duan, Ming-Rui; Nan, Jie; Liang, Yu-He; Mao, Peng; Lu, Lu; Li, Lanfen; Wei, Chunhong; Lai, Luhua; Li, Yi; Su, Xiao-Dong

2007-01-01

WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be involved in the salicylic acid signaling pathway and partially dependent on NPR1; a C-terminal domain of WRKY1, AtWRKY1-C, was constructed for structural studies. Previous investigations showed that DNA binding of the WRKY proteins was localized at the WRKY domains and these domains may define novel zinc-binding motifs. The crystal structure of the AtWRKY1-C determined at 1.6 Å resolution has revealed that this domain is composed of a globular structure with five β strands, forming an antiparallel β-sheet. A novel zinc-binding site is situated at one end of the β-sheet, between strands β4 and β5. Based on this high-resolution crystal structure and site-directed mutagenesis, we have defined and confirmed that the DNA-binding residues of AtWRKY1-C are located at β2 and β3 strands. These results provided us with structural information to understand the mechanism of transcriptional control and signal transduction events of the WRKY proteins. PMID:17264121

Crystal structure of TBC1D15 GTPase‐activating protein (GAP) domain and its activity on Rab GTPases

PubMed Central

Chen, Yan‐Na; Gu, Xin; Zhou, X. Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei

2017-01-01

Abstract TBC1D15 belongs to the TBC (Tre‐2/Bub2/Cdc16) domain family and functions as a GTPase‐activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark‐TBC1D15 and Sus‐TBC1D15 belong to the same subfamily of TBC domain‐containing proteins, and their GAP‐domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. PMID:28168758

Heat capacity, resistivity, and angular dependent magnetization studies of single crystal Nd 1 + ϵ Fe 4 B 4 for ϵ ≈ 1 7

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

Conner, Benjamin S.; Susner, Michael A.; UES Inc., Beavercreek, OH

Advances in crystal growth have allowed for synthesis of large single crystals of Nd 1+ϵFe 4B 4, a well-known phase with a modulated structure. As a result we are able to report heat capacity and resistivity measurements on a single crystal Nd 1+ϵFe 4B 4 sample with a distribution of ϵ that skews towards the solubility limit of Nd near ϵ ≈ 17. Heat capacity measurements show evidence of crystal field splitting at temperatures higher than the long-range ferromagnetic Curie temperature. Heat capacity, resistivity, and magnetization measurements all confirm a Curie temperature of 7 K which is lower than previouslymore » reported values in the Nd 1+ϵFe 4B 4 system. Here, we also perform measurements of the angular dependence of the magnetization and discover behavior associated with the magnetic anisotropy that is inconsistent with the simple description previously proposed.« less

Heat capacity, resistivity, and angular dependent magnetization studies of single crystal Nd 1 + ϵ Fe 4 B 4 for ϵ ≈ 1 7

DOE PAGES

Conner, Benjamin S.; Susner, Michael A.; UES Inc., Beavercreek, OH; ...

2017-04-04

Advances in crystal growth have allowed for synthesis of large single crystals of Nd 1+ϵFe 4B 4, a well-known phase with a modulated structure. As a result we are able to report heat capacity and resistivity measurements on a single crystal Nd 1+ϵFe 4B 4 sample with a distribution of ϵ that skews towards the solubility limit of Nd near ϵ ≈ 17. Heat capacity measurements show evidence of crystal field splitting at temperatures higher than the long-range ferromagnetic Curie temperature. Heat capacity, resistivity, and magnetization measurements all confirm a Curie temperature of 7 K which is lower than previouslymore » reported values in the Nd 1+ϵFe 4B 4 system. Here, we also perform measurements of the angular dependence of the magnetization and discover behavior associated with the magnetic anisotropy that is inconsistent with the simple description previously proposed.« less

Epitaxy: Programmable Atom Equivalents Versus Atoms

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

Wang, Mary X.; Seo, Soyoung E.; Gabrys, Paul A.

The programmability of DNA makes it an attractive structure-directing ligand for the assembly of nanoparticle superlattices in a manner that mimics many aspects of atomic crystallization. However, the synthesis of multilayer single crystals of defined size remains a challenge. Though previous studies considered lattice mismatch as the major limiting factor for multilayer assembly, thin film growth depends on many interlinked variables. Here, a more comprehensive approach is taken to study fundamental elements, such as the growth temperature and the thermodynamics of interfacial energetics, to achieve epitaxial growth of nanoparticle thin films. Under optimized equilibrium conditions, single crystal, multilayer thin filmsmore » can be synthesized over 500 × 500 μm2 areas on lithographically patterned templates. Importantly, these superlattices follow the same patterns of crystal growth demonstrated in thin film atomic deposition, allowing for these processes to be understood in the context of well-studied atomic epitaxy, and potentially enabling a nanoscale model to study fundamental crystallization processes.« less

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

PubMed Central

Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

2011-01-01

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PMID:20859960

Crystal growth and physical properties of SrCu2As2, SrCu2Sb2, and BaCu2Sb2

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

Anand, V.K.; Perera, P. Kanchana; Pandey, Abhishek

2012-06-25

We report the growth of single crystals of SrCu2As2, SrCu2Sb2, SrCu2(As0.84Sb0.16)2, and BaCu2Sb2 using the self-flux technique and their structural, magnetic, thermal, and transport properties that were investigated by powder x-ray diffraction (XRD), magnetic susceptibility χ, specific heat Cp, and electrical resistivity ρ measurements versus temperature T from 1.8 to 350 K. Rietveld refinements of XRD patterns for crushed crystals confirm that SrCu2As2 crystallizes in the ThCr2Si2-type body-centered tetragonal structure (space group I4/mmm) and SrCu2Sb2 crystallizes in the CaBe2Ge2-type primitive tetragonal structure (space group P4/nmm). However, as reported previously, BaCu2Sb2 is found to have a large unit cell consisting ofmore » three blocks. Here a ThCr2Si2-type block is sandwiched between two CaBe2Ge2-type blocks along the c axis with an overall symmetry of I4/mmm, as reported, but likely with a monoclinic distortion. The χ data of all these compounds are diamagnetic and reveal nearly T-independent anisotropic behavior. The χ of SrCu2As2 is found to be larger in the ab plane than along the c axis, as also previously reported for pure and doped BaFe2As2, whereas the χ values of SrCu2Sb2 and BaCu2Sb2 are larger along the c axis. This difference in anisotropy appears to arise from the differences between the crystal structures. The finite values of the Sommerfeld linear specific heat coefficients γ and the T dependences of ρ reveal metallic character of all four compounds. The electronic and magnetic properties indicate that these compounds are sp metals with Cu in the nonmagnetic 3d10 electronic configuration corresponding to the oxidation state Cu+1, as previously predicted theoretically for SrCu2As2 by Singh [ Phys. Rev. B 79 153102 (2009)]. We present a brief review of theoretical and experimental work on the doping character of transition metals for Fe in BaFe2As2. The As–As covalent interlayer bond distances in the collapsed-tetragonal (Ca,Sr,Ba)Cu2As2 compounds are much shorter than the nonbonding As–As distances in BaFe2As2. Thus, the electronic character of the Cu and the strength of the As–As interlayer bonding are both expected to drastically change between weakly Cu-substituted BaFe2As2 and pure BaCu2As2, perhaps via a first-order lattice instability such as a miscibility gap in the Ba(Fe1−xCux)2As2 system.« less

Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

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

Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

2012-10-15

Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

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.

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

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

Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara

The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing amore » sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.« less

Insights from soft X-rays: the chlorine and sulfur sub-structures of a CK2alpha/DRB complex.

PubMed

Raaf, Jennifer; Issinger, Olaf-Georg; Niefind, Karsten

2008-09-01

The diffraction pattern of a protein crystal is normally a product of the interference of electromagnetic waves scattered by electrons of the crystalline sample. The diffraction pattern undergoes systematic changes in case additionally X-ray absorption occurs, meaning if the wavelength of the primary X-ray beam is relatively close to the absorption edge of selected elements of the sample. The resulting effects are summarized as "anomalous dispersion" and can be always observed with "soft" X-rays (wavelength around 2 A) since they match the absorption edges of sulfur and chlorine. A particularly useful application of this phenomenon is the experimental detection of the sub-structures of the anomalous scatterers in protein crystals. We demonstrate this here with a crystal of a C-terminally truncated variant of human CK2alpha to which two molecules of the inhibitor 5,6-dichloro-1-beta-D-ribo-furanosyl-benzimidazole (DRB) are bound. The structure of this co-crystal has been solved recently. For this study we measured an additional diffraction data set at a wavelength of 2 A which showed strong anomalous dispersion effects. On the basis of these effects we detected all sulfur atoms of the protein, the two liganded DRB molecules and a total of 16 additional chloride ions some of them emerging at positions filled with water molecules in previous structure determinations. A number of chloride ions are bound to structural and functional important locations fitting to the constitutive activity and the acidophilic substrate specificity of the enzyme.

Structure and thermal expansion of Ca9Gd(VO4)7: A combined powder-diffraction and dilatometric study of a Czochralski-grown crystal

NASA Astrophysics Data System (ADS)

Paszkowicz, Wojciech; Shekhovtsov, Alexei; Kosmyna, Miron; Loiko, Pavel; Vilejshikova, Elena; Minikayev, Roman; Romanowski, Przemysław; Wierzchowski, Wojciech; Wieteska, Krzysztof; Paulmann, Carsten; Bryleva, Ekaterina; Belikov, Konstantin; Fitch, Andrew

2017-11-01

Materials of the Ca9RE(VO4)7 (CRVO) formula (RE = rare earth) and whitlockite-related structures are considered for applications in optoelectronics, e.g., in white-light emitting diodes and lasers. In the CRVO structure, the RE atoms are known to share the site occupation with Ca atoms at two or three among four Ca sites, with partial occupancy values depending on the choice of the RE atom. In this work, the structure and quality of a Czochralski-grown crystal of this family, Ca9Gd(VO4)7 (CGVO), are studied using X-ray diffraction methods. The room-temperature structure is refined using the powder diffraction data collected at a high-resolution synchrotron beamline ID22 (ESRF, Grenoble); for comparison purposes, a laboratory diffraction pattern was collected and analyzed, as well. The site occupancies are discussed on the basis of comparison with literature data of isostructural synthetic crystals of the CRVO series. The results confirm the previously reported site-occupation scheme and indicate a tendency of the CGVO compound to adopt a Gd-deficient composition. Moreover, the thermal expansion coefficient is determined for CGVO as a function of temperature in the 302-1023 K range using laboratory diffraction data. Additionally, for CGVO and six other single crystals of the same family, thermal expansion is studied in the 298-473 K range, using the dilatometric data. The magnitude and anisotropy of thermal expansion, being of importance for laser applications, are discussed for these materials.

Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase.

PubMed

Lunev, Sergey; Bosch, Soraya S; Batista, Fernando A; Wang, Chao; Li, Jingyao; Linzke, Marleen; Kruithof, Paul; Chamoun, George; Dömling, Alexander S S; Wrenger, Carsten; Groves, Matthew R

2018-03-11

Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis. Copyright © 2018 Elsevier Inc. All rights reserved.

The magnetic properties and structure of the quasi-two-dimensional antiferromagnet CoPS3

NASA Astrophysics Data System (ADS)

Wildes, A. R.; Simonet, V.; Ressouche, E.; Ballou, R.; McIntyre, G. J.

2017-11-01

The magnetic properties and magnetic structure are presented for CoPS3, a quasi-two-dimensional antiferromagnet on a honeycomb lattice with a Néel temperature of TN ∼120 K. The compound is shown to have XY-like anisotropy in its susceptibility, and the anisotropy is analysed to extract crystal field parameters. For temperatures between 2 K and 300 K, no phase transitions were observed in the field-dependent magnetization up to 10 Tesla. Single-crystal neutron diffraction shows that the magnetic propagation vector is k  =  (0 1 0) with the moments mostly along the {a} axis and with a small component along the {c} axis, which largely verifies the previously-published magnetic structure for this compound. The magnetic Bragg peak intensity decreases with increasing temperature as a power law with exponent 2β = 0.60 +/- 0.01 for T > 0.9~TN .

A model for the solution structure of the rod arrestin tetramer.

PubMed

Hanson, Susan M; Dawson, Eric S; Francis, Derek J; Van Eps, Ned; Klug, Candice S; Hubbell, Wayne L; Meiler, Jens; Gurevich, Vsevolod V

2008-06-01

Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

PubMed

Bailey, Lucas J; Sheehy, Kimberly M; Dominik, Pawel K; Liang, Wenguang G; Rui, Huan; Clark, Michael; Jaskolowski, Mateusz; Kim, Yejoon; Deneka, Dawid; Tang, Wei-Jen; Kossiakoff, Anthony A

2018-02-02

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones. Copyright © 2017 Elsevier Ltd. All rights reserved.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals.

PubMed

Wilson, S R; Mendelev, M I

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Mendelev, M. I.

2016-04-01

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

PubMed

Clifton, Matthew C; Bruhn, Jessica F; Atkins, Kateri; Webb, Terry L; Baydo, Ruth O; Raymond, Amy; Lorimer, Donald D; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

2015-10-01

Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Altering the Polymorphic Accessibility of Polycyclic Aromatic Hydrocarbons with Fluorination

DOE PAGES

Hiszpanski, Anna M.; Woll, Arthur R.; Kim, Bumjung; ...

2017-04-25

Here, substituting hydrogen with fluorine is an extensively employed strategy to improve the macroscopic properties of compounds for use in fields as diverse as pharmaceutics and optoelectronics. The role fluorine substitution plays on polymorphism—the ability of a compound to adopt more than one crystal structure—has not been previously studied. Yet, this understanding is important as different polymorphs of the same compound can result in drastically different bulk properties (e.g., solubility, absorptivity, and conductivity). Strategies to either promote or suppress the crystallization of particular polymorphs are thus desired. Here, we show that substituting hydrogen with fluorine affects the polymorphic behavior ofmore » contorted hexabenzocoronene (cHBC). A polycyclic aromatic hydrocarbon and molecular semiconductor, cHBC exhibits two polymorphs (i.e., P2 1/c crystal structure which we refer to as polymorph I and a triclinic crystal structure which we refer to as polymorph II) that are accessible through postdeposition processing of amorphous films. While the same two polymorphs remain accessible in fluorinated derivatives of cHBC, fluorination appears to favor the formation of polymorph I, with progressively smaller energy barrier for transformation from polymorph II to polymorph I with fluorination.« less

Altering the Polymorphic Accessibility of Polycyclic Aromatic Hydrocarbons with Fluorination

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

Hiszpanski, Anna M.; Woll, Arthur R.; Kim, Bumjung

Here, substituting hydrogen with fluorine is an extensively employed strategy to improve the macroscopic properties of compounds for use in fields as diverse as pharmaceutics and optoelectronics. The role fluorine substitution plays on polymorphism—the ability of a compound to adopt more than one crystal structure—has not been previously studied. Yet, this understanding is important as different polymorphs of the same compound can result in drastically different bulk properties (e.g., solubility, absorptivity, and conductivity). Strategies to either promote or suppress the crystallization of particular polymorphs are thus desired. Here, we show that substituting hydrogen with fluorine affects the polymorphic behavior ofmore » contorted hexabenzocoronene (cHBC). A polycyclic aromatic hydrocarbon and molecular semiconductor, cHBC exhibits two polymorphs (i.e., P2 1/c crystal structure which we refer to as polymorph I and a triclinic crystal structure which we refer to as polymorph II) that are accessible through postdeposition processing of amorphous films. While the same two polymorphs remain accessible in fluorinated derivatives of cHBC, fluorination appears to favor the formation of polymorph I, with progressively smaller energy barrier for transformation from polymorph II to polymorph I with fluorination.« less

A catalytic metal ion interacts with the cleavage site G•U wobble in the HDV ribozyme†

PubMed Central

Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C.; Carey, Paul R.; Golden, Barbara L.

2009-01-01

The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate a 2′,3′-cyclic phosphate and a 5′-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pKa shifted > 2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335–13342.], while in crystal structures, it is well-positioned for proton transfer. However no crystallographic evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on rate and Mg2+-binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously-unobserved hydrated magnesium ion interacts with the N7 of the cleavage site G•U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data. PMID:19178151

A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme.

PubMed

Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C; Carey, Paul R; Golden, Barbara L

2009-02-24

The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate 2',3'-cyclic phosphate and 5'-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pK(a) shifted >2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335-13342], while in crystal structures, it is well-positioned for proton transfer. However, no evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on the rate and Mg(2+) binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously unobserved hydrated magnesium ion interacts with N7 of the cleavage site G.U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data.

Crystallization, structure and dynamics of the proton-translocating P-type ATPase.

PubMed

Scarborough, G A

2000-01-01

Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange experiments indicate that these conformational changes are probably rigid-body interdomain movements that lead to cleft closure. When interpreted within the framework of established principles of enzyme catalysis, this information on the structure and dynamics of the H(+) P-ATPase molecule provides the basis of a rational model for the sequence of events that occurs as the ATPase proceeds through its transport cycle. The forces that drive the sequence can also be clearly stipulated. However, an understanding of the molecular mechanism of ion transport catalyzed by the H(+) P-ATPase awaits an atomic resolution structure.

Design of Silicon Photonic Crystal Waveguides for High Gain Raman Amplification Using Two Symmetric Transvers-Electric-Like Slow-Light Modes

NASA Astrophysics Data System (ADS)

Hsiao, Yi-Hua; Iwamoto, Satoshi; Arakawa, Yasuhiko

2013-04-01

We designed silicon photonic crystal (PhC) waveguides (WGs) for efficient silicon Raman amplifiers and lasers. We adopted narrow-width WGs to utilize two symmetric transvers-electric-like (TE-like) guided modes, which permit efficient external coupling for both the pump and Stokes waves. Modifying the size and shape of air holes surrounding the line-defect WG structures could tune the frequency difference between these two modes, at the Brillouin-zone edge, to match the Raman shift of silicon. Thus, small group velocities are also available both for pump and Stokes waves simultaneously, which results in a large enhancement of Raman gain. The enhancement factor of the Raman gain in the designed structure is more than 100 times that reported previously.

Peculiarities of the crystal structure of modified banana-shaped mesogen

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

Zharova, M. A.; Usol'tseva, N. V., E-mail: nadezhda_usoltseva@yahoo.com; Ungar, G.

The structure and phase behavior of an achiral banana-shaped compound-bis-{l_brace}3,4,5-tri[4-(4-n-nonyloxybenzoyloxy)] benzoylamino{r_brace}-1,3-phenylene (I)-have been investigated. This compound exhibits an enantiotropic high-temperature chiral mesophase; upon cooling it successively passes to the crystalline (Cr) phases: Cr{alpha} (281.0-176.0 deg. C), Cr{beta} (175.0-72.0 deg. C), and Cr{gamma} (71.0-40.0 deg. C) (their temperature ranges of existence are indicated). The surface topology and results of linear measurements along the cross sections of certain portions of thin films of compound I in the Cr {gamma} phase clearly prove the effect of the preserved chirality of the previous liquid-crystal phase in the crystalline state.

Ion-exchange synthesis and superconductivity at 8.6 K of Na2Cr3As3 with quasi-one-dimensional crystal structure

NASA Astrophysics Data System (ADS)

Mu, Qing-Ge; Ruan, Bin-Bin; Pan, Bo-Jin; Liu, Tong; Yu, Jia; Zhao, Kang; Chen, Gen-Fu; Ren, Zhi-An

2018-03-01

A Cr-based quasi-one-dimensional superconductor N a2 Cr3As3 was synthesized by an ion-exchange method in a sodium naphthalenide solution. The crystals are threadlike and the structure was analyzed by x-ray diffraction with a noncentrosymmetric hexagonal space group P -6 m 2 (No. 187), in which the (Cr3As3 )2 - linear chains are separated by N a+ ions, and the refined lattice parameters are a =9.239 (2 )Å and c =4.209 (6 )Å . The measurements for electrical resistivity, magnetic susceptibility, and heat capacity reveal a superconducting transition with unconventional characteristic at 8.6 K, which exceeds that of all previously reported Cr-based superconductors.

Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

PubMed

Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

2006-03-31

Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

The high-pressure behavior of spherocobaltite (CoCO3): a single crystal Raman spectroscopy and XRD study

NASA Astrophysics Data System (ADS)

Chariton, Stella; Cerantola, Valerio; Ismailova, Leyla; Bykova, Elena; Bykov, Maxim; Kupenko, Ilya; McCammon, Catherine; Dubrovinsky, Leonid

2018-01-01

Magnesite (MgCO3), calcite (CaCO3), dolomite [(Ca, Mg)CO3], and siderite (FeCO3) are among the best-studied carbonate minerals at high pressures and temperatures. Although they all exhibit the calcite-type structure ({R}\\bar{3}{c}) at ambient conditions, they display very different behavior at mantle pressures. To broaden the knowledge of the high-pressure crystal chemistry of carbonates, we studied spherocobaltite (CoCO3), which contains Co2+ with cation radius in between those of Ca2+ and Mg2+ in calcite and magnesite, respectively. We synthesized single crystals of pure spherocobaltite and studied them using Raman spectroscopy and X-ray diffraction in diamond anvil cells at pressures to over 55 GPa. Based on single crystal diffraction data, we found that the bulk modulus of spherocobaltite is 128 (2) GPa and K' = 4.28 (17). CoCO3 is stable in the calcite-type structure up to at least 56 GPa and 1200 K. At 57 GPa and after laser heating above 2000 K, CoCO3 partially decomposes and forms CoO. In comparison to previously studied carbonates, our results suggest that at lower mantle conditions carbonates can be stable in the calcite-type structure if the radius of the incorporated cation(s) is equal or smaller than that of Co2+ (i.e., 0.745 Å).

Structural differences between single crystal and polycrystalline UBe 13

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

Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia

Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

Structural differences between single crystal and polycrystalline UBe 13

DOE PAGES

Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia; ...

2018-05-16

Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

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

Bae, Brian; Cobb, Ryan E.; DeSieno, Matthew A.

The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5'-monophosphate-3-aminopropylphosphonate and cytidine 5'-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 {angstrom} resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-functionmore » studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.« less

Flux Crystal Growth of the RE 2Ru 3Ge 5 ( RE = La, Ce, Nd, Gd, Tb) Series and Their Magnetic and Metamagnetic Transitions

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

Bugaris, Daniel E.; Malliakas, Christos D.; Bud?ko, Sergey L.

Previously synthesized only as powders, single crystals of the RE 2Ru 3Ge 5 (RE = La, Ce, Nd, Gd, Tb) series of compounds have been now been obtained from molten In. We report that these materials crystallize with the U 2Co 3Si 5-type structure in orthorhombic space group Ibam with lattice parameters a ~ 10.00-9.77 Å (La-Tb), b ~ 12.51-12.35 Å, and c ~ 5.92-5.72 Å. The structure is a three-dimensional framework consisting of RuGe 5 and RuGe 6 units, as well as Ge-Ge zigzag chains. This structure type, along with the other five (Sc 2Fe 3Si 5, Lu 2Comore » 3Si 5, Y 2Rh 3Sn 5, Yb 2Ir 3Ge 5, and Yb 2Pt 3Sn 5) to compose the RE 2T 3X 5 phase space, are discussed in depth. For the three compounds with RE = Nd, Gd, and Tb, multiple magnetic transitions and metamagnetic behavior are observed. Lastly, electronic band structure calculations performed on La 2Ru 3Ge 5 indicate that these materials have a negative band gap and are semimetallic in nature.« less

Electrostatic assembly of binary nanoparticle superlattices using protein cages

NASA Astrophysics Data System (ADS)

Kostiainen, Mauri A.; Hiekkataipale, Panu; Laiho, Ari; Lemieux, Vincent; Seitsonen, Jani; Ruokolainen, Janne; Ceci, Pierpaolo

2013-01-01

Binary nanoparticle superlattices are periodic nanostructures with lattice constants much shorter than the wavelength of light and could be used to prepare multifunctional metamaterials. Such superlattices are typically made from synthetic nanoparticles, and although biohybrid structures have been developed, incorporating biological building blocks into binary nanoparticle superlattices remains challenging. Protein-based nanocages provide a complex yet monodisperse and geometrically well-defined hollow cage that can be used to encapsulate different materials. Such protein cages have been used to program the self-assembly of encapsulated materials to form free-standing crystals and superlattices at interfaces or in solution. Here, we show that electrostatically patchy protein cages--cowpea chlorotic mottle virus and ferritin cages--can be used to direct the self-assembly of three-dimensional binary superlattices. The negatively charged cages can encapsulate RNA or superparamagnetic iron oxide nanoparticles, and the superlattices are formed through tunable electrostatic interactions with positively charged gold nanoparticles. Gold nanoparticles and viruses form an AB8fcc crystal structure that is not isostructural with any known atomic or molecular crystal structure and has previously been observed only with large colloidal polymer particles. Gold nanoparticles and empty or nanoparticle-loaded ferritin cages form an interpenetrating simple cubic AB structure (isostructural with CsCl). We also show that these magnetic assemblies provide contrast enhancement in magnetic resonance imaging.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Flux Crystal Growth of the RE 2Ru 3Ge 5 ( RE = La, Ce, Nd, Gd, Tb) Series and Their Magnetic and Metamagnetic Transitions

DOE PAGES

Bugaris, Daniel E.; Malliakas, Christos D.; Bud?ko, Sergey L.; ...

2017-11-21

Previously synthesized only as powders, single crystals of the RE 2Ru 3Ge 5 (RE = La, Ce, Nd, Gd, Tb) series of compounds have been now been obtained from molten In. We report that these materials crystallize with the U 2Co 3Si 5-type structure in orthorhombic space group Ibam with lattice parameters a ~ 10.00-9.77 Å (La-Tb), b ~ 12.51-12.35 Å, and c ~ 5.92-5.72 Å. The structure is a three-dimensional framework consisting of RuGe 5 and RuGe 6 units, as well as Ge-Ge zigzag chains. This structure type, along with the other five (Sc 2Fe 3Si 5, Lu 2Comore » 3Si 5, Y 2Rh 3Sn 5, Yb 2Ir 3Ge 5, and Yb 2Pt 3Sn 5) to compose the RE 2T 3X 5 phase space, are discussed in depth. For the three compounds with RE = Nd, Gd, and Tb, multiple magnetic transitions and metamagnetic behavior are observed. Lastly, electronic band structure calculations performed on La 2Ru 3Ge 5 indicate that these materials have a negative band gap and are semimetallic in nature.« less

Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device.

PubMed

Solis, Armando D

2014-01-01

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.

The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition

PubMed Central

Okamoto, Ken; Matsumoto, Koji; Hille, Russ; Eger, Bryan T.; Pai, Emil F.; Nishino, Takeshi

2004-01-01

Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon–oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge–transfer band at ≈640 nm. The crystal structure of the complex indicates that the catalytically labile Mo—OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the Mo⋕S group of the oxidized enzyme has become protonated to afford Mo—SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide. PMID:15148401

Improved synthesis and crystal structure of the flexible pillared layer porous coordination polymer: Ni(1,2-bis(4-pyridyl)ethylene)[Ni(CN) 4

DOE PAGES

Wong-Ng, W.; Culp, J. T.; Chen, Y. S.; ...

2013-01-01

This paper reports our synthesis of flexible coordination polymer, Ni(L)[Ni(CN) 4], (L = 1,2-bis(4-pyridyl)ethylene (nicknamed bpene)), and its structural characterization using synchrotron single crystal X-ray diffraction. The structure of the purplish crystals has been determined to be monoclinic, space group P2 1/m, a = 13.5941(12) Å, b = 14.3621(12) Å, c = 14.2561(12) Å, β = 96.141(2)°, V = 2767.4(4) Å 3, Z = 4, D c = 1.46 g cm -1. Ni(bpene)[Ni(CN) 4] assumes a pillared layer structure with layers defined by Ni[Ni(CN) 4] n nets and bpene ligands acting as pillars. With the present crystallization technique which involvesmore » the use of concentrated ammonium hydroxide solution and dimethyl sulfoxide (DMSO), disordered free bpene ligands and solvents of crystallization (DMSO and water molecules) occupy the pores, resulting in a formula of Ni(bpene)[Ni(CN) 4](1/2)bpene∙DMSO 2H 2O, or Ni 2N 7C 24H 25SO 3. Without the inclusion of free bpene ligands and solvent molecules, the free volume is approximately 61% of the total volume; this free volume fraction is reduced to 50% with the free ligands present. Pores without the free ligands were found to have a local diameter of 5.7 Å and a main aperture of 3.5 Å. Based on the successful crystal synthesis, we also devised a new bulk synthetic technique which yielded a polycrystalline material with a significantly improved CO 2 uptake as compared to the originally reported powder material. The improved synthetic technique yielded a polycrystalline material with 40% higher CO 2 uptake compared to the previously reported powder material. An estimated 14.4 molecules of CO 2 per unit cell was obtained.« less

Automatic procedure for stable tetragonal or hexagonal structures: application to tetragonal Y and Cd

NASA Astrophysics Data System (ADS)

Marcus, P. M.; Jona, F.

2005-05-01

A simple effective procedure (MNP) for finding equilibrium tetragonal and hexagonal states under pressure is described and applied. The MNP procedure finds a path to minima of the Gibbs free energy G at T=0 K (G=E+pV, E=energy per atom, p=pressure, V=volume per atom) for tetragonal and hexagonal structures by using the approximate expansion of G in linear and quadratic strains at an arbitrary initial structure to find a change in the strains which moves toward a minimum of G. Iteration automatically proceeds to a minimum within preset convergence criteria on the calculation of the minimum. Comparison is made with experimental results for the ground states of seven metallic elements in hexagonal close-packed (hcp), face- and body-centered cubic structures, and with a previous procedure for finding minima based on tracing G along the epitaxial Bain path (EBP) to a minimum; the MNP is more easily generalized than the EBP procedure to lower symmetry and more atoms in the unit cell. Comparison is also made with a molecular-dynamics program for crystal equilibrium structures under pressure and with CRYSTAL, a program for crystal equilibrium structures at zero pressure. Application of MNP to the elements Y and Cd, which have hcp ground states at zero pressure, finds minima of E at face-centered cubic (fcc) structure for both Y and Cd. Evaluation of all the elastic constants shows that fcc Y is stable, hence a metastable phase, but fcc Cd is unstable.

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

DOE PAGES

Zhang, Li; Popov, Dmitry; Meng, Yue; ...

2016-01-01

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

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

Zhang, Li; Popov, Dmitry; Meng, Yue

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

IMAGINE: first neutron protein structure and new capabilities for neutron macromolecular crystallography

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

Munshi, Parthapratim; Myles, Dean A A; Robertson, Lee

2013-01-01

We report the first high resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory. Neutron diffraction data extending to 1.65 resolution were collected from a relatively small 0.7 mm3 PfRd crystal using 2.5 days (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the deuterium atoms of the protein, and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolutions (1.5 ) from crystals with volume < 1.0 mm3more » and with unit cell edges < 100 . Beam line features include elliptical focusing mirrors that deliver 3x107 n s-1 cm-2 into a 3.5 x 2.0 mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations ( min=2.0 , 2.8 , 3.3 - max =3.0 , 4.0 , 4.5 , ~20 ). Notably, the crystal used to collect this PfRd data is 5-10 times smaller than has been previously reported.« less

Structural studies of crystalline forms of triamterene with carboxylic acid, GRAS and API molecules

PubMed Central

Rehman, Abida

2018-01-01

Pharmaceutical salt solvates (dimethyl sulfoxide, DMSO) of the drug triamterene with the coformers acetic, succinic, adipic, pimelic, azelaic and nicotinic acid and ibuprofen are prepared by liquid-assisted grinding and solvent-evaporative crystallization. The modified ΔpK a rule as proposed by Cruz-Cabeza [(2012 ▸). CrystEngComm, 14, 6362–6365] is in close agreement with the results of this study. All adducts were characterized by X-ray diffraction and thermal analytical techniques, including single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermal gravimetric analysis. Hydrogen-bonded motifs combined to form a variety of extended tapes and sheets. Analysis of the crystal structures showed that all adducts existed as salt solvates and contained the amino­pyridinium–carboxyl­ate heterodimer, except for the solvate containing triamterene, ibuprofen and DMSO, as a result of the presence of a strong and stable hemitriamterenium duplex. A search of the Cambridge Structural Database (CSD 5.36, Version 1.18) to determine the frequency of occurrence of the putative supramolecular synthons found in this study showed good agreement with previous work. PMID:29755747

Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization.

PubMed

Hameed, Uzma; Price, Ian; Ikram-Ul-Haq; Ke, Ailong; Wilson, David B; Mirza, Osman

2017-10-01

Thermostable α-amylases have many industrial applications and are therefore continuously explored from novel sources. We present the characterization of a novel putative α-amylase gene product (Tp-AmyS) cloned from Thermotoga petrophila. The purified recombinant enzyme is highly thermostable and able to hydrolyze starch into dextrin between 90 and 100°C, with optimum activity at 98°C and pH8.5. The activity increased in the presence of Rb 1+ , K 1+ and Ca 2+ ions, whereas other ions inhibited activity. The crystal structure of Tp-AmyS at 1.7Å resolution showed common features of the GH-13 family, however was apparently found to be a dimer. Several residues from one monomer interacted with a docked acarbose, an inhibitor of Tp-AmyS, in the other monomer, suggesting catalytic cooperativity within the dimer. The most striking feature of the dimer was that it resembled the dimerization of salivary amylase from a previous crystal structure, and thus could be a functional feature of some amylases. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal Structure of Chicken γS-Crystallin Reveals Lattice Contacts with Implications for Function in the Lens and the Evolution of the βγ-Crystallins.

PubMed

Sagar, Vatsala; Chaturvedi, Sumit K; Schuck, Peter; Wistow, Graeme

2017-07-05

Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16 chicken γS crystallized avidly while the Q16 mutant did not. The X-ray structure for chicken γS at 2.3 Å resolution shows the canonical structure of the superfamily plus a well-ordered N arm aligned with a β sheet of a neighboring N domain. L16 is also in a lattice contact, partially shielded from solvent. Unexpectedly, the major lattice contact matches a conserved interface (QR) in the multimeric β-crystallins. QR shows little conservation of residue contacts, except for one between symmetry-related tyrosines, but molecular dipoles for the proteins with QR show striking similarities while other γ-crystallins differ. In γS, QR has few hydrophobic contacts and features a thin layer of tightly bound water. The free energy of QR is slightly repulsive and analytical ultracentrifugation confirms no dimerization in solution. The lattice contacts suggest how γ-crystallins allow close packing without aggregation in the crowded environment of the lens. Published by Elsevier Ltd.

Facile synthesis and structure characterization of hexagonal tungsten bronzes crystals

NASA Astrophysics Data System (ADS)

Lee, Jiann-Shing; Liu, Hao-Chuan; Peng, Gao-De; Tseng, Yawteng

2017-05-01

A facile molten-salt route was used to synthesize hexagonal Cs0.33WO3, Rb0.33WO3 and K0.30WO3 crystals. The three isostructural compounds were successfully prepared from the reaction of MxWO3 powders (M = Cs, Rb, K) in the CsCl/NaCl, RbCl/NaCl and KCl/NaCl fluxes, respectively. The structure determination and refinement, based on single-crystal X-ray diffraction data, are in agreement with previous works, possessing space group P63/mcm. The a and c parameters vary non-linearly with increasing radii of the M+ cations (rM) that is coordinated to twelve oxygen atoms. Both the volumes of unit-cell and WO6 octahedra vary linearly with rM, which become smaller from Cs0.33WO3 to K0.30WO3. The distortion of WO6 octahedra as well as isotropic displacement parameters increases from Cs0.33WO3 to K0.30WO3. The geometry of the WO6 octahedron becomes more regular with increasing rM. These structural trends arise from the effective size of the M+ cation.

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryocrystallography

NASA Technical Reports Server (NTRS)

Snell, Eddie

2003-01-01

We have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. Cryocooling is a common technique used for structural data collection to reduce radiation damage in intense X-ray beams and decrease the thermal motion of the atoms. From the thermal images it was clear that during cryocooling a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. As an extension to this work, we used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop for automated structural genomics studies. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryocooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Nakhla: a Martian Meteorite with Indigenous Organic Carbonaceous Features

NASA Technical Reports Server (NTRS)

McKay, D. S.; Gibson, E. K.; Thomas-Keprta, K. L.; Clemett, S. J.; Le, L.; Rahman, Z.; Wentworth, S. J.

2011-01-01

The Nakhla meteorite possesses discrete, well defined, structurally coherent morphologies of carbonaceous phases present within iddingsite alteration zones. Based upon both isotopic measurements and analysis of organic phases the presence of pre-terrestrial organics is now recognized. Within the microcrystalline layers of Nakhla s iddingsite, discrete clusters of salt crystals are present. These salts are predominantly halite (NaCl) with minor MgCl2 crystals. Some CaSO4, likely gypsum, appears to be partially intergrown with some of the halite. EDX mapping shows discrete C-rich features are interspersed among these crystals. A hollow semi-spherical bowl structure ( 3 m ) has been identified and analyzed after using a focused ion beam (FIB) to cut a transverse TEM thin section of the feature and the underlying iddingsite. TEM/EDX analysis reveals that the feature is primarily carbonaceous containing C with lesser amounts of Si, S, Ca, Cl, F, Na, and minor Mn and Fe; additionally a small peak consistent with N, which has been previously seen in Nakhla carbonaceous matter, is also present. Selected area electron diffraction (SAED) shows that this C-rich material is amorphous (lacking any long-range crystallographic order) and is not graphite or carbonate. Micro-Raman spectra acquired from the same surface from which the FIB section was extracted demonstrate a typical kerogen-like D and G band structure with a weak absorption peak at 1350 and a stronger peak at 1600/cm. The C-rich feature is intimately associated with both the surrounding halite and underlying iddingsite matrix. Both iddingsite and salts are interpreted as having formed as evaporate assemblages from progressive evaporation of water bodies on Mars. This assemblage, sans the carbonaceous moieties, closely resembles iddingsite alteration features previously described which were interpreted as indigenous Martian assemblages. These distinctive macromolecular carbonaceous structures in Nakhla may represent one of the sources of the high molecular weight organic material previously identified in Nakhla. While we do not speculate on the origin of these unique carbonaceous structures, we note that the significance of such observations is that it may allow us to construct a C-cycle for Mars based on the C chemistry of the Martian meteorites with obvious implications for astrobiology and the prebiotic evolution of Mars. In any case, our observations strongly suggest that organic C exists as micrometersize, discrete structures on Mars.

Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

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

Lewis, H.A.; Wang, C.; Zhao, X.

2012-04-30

The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutationsmore » that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.« less

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

NASA Technical Reports Server (NTRS)

Egli, M.; Usman, N.; Rich, A.

1993-01-01

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

Growth and characterization of single crystal rocksalt LaAs using LuAs barrier layers

NASA Astrophysics Data System (ADS)

Krivoy, E. M.; Rahimi, S.; Nair, H. P.; Salas, R.; Maddox, S. J.; Ironside, D. J.; Jiang, Y.; Dasika, V. D.; Ferrer, D. A.; Kelp, G.; Shvets, G.; Akinwande, D.; Bank, S. R.

2012-11-01

We demonstrate the growth of high-quality, single crystal, rocksalt LaAs on III-V substrates; employing thin well-behaved LuAs barriers layers at the III-V/LaAs interfaces to suppress nucleation of other LaAs phases, interfacial reactions between GaAs and LaAs, and polycrystalline LaAs growth. This method enables growth of single crystal epitaxial rocksalt LaAs with enhanced structural and electrical properties. Temperature-dependent resistivity and optical reflectivity measurements suggest that epitaxial LaAs is semimetallic, consistent with bandstructure calculations in literature. LaAs exhibits distinct electrical and optical properties, as compared with previously reported rare-earth arsenide materials, with a room-temperature resistivity of ˜459 μΩ-cm and an optical transmission window >50% between ˜3-5 μm.

Expression, Purification And Preliminary X-Ray Analysis of the C-Terminal Domain of An Arginine Repressor Protein From Mycobacterium Tuberculosis

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

Lu, G.J.; Garen, C.R.; Cherney, M.M.

2009-06-03

The gene product of an open reading frame Rv1657 from Mycobacterium tuberculosis is a putative arginine repressor protein (ArgR), a transcriptional factor that regulates the expression of arginine-biosynthetic enzymes. Rv1657 was expressed and purified and a C-terminal domain was crystallized using the hanging-drop vapour-diffusion method. Diffraction data were collected and processed to a resolution of 2.15 {angstrom}. The crystals belong to space group P1 and the Matthews coefficient suggests that the crystals contain six C-terminal domain molecules per unit cell. Previous structural and biochemical studies on the arginine repressor proteins from other organisms have likewise shown the presence of sixmore » molecules per unit cell.« less

Structural and electronic evolution of Cr[subscript 2]O[subscript 3] on compression to 55 GPa

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

Dera, Przemyslaw; Lavina, Barbara; Meng, Yue

2016-08-15

Synchrotron single-crystal x-ray diffraction experiments have been performed on corundum-type Cr{sub 2}O{sub 3} up to a pressure of 55 GPa in Ne and He pressure transmitting media. Diffraction experiments were complemented by measurements of optical absorption spectra with single crystal samples up to 60 GPa. Results of the diffraction data analysis rule out the earlier reported monoclinic distortion at 15-30 GPa, but indicate evidence of two discontinuous transitions of electronic or magnetic nature, most likely associated with a change in magnetic ordering and charge transfer. The compression mechanism established from single crystal refinements indicates much smaller distortion of the Cr{supmore » 3+} coordination environment than was previously assumed.« less

Single-crystal perovskite CH3NH3PbBr3 prepared by cast capping method for light-emitting diodes

NASA Astrophysics Data System (ADS)

Nguyen, Van-Cao; Katsuki, Hiroyuki; Sasaki, Fumio; Yanagi, Hisao

2018-04-01

In this study, electroluminescence from single crystals of CH3NH3PbBr3 perovskite is explored. The cast capping method was applied to fabricate simple devices with an ITO/CH3NH3PbBr3/ITO structure. The devices showed a low operation voltage of 2 V and a pure green luminescence with full width at half maximum of ∼20 nm. However, the emission occurring at the crystal edges demonstrated blinking with a subsecond time interval, which is similar to the previously reported photoluminescence behavior of nanocrystal perovskites. This electroluminescence blinking may provide new insight into the recombination processes depending on the carrier traps and defects of emission layers in perovskite light-emitting devices.

Diffusion paths formation for Cu{sup +} ions in superionic Cu{sub 6}PS{sub 5}I single crystals studied in terms of structural phase transition

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

Gagor, A.; Pietraszko, A.; Kaynts, D.

2005-11-15

In order to understand the structural transformations leading to high ionic conductivity of Cu{sup +} ions in Cu{sub 6}PS{sub 5}I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T{sub c}=(144-169)K Cu{sub 6}PS{sub 5}I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above T{sub c} delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43c (a{sup '}=19.528A, z=32). Finally, above T{sub 1}=274K increasing disordering of the Cu{sup +} ions heightens the symmetry to F-43m (a=9.794A, z=4). In this work,more » the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions (R{sub 1}=0.0397 for F-43c phase, and 0.0245 for F-43m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.« less

Crystal Structure of a Ube2S-Ubiquitin Conjugate

PubMed Central

Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

2016-01-01

Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

Investigations on the Crystal Structure and the Stability Field of FCAM-I (Ca3MgAl6Fe10O28), an Iso-structure to SFCA-I

NASA Astrophysics Data System (ADS)

Zöll, Klaus; Manninger, Tanja; Kahlenberg, Volker; Krüger, Hannes; Tropper, Peter

2017-08-01

In a study on parts of the system Fe2O3-CaO-Al2O3-MgO, the previously unknown compound Ca3MgAl6Fe10O28 or FCAM-I (iso-structural with SFCA-I) has been synthesized. The two principal aims of our investigations have been (i) analysis of the stability field of the new phase as a function of T and fO2 and (ii) determination of its crystal structure. Two experimental series in air and under controlled oxygen fugacity via the hematite-magnetite buffer were conducted. Pure polycrystalline FCAM-I has been obtained at 1463.15 K (1190 °C) in air. While increasing the temperature from 1573.15 K to 1673.15 K (1300 °C to 1400 °C), the FCAM-I phase breaks down forming a variety of new compounds depending on T and fO2. Ca3MgAl6Fe10O28 has a triclinic crystal structure (space group P \\overline{1} ). Basic crystallographic data are as follows: a = 10.2980(4) Å, b = 10.4677(4) Å, c = 11.6399(4) Å, α = 94.363(3)°, β = 111.498(3)°, γ = 109.744(3)°, V = 1069.81(7) Å3, Z = 2.

Crystal structures of (Mg1-x,Fe(x))SiO3 postperovskite at high pressures.

PubMed

Yamanaka, Takamitsu; Hirose, Kei; Mao, Wendy L; Meng, Yue; Ganesh, P; Shulenburger, Luke; Shen, Guoyin; Hemley, Russell J

2012-01-24

X-ray diffraction experiments on postperovskite (ppv) with compositions (Mg(0.9)Fe(0.1))SiO(3) and (Mg(0.6)Fe(0.4))SiO(3) at Earth core-mantle boundary pressures reveal different crystal structures. The former adopts the CaIrO(3)-type structure with space group Cmcm, whereas the latter crystallizes in a structure with the Pmcm (Pmma) space group. The latter has a significantly higher density (ρ = 6.119(1) g/cm(3)) than the former (ρ = 5.694(8) g/cm(3)) due to both the larger amount of iron and the smaller ionic radius of Fe(2+) as a result of an electronic spin transition observed by X-ray emission spectroscopy (XES). The smaller ionic radius for low-spin compared to high-spin Fe(2+) also leads to an ordered cation distribution in the M1 and M2 crystallographic sites of the higher density ppv structure. Rietveld structure refinement indicates that approximately 70% of the total Fe(2+) in that phase occupies the M2 site. XES results indicate a loss of 70% of the unpaired electronic spins consistent with a low spin M2 site and high spin M1 site. First-principles calculations of the magnetic ordering confirm that Pmcm with a two-site model is energetically more favorable at high pressure, and predict that the ordered structure is anisotropic in its electrical and elastic properties. These results suggest that interpretations of seismic structure in the deep mantle need to treat a broader range of mineral structures than previously considered.

Oxide surfaces in practical and model catalytic systems

NASA Astrophysics Data System (ADS)

Lanier, Courtney H.

Oxide surface structures play a key role in many technological processes, including catalysis, thin film growth, and layered structures, and a thorough understanding of surface structures and surface structure dynamics is required in order to better engineer materials systems for these processes. This research works towards understanding these fundamental principles through an investigation of practical and model catalytic systems. In this work, the surface structures and dynamics of Mg3(VO4)2, LaAlO3, SrTiO3, and alpha-Fe2O3/Fe3O 4 are investigated under a variety of conditions and by a range of experimental and computational techniques. The structure and morphology of LaAlO3 has been investigated over a range of annealing temperatures, and the ( 5x5 )R26.6° reconstruction of LaAlO3 (001) has been determined using transmission electron diffraction combined with direct methods. The structure is relatively simple, consisting of a lanthanum oxide termination with one lanthanum cation vacancy per surface unit cell. The electronic structure is unusual since a fractional number of holes or atomic occupancies per surface unit cell are required to achieve charge neutrality. The reconstruction can be understood in terms of expulsion of the more electropositive cation from the surface followed by an increased covalency between the remaining surface lanthanum atoms and adjacent oxygen atoms. The c(6x2) is a reconstruction of the SrTiO3 (001) surface that is formed between 1050-1100°C in oxidizing annealing conditions. This work proposes a model for the atomic structure for the c(6x2) obtained through a combination of results from transmission electron diffraction, surface x-ray diffraction, direct methods analysis, computational combinational screening, and density functional theory. As it is formed at high temperatures, the surface is complex and can be described as a short-range ordered phase featuring microscopic domains composed of four main structural motifs. Additionally, non-periodic TiO2 units are present on the surface. The surface and bulk of oriented single crystal Mg3(VO 4)2 have been characterized after treatment in a reducing environment. Annealing in a flow of 7% H2 in N2 causes the reduction of Mg3(VO4)2 to Mg3V 2O6, which is shown to be single-crystal to single-crystal and occurs in such a way that the oxygen framework of the crystal is preserved. Transmission electron microscopy images of crystals at the early stages of reduction show low angle grain boundaries and the formation of channels approximately 50nm in diameter. A model for reduction of Mg3(VO4) 2 to Mg3V2O6 based on the experimental observations and derived from classic nucleation theory is proposed. The so-called Biphase structure on alpha-Fe2O3 has been previously reported and described as islands of Fe1-xO and alpha-Fe2O3 arranged in a 40A periodic unit cell. Based on thermodynamic arguments and experimental evidence, including transmission electron diffraction, we find that the previous structure model was incorrect. Rather, it is found that the Biphase structure is, in fact, related to the reduction of alpha-Fe2O3 to Fe 3O4, is a layered structure, and does not contain islands of Fe1-xO. A model for the Biphase termination consisting of bulk alpha-Fe 2O3 with an Fe3O4 -derived overlayer is developed and is consistent with all current and previously reported experimental findings.

Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin

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

Kusunoki, H.; Minasov, G.; Macdonald, R.I.

Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain {alpha}-spectrin and human erythroid {beta}-spectrin repeats can undergo bending without losing their {alpha}-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain {alpha}-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, themore » three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of {alpha}-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and {alpha}-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.« less

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

Meagher, Martin; Enemark, Eric J.

The crystal structure of the N-terminal domain of thePyrococcus furiosusminichromosome maintenance (MCM) protein as a double hexamer is described. The MCM complex is a ring-shaped helicase that unwinds DNA at the replication fork of eukaryotes and archaea. Prior to replication initiation, the MCM complex assembles as an inactive double hexamer at specific sites of DNA. The presented structure is highly consistent with previous MCM double-hexamer structures and shows two MCM hexamers with a head-to-head interaction mediated by the N-terminal domain. Minor differences include a diminished head-to-head interaction and a slightly reduced inter-hexamer rotation.

Structural difference rule for amorphous alloy formation by ion mixing

NASA Technical Reports Server (NTRS)

Liu, B.-X.; Johnson, W. L.; Nicolet, M.A.; Lau, S. S.

1983-01-01

A rule is formulated which establishes a sufficient condition that an amorphous binary alloy will be formed by ion mixing of multilayered samples when the two constituent metals are of different crystalline structure, regardless of their atomic sizes and electronegativities. The rule is supported by the experimental results obtained on six selected binary metal systems, as well as by the previous data reported in the literature. The amorphization mechanism is discussed in terms of the competition between two different structures resulting in frustration of the crystallization process.

Crystal structure of tetra-kis-(μ3-2-{[1,1-bis-(hy-droxy-meth-yl)-2-oxidoeth-yl]imino-meth-yl}-6-meth-oxy-phenolato)tetra-kis-[aqua-copper(II)]: a redetermination at 200 K.

PubMed

Buvaylo, Elena A; Vassilyeva, Olga Yu; Skelton, Brian W

2015-10-01

The crystal structure of the tetra-nuclear title compound, [Cu4(C12H15NO5)4(H2O)4], has been previously reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem. (2015), 641, 941-947], based on room-temperature data. In the previously published structure, no standard uncertainties are recorded for the deprotonated hy-droxy-methyl group and water mol-ecule O atoms coordinating to the metal atom indicating that they were not refined; furthermore, the H atoms of some OH groups and water mol-ecules have not been positioned accurately. Since the current structure was determined at a lower temperature, all atoms, including the H atoms of these hy-droxy groups and the water mol-ecule, have been determined more accurately resulting in improved standard uncertainties in the bond lengths and angles. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. In addition, it is now possible to report intra- and inter-molecular O-H⋯O inter-actions. In the title complex molecule, which has crystallographic -4 symmetry, the Cu(II) ions are coordinated by the tridentate Schiff base ligands and water mol-ecules, forming a tetra-nuclear Cu4O4 cubane-like core. The Cu(II) ion adopts a CuNO5 elongated octa-hedral environment. The coordination environment of Cu(II) at 200 K displays a small contraction of the Cu-N/O bonds, compared with the room-temperature structure. In the crystal lattice, the neutral clusters are linked by inter-molecular O-H⋯O hydrogen bonds into a one-dimensional hydrogen-bonding network propagating along the b axis.

Molecular dynamics simulations of steady-state crystal growth and homogeneous nucleation in polyethylene-like polymer

NASA Astrophysics Data System (ADS)

Yamamoto, Takashi

2008-11-01

Molecular mechanisms of crystal growth and homogeneous nucleation from the melt of polyethylene-like linear polymer are investigated by molecular dynamics simulations. The present paper is aimed at extending our previous work with respect to the system size and the boundary condition, thereby enabling detailed studies on the structures of sufficiently large lamellae and fully equilibrated melt. Lamellae of uniform thickness but with marked tapered edges are found to grow at constant velocity from the substrate. Three-dimensional shape of the growing lamellae exhibits peculiar undulation at the growth front, the origin of which is suggested to be the inhomogeneous thickness distribution within the lamellae. Trajectories of chains crystallizing onto the growth front reveal an unexpected pathway for chain folding, where a partially attached chain stem forms a new fold by plunging its head back into a neighboring stem position through slithering snake motions of the chain. Detailed statistics of folds and cilia show that the folds are rather neat and mostly make re-entries into the nearest or the second or third nearest neighboring stem positions, whereas the cilia are generally short but with a small number of longer cilia forming thick amorphous layers. Structure of supercooled melt investigated versus temperature reveals that, at moderate degree of supercooling, the overall chain conformation remains Gaussian random coil but the persistent length of chains increases monotonically with increasing supercooling. Exceptions are at the largest supercooling where homogeneous nucleation takes place; usual melt structure becomes rapidly unstable and emerges many crystallites of random orientations. During early 10-20ns after the quench, density of melt, radius of gyration of chains, and fraction of kinked bonds show marked alterations. These structural changes are highly cooperative and are considered simply due to the emergence of many embryonic crystals in the melt. Conformations of the chains forming nuclei are also traced to reveal that the homogeneous nuclei are fringed micelle like aggregates of chains, but the chains as a whole have folded conformations, which are similar to those reported in previous simulations on a single polyethylene in a vacuum.

Investigation of intermolecular interactions in finasteride drug crystals in view of X-ray and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Bojarska, Joanna; Maniukiewicz, Waldemar

2015-11-01

The N,N-dimethylformamide (DMF) solvate hemihydrate (1) of finasteride, has been structurally characterized by single-crystal X-ray diffraction at 100 K and compared with previously reported finasteride crystalline forms. In addition, in order to resolve ambiguity concerning H-bond interactions, the crystal structure of finasteride hemihydrate, (2), originally reported by Schultheiss et al. in 2009, has been redetermined with higher precision. The (1) and (2) pseudopolymorphs of finasteride crystallize as orthorhombic in chiral P212121 space group with two very similar host molecules in the asymmetric unit. The conformation of fused 6-membered rings are screw-boat, chair and chair for both molecules, while 5-membered rings assume chair in (1), and half-chair in (2). There is a fairly close resemblance of the molecular geometry for all analyzed compounds, arising due to the rigid host molecule. Inter- and intramolecular host-host, host-guest strong O-H⋯O, N-H⋯O hydrogen bonds and weak C-H⋯O interactions form 3D net conferring stability to the crystal packing. Finasterides can be classified as synthon pseudopolymorphs. Isostructural solvates crystallizing in the orthorhombic space group P212121, with Z‧ = 2, exhibit R22(8) C22(15) network, monoclinic solvate (Z‧ = 1) possess D11(2), while both orthorhombic and monoclinic polymorphs have C(4) motifs, respectively. The structural similarities and subtle differences have been interpreted in view of the 3D Hirshfeld surface analysis and associated 2D fingerprint plots, which enabled detailed qualitative and quantitative insight into the intermolecular interactions. The 97-100% of Hirshfeld surface areas are due to H···H, O···H/H⋯O, C···H/H⋯C and N⋯H/H⋯N contacts. Furthermore, the electrostatic potential has been mapped over the Hirshfeld surfaces to decode the electrostatic complementarities, which exist in the crystal packing.

Monoclonal Antibody Analysis and Insecticidal Spectrum of Three Types of Lepidopteran-Specific Insecticidal Crystal Proteins of Bacillus thuringiensis

PubMed Central

Höfte, Herman; Van Rie, Jeroen; Jansens, Stefan; Van Houtven, Annemie; Vanderbruggen, Hilde; Vaeck, Mark

1988-01-01

We have investigated the protein composition and the insecticidal spectrum of crystals of 29 Bacillus thuringiensis strains active against lepidopteran larvae. All crystals contained proteins of 130 to 140 kilodaltons (kDa) which could be grouped into three types by the molecular weight of the protoxin and the trypsin-activated core fragment. Proteins of the three types showed a characteristic insecticidal spectrum when tested against five lepidopteran species. Type A crystal proteins were protoxins of 130 or 133 kDa, which were processed into 60-kDa toxins by trypsin. Several genes encoding crystal proteins of this type have been cloned and sequenced earlier. They are highly conserved in the N-terminal half of the toxic fragment and were previously classified in three subtypes (the 4.5-, 5.3-, and 6.6-kilobase subtypes) based on the restriction map of their genes. The present study shows that different proteins of these three subtypes were equally toxic against Manduca sexta and Pieris brassicae and had no detectable activity against Spodoptera littoralis. However, the 4.5-, 5.3-, and 6.6-kilobase subtypes differed in their toxicity against Heliothis virescens and Mamestra brassicae. Type B crystal proteins consisted of 140-kDa protoxins with a 55-kDa tryptic core fragment. These were only active against one of the five insect species tested (P. brassicae). The protoxin and the trypsin-activated toxin of type C were 135- and 63-kDa proteins, respectively. Proteins of this type were associated with high toxicity against S. littoralis and M. brassicae. A panel of 35 monoclonal antibodies was used to compare the structural characteristics of crystal proteins of the three different types and subtypes. Each type of protein could be associated with a typical epitope structure, indicating an unambiguous correlation between antigenic structure and insect specificity. Images PMID:16347711

Flow induced/ refined solution crystallization of a semiconducting polymer

NASA Astrophysics Data System (ADS)

Nguyen, Ngoc A.

Organic photovoltaics, a new generation of solar cells, has gained scientific and economic interests due to the ability of solution-processing and potentially low-cost power production. Though, the low power conversion efficiency of organic/ plastic solar cells is one of the most pertinent challenges that has appealed to research communities from many different fields including materials science and engineering, electrical engineering, chemical engineering, physics and chemistry. This thesis focuses on investigating and controlling the morphology of a semi-conducting, semi-crystalline polymer formed under shear-flow. Molecular structures and processing techniques are critical factors that significantly affect the morphology formation in the plastic solar cells, thus influencing device performance. In this study, flow-induced solution crystallization of poly (3-hexylthiophene) (P3HT) in a poor solvent, 2-ethylnapthalene (2-EN) was utilized to make a paint-like, structural liquid. The polymer crystals observed in this structured paint are micrometers long, nanometers in cross section and have a structure similar to that formed under quiescent conditions. There is pi-pi stacking order along the fibril axis, while polymer chain folding occurs along the fibril width and the order of the side-chain stacking is along fibril height. It was revealed that shear-flow not only induces P3HT crystallization from solution, but also refines and perfects the P3HT crystals. Thus, a general strategy to refine the semiconducting polymer crystals from solution under shear-flow has been developed and employed by simply tuning the processing (shearing) conditions with respect to the dissolution temperature of P3HT in 2-EN. The experimental results demonstrated that shear removes defects and allows more perfect crystals to be formed. There is no glass transition temperature observed in the crystals formed using the flow-induced crystallization indicating a significantly different morphology formation in comparison to that of the pristine (as-received) P3HT. As a result, single P3HT crystals with high surface energy chain folds were analyzed and determined. Previous reported results of infinite melting enthalpy of extended chain P3HT crystals are much higher than the result discovered in this study. The findings in this study revealed that the infinite melting enthalpy of chain-folded P3HT crystals is considerably decreased due to the presence of this P3HT chain-folded surface energy. In this study, the kinetics and mechanism of P3HT crystallization under shear-flow was thoroughly investigated as well. A homogeneous nucleation of P3HT was observed that allows one dimensional fibril crystal growth. The micrometer long P3HT crystals are formed and limited by the contact time between the P3HT molecules. Furthermore, it was found that phenyl-C61-butyric acid methyl ester (PCBM) nanoparticles inhibit the crystallization of P3HT under shear. However, the shear-flow leads to nanophase agglomeration of PCBM and creates percolation of P3HT fibril crystal networks and the PCBM phase separated domains that apparently present better pathways for transporting electrons and holes. Interestingly, the structured liquid was simply applied onto substrates with a paintbrush resulting in similar device performance to those made with current techniques in which the morphology is commonly formed during application or post-processing steps. These detailed findings are given and discussed in the thesis.

The bipolar filaments formed by Herpes simplex virus type 1 SSB/recombination protein (ICP8) suggest a mechanism for DNA annealing

PubMed Central

Makhov, Alexander M.; Sen, Anindito; Yu, Xiong; Simon, Martha N.; Griffith, Jack D.; Egelman, Edward H.

2009-01-01

Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single strand binding protein and recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic (EM) studies showed that ICP8 will form long left-handed helical filaments. Here EM image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using Scanning Transmission Electron Microscopy. The pitch of the filaments is ~ 250 Å, with ~ 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing ~ 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA, based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary single stranded DNA into double-stranded DNA, where each strand runs in opposite directions. PMID:19138689

The bipolar filaments formed by herpes simplex virus type 1 SSB/recombination protein (ICP8) suggest a mechanism for DNA annealing.

PubMed

Makhov, Alexander M; Sen, Anindito; Yu, Xiong; Simon, Martha N; Griffith, Jack D; Egelman, Edward H

2009-02-20

Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single-strand binding protein and as a recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic studies showed that ICP8 will form long left-handed helical filaments. Here, electron microscopic image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using scanning transmission electron microscopy. The pitch of the filaments is approximately 250 A, with approximately 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing approximately 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA (ssDNA), based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary ssDNA into double-stranded DNA, where each strand runs in opposite directions.

The Bipolar Filaments Formed by Herpes Simplex Virus Type 1 SSB/Recombination Protein (ICP8) Suggest a Mechanism for DNA Annealing

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

Makhov, A.M.; Simon, M.; Sen, A.

2009-02-20

Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single-strand binding protein and as a recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic studies showed that ICP8 will form long left-handed helical filaments. Here, electron microscopic image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using scanning transmission electron microscopy. The pitch of the filaments ismore » {approx} 250 {angstrom}, with {approx} 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing {approx} 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA (ssDNA), based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary ssDNA into double-stranded DNA, where each strand runs in opposite directions.« less

Adsorption calorimetry during metal vapor deposition on single crystal surfaces: Increased flux, reduced optical radiation, and real-time flux and reflectivity measurements

NASA Astrophysics Data System (ADS)

Sellers, Jason R. V.; James, Trevor E.; Hemmingson, Stephanie L.; Farmer, Jason A.; Campbell, Charles T.

2013-12-01

Thin films of metals and other materials are often grown by physical vapor deposition. To understand such processes, it is desirable to measure the adsorption energy of the deposited species as the film grows, especially when grown on single crystal substrates where the structure of the adsorbed species, evolving interface, and thin film are more homogeneous and well-defined in structure. Our group previously described in this journal an adsorption calorimeter capable of such measurements on single-crystal surfaces under the clean conditions of ultrahigh vacuum [J. T. Stuckless, N. A. Frei, and C. T. Campbell, Rev. Sci. Instrum. 69, 2427 (1998)]. Here we describe several improvements to that original design that allow for heat measurements with ˜18-fold smaller standard deviation, greater absolute accuracy in energy calibration, and, most importantly, measurements of the adsorption of lower vapor-pressure materials which would have previously been impossible. These improvements are accomplished by: (1) using an electron beam evaporator instead of a Knudsen cell to generate the metal vapor at the source of the pulsed atomic beam, (2) changing the atomic beam design to decrease the relative amount of optical radiation that accompanies evaporation, (3) adding an off-axis quartz crystal microbalance for real-time measurement of the flux of the atomic beam during calorimetry experiments, and (4) adding capabilities for in situ relative diffuse optical reflectivity determinations (necessary for heat signal calibration). These improvements are not limited to adsorption calorimetry during metal deposition, but also could be applied to better study film growth of other elements and even molecular adsorbates.

Adsorption calorimetry during metal vapor deposition on single crystal surfaces: increased flux, reduced optical radiation, and real-time flux and reflectivity measurements.

PubMed

Sellers, Jason R V; James, Trevor E; Hemmingson, Stephanie L; Farmer, Jason A; Campbell, Charles T

2013-12-01

Thin films of metals and other materials are often grown by physical vapor deposition. To understand such processes, it is desirable to measure the adsorption energy of the deposited species as the film grows, especially when grown on single crystal substrates where the structure of the adsorbed species, evolving interface, and thin film are more homogeneous and well-defined in structure. Our group previously described in this journal an adsorption calorimeter capable of such measurements on single-crystal surfaces under the clean conditions of ultrahigh vacuum [J. T. Stuckless, N. A. Frei, and C. T. Campbell, Rev. Sci. Instrum. 69, 2427 (1998)]. Here we describe several improvements to that original design that allow for heat measurements with ~18-fold smaller standard deviation, greater absolute accuracy in energy calibration, and, most importantly, measurements of the adsorption of lower vapor-pressure materials which would have previously been impossible. These improvements are accomplished by: (1) using an electron beam evaporator instead of a Knudsen cell to generate the metal vapor at the source of the pulsed atomic beam, (2) changing the atomic beam design to decrease the relative amount of optical radiation that accompanies evaporation, (3) adding an off-axis quartz crystal microbalance for real-time measurement of the flux of the atomic beam during calorimetry experiments, and (4) adding capabilities for in situ relative diffuse optical reflectivity determinations (necessary for heat signal calibration). These improvements are not limited to adsorption calorimetry during metal deposition, but also could be applied to better study film growth of other elements and even molecular adsorbates.

Molecular Genetic and Crystal Structural Analysis of 1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from 'Aromatoleum aromaticum' EbN1.

PubMed

Büsing, Imke; Höffken, H Wolfgang; Breuer, Michael; Wöhlbrand, Lars; Hauer, Bernhard; Rabus, Ralf

2015-01-01

The dehydrogenation of 1-(4-hydroxyphenyl)-ethanol to 4-hydroxyacetophenone represents the second reaction step during anaerobic degradation of p-ethylphenol in the denitrifying bacterium 'Aromatoleum aromaticum' EbN1. Previous proteogenomic studies identified two different proteins (ChnA and EbA309) as possible candidates for catalyzing this reaction [Wöhlbrand et al: J Bacteriol 2008;190:5699-5709]. Physiological-molecular characterization of newly generated unmarked in-frame deletion and complementation mutants allowed defining ChnA (renamed here as Hped) as the enzyme responsible for 1-(4-hydroxyphenyl)-ethanol oxidation. Hped [1-(4-hydroxyphenyl)-ethanol dehydrogenase] belongs to the 'classical' family within the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Hped was overproduced in Escherichia coli, purified and crystallized. The X-ray structures of the apo- and NAD(+)-soaked form were resolved at 1.5 and 1.1 Å, respectively, and revealed Hped as a typical homotetrameric SDR. Modeling of the substrate 4-hydroxyacetophenone (reductive direction of Hped) into the active site revealed the structural determinants of the strict (R)-specificity of Hped (Phe(187)), contrasting the (S)-specificity of previously reported 1-phenylethanol dehydrogenase (Ped; Tyr(93)) from strain EbN1 [Höffken et al: Biochemistry 2006;45:82-93]. © 2015 S. Karger AG, Basel.

Structure of Human Pancreatic Lipase-Related Protein 2 with the Lid in an Open Conformation

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

Eydoux, Cecilia; Spinelli, Silvia; Davis, Tara L.

2008-10-02

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lidmore » is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.« less

Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

PubMed

Eydoux, Cécilia; Spinelli, Silvia; Davis, Tara L; Walker, John R; Seitova, Alma; Dhe-Paganon, Sirano; De Caro, Alain; Cambillau, Christian; Carrière, Frédéric

2008-09-09

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.

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

AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited formore » structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.« less

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.

PubMed Central

Qian, M.; Haser, R.; Payan, F.

1995-01-01

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high-resolution study of a complex between PPA and a carbohydrate inhibitor (Qian M, Buisson G, Duée E, Haser H, Payan F, 1994, Biochemistry 33:6284-6294). One of the binding sites previously identified in a 5-A-resolution electron density map, lies at a distance of 20 A from the active site cleft and can accommodate two glucose units. The second affinity site for sugar units is located close to the calcium binding site. The crystal structure of the maltopentaose complex was refined at 2.1 A resolution, to an R-factor of 17.5%, with an RMS deviation in bond distances of 0.007 A. The model includes all 496 residues of the enzyme, 1 calcium ion, 1 chloride ion, 425 water molecules, and 3 bound sugar rings. The binding sites are characterized and described in detail. The present complex structure provides the evidence of an increased stability of the structure upon interaction with the substrate and allows identification of an N-terminal pyrrolidonecarboxylic acid in PPA. PMID:7613472

Structure of Leishmania major Methionyl-tRNA Synthetase in Complex with Intermediate Products Methionyladenylate and Pyrophosphate

PubMed Central

Larson, Eric T.; Kim, Jessica E.; Zucker, Frank H.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G.J.

2011-01-01

Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNAMet complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme. PMID:21144880

Nodal lines and nodal loops in nonsymmorphic odd-parity superconductors

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

Micklitz, T.; Norman, M. R.

2017-01-01

We discuss the nodal structure of odd-parity superconductors in the presence of nonsymmorphic crystal symmetries, both with and without spin-orbit coupling, and with and without time-reversal symmetry. We comment on the relation of our work to previous work in the literature, and also the implications for unconventional superconductors such as UPt3.

Determining the crystal structure of fibrinogen.

PubMed

Doolittle, R F

2004-05-01

Summary. I have enjoyed reading previous historical sketches that have appeared in Journal of Thrombosis and Haemostasis, and especially those by Ted Tuddenham on factor VIII and Bjorn Dahlback on activated protein C resistance. Like those authors, I have tried to capture some of the excitement-as well as the disappointments-that occurred along the way to a long-term goal.

Crystal structure of the human astrovirus capsid spike.

PubMed

Dong, Jinhui; Dong, Liping; Méndez, Ernesto; Tao, Yizhi

2011-08-02

Astroviruses are single-stranded, plus-sense RNA viruses that infect both mammals and birds, causing gastroenteritis and other extraintestinal diseases. Clinical studies have established astroviruses as the second leading cause of viral diarrhea in young children. Here we report the crystal structure of the human astrovirus dimeric surface spike determined to 1.8-Å resolution. The overall structure of each spike/projection domain has a unique three-layered β-sandwiches fold, with a core, six-stranded β-barrel structure that is also found in the hepatitis E virus capsid protrusions, suggesting a closer phylogenetic relationship between these two viruses than previously acknowledged. Based on a hepatitis E virus capsid model, we performed homology modeling and produced a complete, T = 3 astrovirus capsid model with features remarkably similar to those observed in a cryoelectron microscopy reconstruction image of a human astrovirus. Mapping conserved residues onto the astrovirus projection domain revealed a putative receptor binding site with amino acid compositions characteristic for polysaccharide recognition. Our results will have an important impact on future characterization of astrovirus structure and function, and will likely have practical applications in the development of vaccines and antivirals.

Crystal Structure and Regulation of the Citrus Pol III Repressor MAF1 by Auxin and Phosphorylation.

PubMed

Soprano, Adriana Santos; Giuseppe, Priscila Oliveira de; Shimo, Hugo Massayoshi; Lima, Tatiani Brenelli; Batista, Fernanda Aparecida Heleno; Righetto, Germanna Lima; Pereira, José Geraldo de Carvalho; Granato, Daniela Campos; Nascimento, Andrey Fabricio Ziem; Gozzo, Fabio Cesar; de Oliveira, Paulo Sérgio Lopes; Figueira, Ana Carolina Migliorini; Smetana, Juliana Helena Costa; Paes Leme, Adriana Franco; Murakami, Mario Tyago; Benedetti, Celso Eduardo

2017-09-05

MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrus. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.

PubMed

Williamson, Adele; Rothweiler, Ulli; Leiros, Hanna Kirsti Schrøder

2014-11-01

DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.

The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6.

PubMed

Usenik, Aleksandra; Renko, Miha; Mihelič, Marko; Lindič, Nataša; Borišek, Jure; Perdih, Andrej; Pretnar, Gregor; Müller, Uwe; Turk, Dušan

2017-03-07

Bacterial cell wall proteins play crucial roles in cell survival, growth, and environmental interactions. In Gram-positive bacteria, cell wall proteins include several types that are non-covalently attached via cell wall binding domains. Of the two conserved surface-layer (S-layer)-anchoring modules composed of three tandem SLH or CWB2 domains, the latter have so far eluded structural insight. The crystal structures of Cwp8 and Cwp6 reveal multi-domain proteins, each containing an embedded CWB2 module. It consists of a triangular trimer of Rossmann-fold CWB2 domains, a feature common to 29 cell wall proteins in Clostridium difficile 630. The structural basis of the intact module fold necessary for its binding to the cell wall is revealed. A comparison with previously reported atomic force microscopy data of S-layers suggests that C. difficile S-layers are complex oligomeric structures, likely composed of several different proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 Å resolution

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

Maraite, Andy; Schmidt, Thomas; Ansörge-Schumacher, Marion B.

2007-07-01

The X-ray crystal structure of the ThDP-dependent enzyme benzaldehyde lyase has been refined to 1.65 Å. Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 Å using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005 ▶), FEBS J.272, 6067–6076]. In this communication of parallel studies, BAL was crystallized in an alternative spacemore » group (P2{sub 1}2{sub 1}2{sub 1}) and its structure refined to a resolution of 1.65 Å, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.« less

Crystal grain growth at the α -uranium phase transformation in praseodymium

NASA Astrophysics Data System (ADS)

Cunningham, Nicholas C.; Velisavljevic, Nenad; Vohra, Yogesh K.

2005-01-01

Structural phase transformations under pressure are examined in praseodymium metal for the range 0-40GPa at ambient temperature. Pressure was generated with a diamond-anvil cell, and data were collected using high-resolution synchrotron x-ray diffraction and the image plate technique. The structural sequence double hexagonal close packed (dhcp)→face centered cubic (fcc)→distorted-fcc (d-fcc)→ α -uranium (α-U) is observed with increasing pressure. Rietveld refinement of all crystallographic phases provided confirmation of the hR24 structure for the d-fcc phase while the previously reported monoclinic phase between the d-fcc and the α-U phase was not confirmed. We observe dramatic crystal grain growth during the volume collapse concurrent with the symmetry-lowering transition to the α-U structure. No preferred orientation axis is observed, and the formation process for these large grains is expected to be via a nucleation and growth mechanism. An analogous effect in rare earth metal cerium suggests that the grain growth during transformation to the α-U structure is a common occurrence in f -electron metals at high pressures.

Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases.

PubMed

Chen, Yan-Na; Gu, Xin; Zhou, X Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei; Xu, H Eric; Lv, Zhengbing

2017-04-01

TBC1D15 belongs to the TBC (Tre-2/Bub2/Cdc16) domain family and functions as a GTPase-activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark-TBC1D15 and Sus-TBC1D15 belong to the same subfamily of TBC domain-containing proteins, and their GAP-domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. © 2017 The Protein Society.

Discovery of black dye crystal structure polymorphs: Implications for dye conformational variation in dye-sensitized solar cells

DOE PAGES

Cole, Jacqueline M.; Low, Kian Sing; Gong, Yun

2015-11-24

Here, we present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world’s leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO 2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiplemore » conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO 2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO 2 interfaces in DSSCs, at least for ruthenium-based dye complexes.« less

Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts.

PubMed

Boehm, M K; Corper, A L; Wan, T; Sohi, M K; Sutton, B J; Thornton, J D; Keep, P A; Chester, K A; Begent, R H; Perkins, S J

2000-03-01

MFE-23 is the first single-chain Fv antibody molecule to be used in patients and is used to target colorectal cancer through its high affinity for carcinoembryonic antigen (CEA), a cell-surface member of the immunoglobulin superfamily. MFE-23 contains an N-terminal variable heavy-chain domain joined by a (Gly(4)Ser)(3) linker to a variable light-chain (V(L)) domain (kappa chain) with an 11-residue C-terminal Myc-tag. Its crystal structure was determined at 2.4 A resolution by molecular replacement with an R(cryst) of 19.0%. Five of the six antigen-binding loops, L1, L2, L3, H1 and H2, conformed to known canonical structures. The sixth loop, H3, displayed a unique structure, with a beta-hairpin loop and a bifurcated apex characterized by a buried Thr residue. In the crystal lattice, two MFE-23 molecules were associated back-to-back in a manner not seen before. The antigen-binding site displayed a large acidic region located mainly within the H2 loop and a large hydrophobic region within the H3 loop. Even though this structure is unliganded within the crystal, there is an unusually large region of contact between the H1, H2 and H3 loops and the beta-sheet of the V(L) domain of an adjacent molecule (strands DEBA) as a result of intermolecular packing. These interactions exhibited remarkably high surface and electrostatic complementarity. Of seven MFE-23 residues predicted to make contact with antigen, five participated in these lattice contacts, and this model for antigen binding is consistent with previously reported site-specific mutagenesis of MFE-23 and its effect on CEA binding.

Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold.

PubMed

Teruya, Kenta; Hattori, Yasunao; Shimamoto, Yasuhiro; Kobayashi, Kazuya; Sanjoh, Akira; Nakagawa, Atsushi; Yamashita, Eiki; Akaji, Kenichi

2016-11-04

Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2)  = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016. © 2015 Wiley Periodicals, Inc.

Single-crystal X-ray diffraction study of SrGeO3 high-pressure perovskite phase at 100 K

NASA Astrophysics Data System (ADS)

Nakatsuka, Akihiko; Arima, Hiroshi; Ohtaka, Osamu; Fujiwara, Keiko; Yoshiasa, Akira

2017-10-01

Single-crystal X-ray diffraction study of SrGeO3 perovskite (cubic; space group Pmɜ¯m) synthesized at 6 GPa and 1223 K was conducted at a low temperature of 100 K. The residual electron density revealed the presence of the bonding electron at the center of the Ge-O bond, in accordance with our previous conclusion that the Ge-O bond is strongly covalent. From comparison with our previous structure-refinement result at 296 K, the mean square displacement (MSD) of the O atom in the direction of the Ge-O bond is suggested to exhibit no significant temperature dependence, in contrast to that in the direction perpendicular to the bond. Thus, the strong covalency of the Ge-O bond can have a large influence on the temperature dependence of thermal vibration of the O atom.

New crystal structures in hexagonal CuInS2 nanocrystals

NASA Astrophysics Data System (ADS)

Shen, Xiao; Hernández-Pagan, Emil A.; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo, Juan C.; MacDonald, Janet E.; Pennycook, Stephen J.; Pantelides, Sokrates T.

2013-03-01

CuInS2 is one of the best candidate materials for solar energy harvesting. Its nanocrystals with a hexagonal lattice structure that is different from the bulk chalcopyrite phase have been synthesized by many groups. The structure of these CuInS2 nanocrystals has been previously identified as the wurtzite structure in which the copper and indium atoms randomly occupy the cation sites. Using first-principles total energy and electronic structure calculations based on density functional theory, UV-vis absorption spectroscopy, X-ray diffraction, and atomic resolution Z-contrast images obtained in an aberration-corrected scanning transmission electron microscope, we show that CuInS2 nanocrystals do not form random wurtzite structure. Instead, the CuInS2 nanocrystals consist of several wurtzite- related crystal structures with ordered cation sublattices, some of which are reported for the first time here. This work is supported by the NSF TN-SCORE (JEM), by NSF (WZ), by ORNL's Shared Research Equipment User Program (JCI) sponsored by DOE BES, by DOE BES Materials Sciences and Engineering Division (SJP, STP), and used resources of the National Energy Research Scientific Computing Center, supported by the DOE Office of Science under Contract No. DE-AC02-05CH11231.

Effect of coccolith polysaccharides isolated from the coccolithophorid, Emiliania huxleyi, on calcite crystal formation in in vitro CaCO3 crystallization.

PubMed

Kayano, Keisuke; Saruwatari, Kazuko; Kogure, Toshihiro; Shiraiwa, Yoshihiro

2011-02-01

Marine coccolithophorids (Haptophyceae) produce calcified scales "coccoliths" which are composed of CaCO(3) and coccolith polysaccharides (CP) in the coccolith vesicles. CP was previously reported to be composed of uronic acids and sulfated residues, etc. attached to the polymannose main chain. Although anionic polymers are generally known to play key roles in biomineralization process, there is no experimental data how CP contributes to calcite crystal formation in the coccolithophorids. CP used was isolated from the most abundant coccolithophorid, Emiliania huxleyi. CaCO(3) crystallization experiment was performed on agar template layered onto a plastic plate that was dipped in the CaCO(3) crystallization solution. The typical rhombohedral calcite crystals were formed in the absence of CP. CaCO(3) crystals formed on the naked plastic plate were obviously changed to stick-like shapes when CP was present in the solution. EBSD analysis proved that the crystal is calcite of which c-axis was elongated. CP in the solution stimulated the formation of tabular crystals with flat edge in the agarose gel. SEM and FIB-TEM observations showed that the calcite crystals were formed in the gel. The formation of crystals without flat edge was stimulated when CP was preliminarily added in the gel. These observations suggest that CP has two functions: namely, one is to elongate the calcite crystal along c-axis and another is to induce tabular calcite crystal formation in the agarose gel. Thus, CP may function for the formation of highly elaborate species-specific structures of coccoliths in coccolithophorids.

Proton-Induced Conductivity Enhancement in AlGaN/GaN HEMT Devices

NASA Astrophysics Data System (ADS)

Lee, In Hak; Lee, Chul; Choi, Byoung Ki; Yun, Yeseul; Chang, Young Jun; Jang, Seung Yup

2018-04-01

We investigated the influence of proton irradiation on the AlGaN/GaN high-electron-mobility transistor (HEMT) devices. Unlike previous studies on the degradation behavior upon proton irradiation, we observed improvements in their electrical conductivity and carrier concentration of up to 25% for the optimal condition. As we increased the proton dose, the carrier concentration and the mobility showed a gradual increase and decrease, respectively. From the photoluminescence measurements, we observed a reduction in the near-band-edge peak of GaN ( 366 nm), which correlate on the observed electrical properties. However, neither the Raman nor the X-ray diffraction analysis showed any changes, implying a negligible influence of protons on the crystal structures. We demonstrated that high-energy proton irradiation could be utilized to modify the transport properties of HEMT devices without damaging their crystal structures.

Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component

DOE PAGES

Hernandez, Carina; Birktoft, Jens J.; Ohayon, Yoel P.; ...

2017-10-05

There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. Furthermore, the work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%,more » and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding.« less

Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.

PubMed

Hernandez, Carina; Birktoft, Jens J; Ohayon, Yoel P; Chandrasekaran, Arun Richard; Abdallah, Hatem; Sha, Ruojie; Stojanoff, Vivian; Mao, Chengde; Seeman, Nadrian C

2017-11-16

There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. The work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%, and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding. Copyright © 2017 Elsevier Ltd. All rights reserved.

The significance of temperature dependence on the piezoelectric energy harvesting by using a phononic crystal

NASA Astrophysics Data System (ADS)

Aly, Arafa H.; Nagaty, Ahmed; Khalifa, Zaki; Mehaney, Ahmed

2018-05-01

In this study, an acoustic energy harvester based on a two-dimensional phononic crystal has been constructed. The present structure consists of silicon cylinders in the air background with a polyvinylidene fluoride cylinder as a defect to confine the acoustic energy. The presented energy harvester depends on the piezoelectric effect (using the piezoelectric material polyvinylidene fluoride) that converts the confined acoustic energy to electric energy. The maximum output voltage obtained equals 170 mV. Moreover, the results revealed that the output voltage can be increased with increasing temperature. In addition, the effects of the load resistance and the geometry of the piezoelectric material on the output voltage have been studied theoretically. Based on these results, all previous studies about energy harvesting in phononic structures must take temperature effects into account.

Projection structure of a ClC-type chloride channel at 6.5Å resolution

NASA Astrophysics Data System (ADS)

Mindell, Joseph A.; Maduke, Merritt; Miller, Christopher; Grigorieff, Nikolaus

2001-01-01

Virtually all cells in all eukaryotic organisms express ion channels of the ClC type, the only known molecular family of chloride-ion-selective channels. The diversity of ClC channels highlights the multitude and range of functions served by gated chloride-ion conduction in biological membranes, such as controlling electrical excitability in skeletal muscle, maintaining systemic blood pressure, acidifying endosomal compartments, and regulating electrical responses of GABA (γ-aminobutyric acid)-containing interneurons in the central nervous system. Previously, we expressed and purified a prokaryotic ClC channel homologue. Here we report the formation of two-dimensional crystals of this ClC channel protein reconstituted into phospholipid bilayer membranes. Cryo-electron microscopic analysis of these crystals yields a projection structure at 6.5Å resolution, which shows off-axis water-filled pores within the dimeric channel complex.

Redetermination of AgPO(3).

PubMed

Terebilenko, Katherina V; Zatovsky, Igor V; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2011-02-09

Single crystals of silver(I) polyphosphate(V), AgPO(3), were prepared via a phospho-ric acid melt method using a solution of Ag(3)PO(4) in H(3)PO(4). In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779-784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO(5)] polyhedra, giving rise to multidirectional ribbons, and from two types of PO(4) tetra-hedra linked into meandering chains (PO(3))(n) spreading parallel to the b axis with a repeat unit of four tetra-hedra. The calculated bond-valence sum value of one of the two Ag(I) ions indicates a significant strain of the structure.

Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component

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

Hernandez, Carina; Birktoft, Jens J.; Ohayon, Yoel P.

There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. Furthermore, the work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%,more » and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding.« less

Ultralight mesoporous magnetic frameworks by interfacial assembly of Prussian blue nanocubes.

PubMed

Kong, Biao; Tang, Jing; Wu, Zhangxiong; Wei, Jing; Wu, Hao; Wang, Yongcheng; Zheng, Gengfeng; Zhao, Dongyuan

2014-03-10

A facile approach for the synthesis of ultralight iron oxide hierarchical structures with tailorable macro- and mesoporosity is reported. This method entails the growth of porous Prussian blue (PB) single crystals on the surface of a polyurethane sponge, followed by in situ thermal conversion of PB crystals into three-dimensional mesoporous iron oxide (3DMI) architectures. Compared to previously reported ultralight materials, the 3DMI architectures possess hierarchical macro- and mesoporous frameworks with multiple advantageous features, including high surface area (ca. 117 m(2) g(-1)) and ultralow density (6-11 mg cm(-3)). Furthermore, they can be synthesized on a kilogram scale. More importantly, these 3DMI structures exhibit superparamagnetism and tunable hydrophilicity/hydrophobicity, thus allowing for efficient multiphase interfacial adsorption and fast multiphase catalysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Disappearance of the metal-insulator transition in iridate pyrochlores on approaching the ideal R2Ir2O7 stoichiometry

NASA Astrophysics Data System (ADS)

Sleight, Arthur W.; Ramirez, Arthur P.

2018-07-01

Recently, rare earth iridates, R2Ir2O7, with the pyrochlore structure have been intensively investigated due to their promise as either topological Mott insulators or Weyl semimetals. Single crystals of such pyrochlores with R = Nd, Sm, Eu, and Dy were prepared hydrothermally in sealed gold tubes at 975 K and show significantly higher electrical resistivities than previously reported for either crystals or polycrystalline samples. Furthermore, none of the present crystals exhibit the metal-insulator transition found for some samples of these phases. Lower resistivities are ascribed to lack of control of x and y in R2-xIr2O7-y in other more commonly used synthesis methods, yielding uncertainty in the Ir oxidation state. We also report resistivity of R2Ru2O7 crystals for R = Yb, Gd, Eu, and Nd, prepared in the same manner. These results suggest that the observed charge transport in hydrothermally grown iridate crystals is that of essentially stoichiometric phases and is consistent a with the existence of Weyl nodes.

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

DOE PAGES

Casadei, Cecilia M.; Tsai, Ching-Ju; Barty, Anton; ...

2018-01-01

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography atmore » X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.« less

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

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

Casadei, Cecilia M.; Tsai, Ching-Ju; Barty, Anton

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography atmore » X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.« less

The Structure of the Metal Transporter Tp34 and its Affinity for Divalent Metal Ions

NASA Astrophysics Data System (ADS)

Knutsen, Gregory; Deka, Ranjit; Brautigam, Chad; Tomchick, Diana; Machius, Mischa; Norgard, Michael

2007-10-01

Tp34 is periplasmic membrane protein of the nonculitvatable spirochete Treponema pallidum, the pathogen of syphillis. It was proposed that Tp34 is a divalent metal transporter, but the identity of the preferred metal ion(s) was unclear. In this study we investigated the ability of divalent metal ions to induce rTp34 dimerization using hydrodynamic techniques and determine the crystal structure of metal bound forms. Using analytical ultracentrifugation sedimentation velocity experiments, we determined that cobalt is superior to nickel at inducing the dimerization of rTp34. rTp34 was crystallized and selected crystals were incubated at a pH 7.5 with CuSO4 and NiSO4. Diffraction experiments were conducted and the processed electron density maps showed that copper was bound to the major metal binding site as well as to three additional minor binding sites. By contrast nickel was only bound to the major metal binding site in one monomer and to three additional minor sites. These results along with previous findings support evidence of Tp34 being involved with metal transport and/or iron utilization.

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex.

PubMed

Fan, Q R; Long, E O; Wiley, D C

2001-05-01

Inhibitory natural killer (NK) cell receptors down-regulate the cytotoxicity of NK cells upon recognition of specific class I major histocompatibility complex (MHC) molecules on target cells. We report here the crystal structure of the inhibitory human killer cell immunoglobulin-like receptor 2DL1 (KIR2DL1) bound to its class I MHC ligand, HLA-Cw4. The KIR2DL1-HLA-Cw4 interface exhibits charge and shape complementarity. Specificity is mediated by a pocket in KIR2DL1 that hosts the Lys80 residue of HLA-Cw4. Many residues conserved in HLA-C and in KIR2DL receptors make different interactions in KIR2DL1-HLA-Cw4 and in a previously reported KIR2DL2-HLA-Cw3 complex. A dimeric aggregate of KIR-HLA-C complexes was observed in one KIR2DL1-HLA-Cw4 crystal. Most of the amino acids that differ between human and chimpanzee KIRs with HLA-C specificities form solvent-accessible clusters outside the KIR-HLA interface, which suggests undiscovered interactions by KIRs.

Revisiting polarimetry near the isotropic point of an optically active, non-enantiomorphous, molecular crystal.

PubMed

Martin, Alexander T; Tan, Melissa; Nichols, Shane M; Timothy, Emily; Kahr, Bart

2018-07-01

Accurate polarimetric measurements of the optical activity of crystals along low symmetry directions are facilitated by isotropic points, frequencies where dispersion curves of eigenrays cross and the linear birefringence disappears. We report here the optical properties and structure of achiral, uniaxial (point group D 2d ) potassium trihydrogen di-(cis-4-cyclohexene-1,2-dicarboxylate) dihydrate, whose isotropic point was previously detected (S. A. Kim, C. Grieswatch, H. Küppers, Zeit. Krist. 1993; 208:219-222) and exploited for a singular measurement of optical activity normal to the optic axis. The crystal structure associated with the aforementioned study was never published. We report it here, confirming the space group assignment I 4¯c2, along with the frequency dependence of the fundamental optical properties and the constitutive tensors by fitting optical dispersion relations to measured Mueller matrix spectra. k-Space maps of circular birefringence and of the Mueller matrix near the isotropic wavelength are measured and simulated. The signs of optical rotation are correlated with the absolute crystallographic directions. © 2018 Wiley Periodicals, Inc.

A Novel High-Sensitivity, Low-Power, Liquid Crystal Temperature Sensor

PubMed Central

Algorri, José Francisco; Urruchi, Virginia; Bennis, Noureddine; Sánchez-Pena, José Manuel

2014-01-01

A novel temperature sensor based on nematic liquid crystal permittivity as a sensing magnitude, is presented. This sensor consists of a specific micrometric structure that gives considerable advantages from other previous related liquid crystal (LC) sensors. The analytical study reveals that permittivity change with temperature is introduced in a hyperbolic cosine function, increasing the sensitivity term considerably. The experimental data has been obtained for ranges from −6 °C to 100 °C. Despite this, following the LC datasheet, theoretical ranges from −40 °C to 109 °C could be achieved. These results have revealed maximum sensitivities of 33 mVrms/°C for certain temperature ranges; three times more than of most silicon temperature sensors. As it was predicted by the analytical study, the micrometric size of the proposed structure produces a high output voltage. Moreover the voltage's sensitivity to temperature response can be controlled by the applied voltage. This response allows temperature measurements to be carried out without any amplification or conditioning circuitry, with very low power consumption. PMID:24721771

Vortex lattice structures in YNi{sub 2}B{sub 2}C

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

Yethiraj, M.; Paul, D.M.; Tomy, C.V.

The authors observe a flux lattice with square symmetry in the superconductor YNi{sub 2}B{sub 2}C when the applied field is parallel to the c-axis of the crystal. A square lattice observed previously in the isostructural magnetic analog ErNi{sub 2}B{sub 2}C was attributed to the interaction between magnetic order in that system and the flux lattice. Since the Y-based compound does not order magnetically, it is clear that the structure of the flux lattice is unrelated to magnetic order. In fact, they show that the flux lines have a square cross-section when the applied field is parallel to the c-axis ofmore » the crystal, since the measured penetration depth along the 100 crystal direction is larger than the penetration depth along the 110 by approximately 60%. This is the likely reason for the square symmetry of the lattice. Although they find considerable disorder in the arrangement of the flux lines at 2.5T, no melting of the vortex lattice was observed.« less

Vortex lattice structures in YNi{sub 2}B{sub 2}C

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

Yethiraj, M.; Paul, D.M.; Tomy, C.V.

We observe a flux lattice with square symmetry in the superconductor YNi{sub 2}B{sub 2}C when the applied field is parallel to the c-axis of the crystal. A square lattice observed previously in the isostructural magnetic analog ErNi{sub 2}B{sub 2}C was attributed to the interaction between magnetic order in that system and the flux lattice. Since the Y-based compound does not order magnetically, it is clear that the structure of the flux lattice is unrelated to magnetic order. In fact, we show that the flux lines have a square cross-section when the applied field is parallel to the c-axis of themore » crystal, since the measured penetration depth along the 110 crystal direction is smaller than the penetration depth along the 100 by approximately 30%. This causes the square symmetry of the lattice. Although we find considerable disorder in the arrangement of the flux lines at 2.5T, no melting of the vortex lattice was observed.« less

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

PubMed Central

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S.; Zatsepin, Nadia A.; Barty, Anton; Benner, W. Henry; Boutet, Sébastien; Feld, Geoffrey K.; Hau-Riege, Stefan P.; Kirian, Richard A.; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I.; Pardini, Tommaso; Segelke, Brent; Williams, Garth J.; Spence, John C. H.; Abela, Rafael; Coleman, Matthew; Evans, James E.; Schertler, Gebhard F. X.; Frank, Matthias; Li, Xiao-Dan

2014-01-01

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution. PMID:24914166

Biomolecular crystals for material applications and a mechanistic study of an iron oxide nanoparticle synthesis

NASA Astrophysics Data System (ADS)

Falkner, Joshua Charles

The three projects within this work address the difficulties of controlling biomolecular crystal formats (i.e. size and shape), producing 3-D ordered composite materials from biomolecular crystal templates, and understanding the mechanism of a practical iron oxide synthesis. The unifying thread consistent throughout these three topics is the development of methods to manipulate nanomaterials using a bottom-up approach. Biomolecular crystals are nanometer to millimeter sized crystals that have well ordered mesoporous solvent channels. The overall physical dimensions of these crystals are highly dependent on crystallization conditions. The controlled growth of micro- and nanoprotein crystals was studied to provide new pathways for creating smaller crystalline protein materials. This method produced tetragonal hen egg-white lysozyme crystals (250--100,000 nm) with near monodisperse size distributions (<15%). With this degree of control, existing protein crystal applications such as drug delivery and analytical sensors can reach their full potential. Applications for larger crystals with inherently ubiquitous pore structures could extend to materials used for membranes or templates. In this work, the porous structure of larger cowpea mosaic virus crystals was used to template metal nanoparticle growth within the body centered cubic crystalline network. The final composite material was found to have long range ordering of palladium and platinum nonocrystal aggregates (10nm) with symmetry consistent to the virus template. Nanoparticle synthesis itself is an immense field of study with an array of diverse applications. The final piece of this work investigates the mechanism behind a previously developed iron oxide synthesis to gain more understanding and direction to future synthesis strategies. The particle growth mechanism was found to proceed by the formation of a solvated iron(III)oleate complex followed by a reduction of iron (III) to iron (II). This unstable iron(II) nucleates to form a wustite (FeO) core which serves as an epitaxial surface for the magnetite (Fe3O4) shell growth. This method produces spherical particles (6-60nm) with relative size distributions of less than 15%.

Architecture of Columnar Nacre, and Implications for Its Formation Mechanism

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

Metzler, Rebecca A.; Olabisi, Ronke M.; Coppersmith, Susan N.

2007-06-29

We analyze the structure of Haliotis rufescens nacre, or mother-of-pearl, using synchrotron spectromicroscopy and x-ray absorption near-edge structure spectroscopy. We observe imaging contrast between adjacent individual nacre tablets, arising because different tablets have different crystal orientations with respect to the radiation's polarization vector. Comparing previous data and our new data with models for columnar nacre growth, we find the data are most consistent with a model in which nacre tablets are nucleated by randomly distributed sites in the organic matrix layers.

L-Cysteine halogenides: A new family of salts with an L-cysteine⋯L-cysteinium dimeric cation

NASA Astrophysics Data System (ADS)

Ghazaryan, V. V.; Minkov, V. S.; Boldyreva, E. V.; Petrosyan, A. M.

2016-10-01

Two L-cysteinium-halogenides with (L-cysteine···L-cysteinium) dimeric cations have been obtained, (L-Cys⋯L-Cys+)·Cl-, and (L-Cys⋯L-Cys+)·Br-. Both salts crystallize in monoclinic space group P21. Although these salts have the same dimeric cations and isotypical halogen anions, crystal packing is different. The main difference between the two salts rests in the conformation of (L-Cys⋯L-Cys+) dimeric cation, which also differs from that of the dimeric cation in the previously reported compound L-Cys+(L-Cys⋯L-Cys+)·F-·(F-⋯HF). The dimeric cation is formed by a very short O-H⋯O hydrogen bond with d(O···O) of 2.449(2) Å and 2.435(11) Å in the chloride and bromide, respectively. In addition to crystal structure analysis, Infrared and Raman spectra have been registered and discussed with a particular focus on intermolecular interactions. The L-Cys+·Br-·H2O salt with a simple L-cysteinium cation was also obtained and the crystal structure solved. It resembles its chloride analogue, L-Cys+·Cl-·H2O.

The Feasibility of Bulk Crystallization as an Industrial Purification and Production Technique for Proteins

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Forsythe, Elizabeth L.; Johns, Michael R.; Pusey, Marc L.; White, Edward T.

1998-01-01

Bulk crystallization in stirred vessels is used industrially for the recovery and purification of many inorganic and organic materials. Although much has been written on the crystallization of proteins for X-ray diffraction analysis, very little has been reported on the application of bulk crystallization in stirred vessels. In this study, a 1-liter, seeded, stirred, batch crystallizer was used with ovalbumin as a model protein to test the feasibility of this crystallization method as a recovery and purification process for proteins. Results were obtained for ovalbumin solubility, nucleation thresholds, crystal breakage and crystal growth kinetics in bulk solution under a range of operating conditions of pH and ammonium sulphate concentration (Judge et al., 1996). Experiments were also performed to determine the degree of purification that can be achieved by the crystallization of ovalbumin from a mixture of proteins. The effect of the presence of these proteins upon the ovalbumin crystal growth kinetics was also investigated (Judge et al., 1995). All of these aspects are essential for the design of bulk crystallization processes which have not previously been reported for proteins. Results from a second study that investigated the effect of structurally different proteins on the solubility, crystal growth rates and crystal purity of chicken egg white lysozyme are also presented (Judge et al., 1997). In this case face growth rates were measured using lysozyme purified by liquid chromatography and the effect of the addition of specific protein impurities were observed on the (110) and (101) crystal faces. In these two studies the results are presented to show the feasibility and purifying ability of crystallization as a production process for proteins.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Cellulose Tailored Anatase TiO2 Nanospindles in Three-Dimensional Graphene Composites for High-Performance Supercapacitors.

PubMed

Ding, Yangbin; Bai, Wei; Sun, Jinhua; Wu, Yu; Memon, Mushtaque A; Wang, Chao; Liu, Chengbin; Huang, Yong; Geng, Jianxin

2016-05-18

The morphologies of transition metal oxides have decisive impact on the performance of their applications. Here, we report a new and facile strategy for in situ preparation of anatase TiO2 nanospindles in three-dimensional reduced graphene oxide (RGO) structure (3D TiO2@RGO) using cellulose as both an intermediate agent eliminating the negative effect of graphene oxide (GO) on the growth of TiO2 crystals and as a structure-directing agent for the shape-controlled synthesis of TiO2 crystals. High-resolution transmission electron microscopy and X-ray diffractometer analysis indicated that the spindle shape of TiO2 crystals was formed through the restriction of the growth of high energy {010} facets due to preferential adsorption of cellulose on these facets. Because of the 3D structure of the composite, the large aspect ratio of the TiO2 nanospindles, and the exposed high-energy {010} facets of the TiO2 crystals, the 3D TiO2@RGO(Ce 1.7) exhibited excellent capacitive performance as an electrode material for supercapacitors, with a high specific capacitance (ca. 397 F g(-1)), a high energy density (55.7 Wh kg(-1)), and a high power density (1327 W kg(-1)) on the basis of the masses of RGO and TiO2. These levels of capacitive performance far exceed those of previously reported TiO2-based composites.

Nematic-like stable glasses without equilibrium liquid crystal phases

DOE Data Explorer

Gomez, Jaritza [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Gujral, Ankit [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Huang, Chengbin [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Bishop, Camille [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Yu, Lian [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Ediger, Mark [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

2017-02-01

We report the thermal and structural properties of glasses of posaconazole, a rod-like molecule, prepared using physical vapor deposition (PVD). PVD glasses of posaconazole can show substantial molecular orientation depending upon the choice of substrate temperature, Tsubstrate, during deposition.Ellipsometry and IR measurements indicate that glasses prepared at Tsubstrate very near the glass transition temperature (Tg) are highly ordered. For these posaconazole glasses, the orientation order parameter is similar to that observed in macroscopically aligned nematic liquid crystals, indicating that the molecules are mostly parallel to one another and perpendicular to the interface. To our knowledge, these are the most anisotropic glasses ever prepared by PVD from a molecule that does not form equilibrium liquid crystal phases. These results are consistent with a previously proposed mechanism in which molecular orientation in PVD glasses is inherited from the orientation present at the free surface of the equilibrium liquid. This mechanism suggests that molecular orientation at the surface of the equilibrium liquid of posaconazole is nematic-like. Posaconazole glasses can show very high kinetic stability; the isothermal transformation of a 400 nm glass into the supercooled liquid occurs via a propagating front that originates at the free surface and requires ~105 times the structural relaxation time of the liquid (τα). We also studied the kinetic stability of PVD glasses of itraconazole, which is a structurally similar molecule with equilibrium liquid crystal phases. While itraconazole glasses can be even more anisotropic than posaconazole glasses, they exhibit lower kinetic stability.

Cooperativity in plastic crystals

NASA Astrophysics Data System (ADS)

Pieruccini, Marco; Tombari, Elpidio

2018-03-01

A statistical mechanical model previously adopted for the analysis of the α -relaxation in structural glass formers is rederived within a general theoretical framework originally developed for systems approaching the ideal glassy state. The interplay between nonexponentiality and cooperativity is reconsidered in the light of energy landscape concepts. The method is used to estimate the cooperativity in orientationally disordered crystals, either from the analysis of literature data on linear dielectric response or from the enthalpy relaxation function obtained by temperature-modulated calorimetry. Knowledge of the specific heat step due to the freezing of the configurational or conformational modes at the glass transition is needed in order to properly account for the extent to which the relaxing system deviates from equilibrium during the rearrangement processes. A number of plastic crystals have been analyzed, and relatively higher cooperativities are found in the presence of hydrogen bonding interaction.

Early Onset of Kinetic Roughening due to a Finite Step Width in Hematin Crystallization

NASA Astrophysics Data System (ADS)

Olafson, Katy N.; Rimer, Jeffrey D.; Vekilov, Peter G.

2017-11-01

The structure of the interface of a growing crystal with its nutrient phase largely determines the growth dynamics. We demonstrate that hematin crystals, crucial for the survival of malaria parasites, transition from faceted to rough growth interfaces at increasing thermodynamic supersaturation Δ μ . Contrary to theoretical predictions and previous observations, this transition occurs at moderate values of Δ μ . Moreover, surface roughness varies nonmonotonically with Δ μ , and the rate constant for rough growth is slower than that resulting from nucleation and spreading of layers. We attribute these unexpected behaviors to the dynamics of step growth dominated by surface diffusion and the loss of identity of nuclei separated by less than the step width w . We put forth a general criterion for the onset of kinetic roughening using w as a critical length scale.

Multi-crystal native SAD analysis at 6 keV.

PubMed

Liu, Qun; Guo, Youzhong; Chang, Yanqi; Cai, Zheng; Assur, Zahra; Mancia, Filippo; Greene, Mark I; Hendrickson, Wayne A

2014-10-01

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121

PubMed Central

Quistgaard, Esben M.; Martinez Molledo, Maria

2017-01-01

Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins. PMID:28264013

Structure of the Intermediate Filament-Binding Region of Desmoplakin

DOE PAGES

Kang, Hyunook; Weiss, Thomas M.; Bang, Injin; ...

2016-01-25

Here, desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of themore » full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with R g = 51.5 Å and D max = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions.« less

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, K.; Ho, J. X.; Keeling, K.; Gilliland, G. L.; Ji, X.; Ruker, F.; Carter, D. C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) (Muster T et al., 1993, J Virol 67:6642-6647) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry 31:10169-10184) was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(3)2(1)2, with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

Expression, purification and preliminary X-ray analysis of the C-terminal domain of an arginine repressor protein from Mycobacterium tuberculosis

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

Lu, George J.; Garen, Craig R.; Cherney, Maia M.

2007-11-01

The C-terminal portion of the arginine repressor protein from M. tuberculosis H37Rv has been crystallized. The complete transcriptional factor regulates arginine biosynthesis by binding operator DNA when arginine is bound at the C-terminal domain. The gene product of an open reading frame Rv1657 from Mycobacterium tuberculosis is a putative arginine repressor protein (ArgR), a transcriptional factor that regulates the expression of arginine-biosynthetic enzymes. Rv1657 was expressed and purified and a C-terminal domain was crystallized using the hanging-drop vapour-diffusion method. Diffraction data were collected and processed to a resolution of 2.15 Å. The crystals belong to space group P1 and themore » Matthews coefficient suggests that the crystals contain six C-terminal domain molecules per unit cell. Previous structural and biochemical studies on the arginine repressor proteins from other organisms have likewise shown the presence of six molecules per unit cell.« less

Structural Studies of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Tetramer in Complex with Its Receptor, Sialyllactose

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

Yuan, Ping; Thompson, Thomas B.; Wurzburg, Beth A.

2010-03-08

The paramyxovirus hemagglutinin-neuraminidase (HN) functions in virus attachment to cells, cleavage of sialic acid from oligosaccharides, and stimulating membrane fusion during virus entry into cells. The structural basis for these diverse functions remains to be fully understood. We report the crystal structures of the parainfluenza virus 5 (SV5) HN and its complexes with sialic acid, the inhibitor DANA, and the receptor sialyllactose. SV5 HN shares common structural features with HN of Newcastle disease virus (NDV) and human parainfluenza 3 (HPIV3), but unlike the previously determined HN structures, the SV5 HN forms a tetramer in solution, which is thought to bemore » the physiological oligomer. The sialyllactose complex reveals intact receptor within the active site, but no major conformational changes in the protein. The SV5 HN structures do not support previously proposed models for HN action in membrane fusion and suggest alternative mechanisms by which HN may promote virus entry into cells.« less

Fabrication of one-dimensional alumina photonic crystals by anodization using a modified pulse-voltage method

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

Li, Shou-Yi; Wang, Jian, E-mail: wangjian@nwnu.edu.cn; Wang, Gang

2015-08-15

Highlights: • The alumina multilayer structure with alternating high and low refractive index is fabricated. • This multilayer shows a strong photonic band gap (PBG) and vivid film colors. • The first PBG could be modulated easily by varying the duration time of constant high or low voltages. • Fabrication of the photonic crystal is obtained by directly electrochemical anodization. • The formation mechanism of multilayer is also discussed. - Abstract: The alumina nanolayer structure with alternating high and low porosities is conveniently fabricated by applying a modified pulse voltage waveform with constant high and low voltage. This structure showsmore » the well-defined layer in a long-range structural periodicity leads to a strong photonic band gap (PBG) from visible to near infrared and brilliant film colors. Compared with the previous reported tuning method, this method is more simple and flexible in tuning the PBG of photonic crystals (PCs). The effect of duration time of high, low and 0 V voltages on PBG is discussed. The first PBG could be modulated easily from the visible to near infrared region by varying the duration time of constant high or low voltages. It is also found that the 0 V lasting for appropriate time is helpful to improve the quality of the PCs. The formation mechanism of multilayer is also discussed.« less

Regulation of Silk Material Structure by Temperature-Controlled Water Vapor Annealing

PubMed Central

Hu, Xiao; Shmelev, Karen; Sun, Lin; Gil, Eun-Seok; Park, Sang-Hyug; Cebe, Peggy; Kaplan, David L.

2011-01-01

We present a simple and effective method to obtain refined control of the molecular structure of silk biomaterials through physical temperature-controlled water vapor annealing (TCWVA). The silk materials can be prepared with control of crystallinity, from a low content using conditions at 4°C (alpha-helix dominated silk I structure), to highest content of ~60% crystallinity at 100°C (beta-sheet dominated silk II structure). This new physical approach covers the range of structures previously reported to govern crystallization during the fabrication of silk materials, yet offers a simpler, green chemistry, approach with tight control of reproducibility. The transition kinetics, thermal, mechanical, and biodegradation properties of the silk films prepared at different temperatures were investigated and compared by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), uniaxial tensile studies, and enzymatic degradation studies. The results revealed that this new physical processing method accurately controls structure, in turn providing control of mechanical properties, thermal stability, enzyme degradation rate, and human mesenchymal stem cell interactions. The mechanistic basis for the control is through the temperature controlled regulation of water vapor, to control crystallization. Control of silk structure via TCWVA represents a significant improvement in the fabrication of silk-based biomaterials, where control of structure-property relationships is key to regulating material properties. This new approach to control crystallization also provides an entirely new green approach, avoiding common methods which use organic solvents (methanol, ethanol) or organic acids. The method described here for silk proteins would also be universal for many other structural proteins (and likely other biopolymers), where water controls chain interactions related to material properties. PMID:21425769

The X-ray Crystal Structure of the Phage Tail Terminator Protein Reveals the Biologically Relevant Hexameric Rang Structure and Demonstrates a Conserved mechanism of Tail Termination among Divrse Long Tailed Phages

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

Pell, L.; Liu, A; Edmonds, L

The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. Here, we present the 2.7-A crystal structure of a hexameric ring of gpU, the TrP of phage ?. Using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. Comparison of the hexameric crystal structure with the solution structure of gpU that we previously solved using NMR spectroscopy shows large structural changesmore » occurring upon multimerization and suggests a mechanism that allows gpU to remain monomeric at high concentrations on its own, yet polymerize readily upon contact with an assembled tail tube. The gpU hexamer displays several flexible loops that play key roles in head and tail binding, implying a role for disorder-to-order transitions in controlling assembly as has been observed with other ? morphogenetic proteins. Finally, we have found that the hexameric structure of gpU is very similar to the structure of a putative TrP from a contractile phage tail even though it displays no detectable sequence similarity. This finding coupled with further bioinformatic investigations has led us to conclude that the TrPs of non-contractile-tailed phages, such as ?, are evolutionarily related to those of contractile-tailed phages, such as P2 and Mu, and that all long-tailed phages may utilize a conserved mechanism for tail termination.« less

Crystal structures of (Mg1-x,Fex)SiO3postperovskite at high pressures

PubMed Central

Yamanaka, Takamitsu; Hirose, Kei; Mao, Wendy L.; Meng, Yue; Ganesh, P.; Shulenburger, Luke; Shen, Guoyin; Hemley, Russell J.

2012-01-01

X-ray diffraction experiments on postperovskite (ppv) with compositions (Mg0.9Fe0.1)SiO3 and (Mg0.6Fe0.4)SiO3 at Earth core-mantle boundary pressures reveal different crystal structures. The former adopts the CaIrO3-type structure with space group Cmcm, whereas the latter crystallizes in a structure with the Pmcm (Pmma) space group. The latter has a significantly higher density (ρ = 6.119(1) g/cm3) than the former (ρ = 5.694(8) g/cm3) due to both the larger amount of iron and the smaller ionic radius of Fe2+ as a result of an electronic spin transition observed by X-ray emission spectroscopy (XES). The smaller ionic radius for low-spin compared to high-spin Fe2+ also leads to an ordered cation distribution in the M1 and M2 crystallographic sites of the higher density ppv structure. Rietveld structure refinement indicates that approximately 70% of the total Fe2+ in that phase occupies the M2 site. XES results indicate a loss of 70% of the unpaired electronic spins consistent with a low spin M2 site and high spin M1 site. First-principles calculations of the magnetic ordering confirm that Pmcm with a two-site model is energetically more favorable at high pressure, and predict that the ordered structure is anisotropic in its electrical and elastic properties. These results suggest that interpretations of seismic structure in the deep mantle need to treat a broader range of mineral structures than previously considered. PMID:22223656

The crystal structure of augmenter of liver regeneration: A mammalian FAD-dependent sulfhydryl oxidase

PubMed Central

Wu, Chia-Kuei; Dailey, Tamara A.; Dailey, Harry A.; Wang, Bi-Cheng; Rose, John P.

2003-01-01

The crystal structure of recombinant rat augmenter of liver regeneration (ALRp) has been determined to 1.8 Å. The protein is a homodimer, stabilized by extensive noncovalent interactions and a network of hydrogen bonds, and possesses a noncovalently bound FAD in a motif previously found only in the related protein ERV2p. ALRp functions in vitro as a disulfide oxidase using dithiothreitol as reductant. Reduction of the flavin by DTT occurs under aerobic conditions resulting in a spectrum characteristic of a neutral semiquinone. This semiquinone is stable and is only fully reduced by addition of dithionite. Mutation of either of two cysteine residues that are located adjacent to the FAD results in inactivation of the oxidase activity. A comparison of ALRp with ERV2p is made that reveals a number of significant structural differences, which are related to the in vivo functions of these two proteins. Possible physiological roles of ALR are examined and a hypothesis that it may serve multiple roles is proposed. PMID:12717032

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.

PubMed

Isupov, Michail N; Schröder, Ewald; Gibson, Robert P; Beecher, Jean; Donadio, Giuliana; Saneei, Vahid; Dcunha, Stephlina A; McGhie, Emma J; Sayer, Christopher; Davenport, Colin F; Lau, Peter C; Hasegawa, Yoshie; Iwaki, Hiroaki; Kadow, Maria; Balke, Kathleen; Bornscheuer, Uwe T; Bourenkov, Gleb; Littlechild, Jennifer A

2015-11-01

The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

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

Wilson, S. R.; Mendelev, M. I., E-mail: mendelev@ameslab.gov

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, wemore » found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).« less

Lattice dynamics of A Sb2O6 (A =Cu , Co) with trirutile structure

NASA Astrophysics Data System (ADS)

Maimone, D. T.; Christian, A. B.; Neumeier, J. J.; Granado, E.

2018-03-01

Raman spectroscopy experiments on single crystals of CuSb2O6 and CoSb2O6 quasi-one-dimensional antiferromagnets with trirutile crystal structure were performed, with a focus on the first material. The observed Raman-active phonon modes and previously reported infrared-active modes were identified with the aid of ab initio lattice dynamics calculations. The structural transition between monoclinic β -CuSb2O6 and tetragonal α -CuSb2O6 phases at Ts=400 K is manifested in our spectra by a "repulsion" of two accidentally quasidegenerate symmetric modes below Ts, caused by a phonon mixing effect that is only operative in the monoclinic β -CuSb2O6 phase due to symmetry restrictions. Also, two specific phonons, associated with CuO6 octahedra rotation and with a Jahn-Teller elongation mode, soften and broaden appreciably as T →Ts . A crossover from a displacive to an order-disorder transition at Ts is inferred.

Proteolysis of truncated hemolysin A yields a stable dimerization interface

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

Novak, Walter R. P.; Bhattacharyya, Basudeb; Grilley, Daniel P.

2017-02-21

Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interfacemore » is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.« less

Crystal Structures of Human and Staphylococcus aureus Pyruvate Carboxylase and Molecular Insights into the Carboxyltransfer Reaction

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

Xiang,S.; Tong, L.

2008-01-01

Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-Angstroms resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in themore » active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.« less

Crystal Structure of the Extracellular Cholinesterase-Like Domain from Neuroligin-2

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

Koehnke,J.; Jin, X.; Budreck, E.

Neuroligins (NLs) are catalytically inactive members of a family of cholinesterase-like transmembrane proteins that mediate cell adhesion at neuronal synapses. Postsynaptic neuroligins engage in Ca2+-dependent transsynaptic interactions via their extracellular cholinesterase domain with presynaptic neurexins (NRXs). These interactions may be regulated by two short splice insertions (termed A and B) in the NL cholinesterase domain. Here, we present the 3.3- Angstroms crystal structure of the ectodomain from NL2 containing splice insertion A (NL2A). The overall structure of NL2A resembles that of cholinesterases, but several structural features are unique to the NL proteins. First, structural elements surrounding the esterase active-site regionmore » differ significantly between active esterases and NL2A. On the opposite surface of the NL2A molecule, the positions of the A and B splice insertions identify a candidate NRX interaction site of the NL protein. Finally, sequence comparisons of NL isoforms allow for mapping the location of residues of previously identified mutations in NL3 and NL4 found in patients with autism spectrum disorders. Overall, the NL2 structure promises to provide a valuable model for dissecting NL isoform- and synapse-specific functions.« less