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Crystallographic Structure (crystallographic + structure)
Kinds of Crystallographic Structure Selected AbstractsEffects of MgCl2 Crystallographic Structure on Active Centre Formation in Immobilized Single-Centre and Ziegler,Natta Catalysts for Ethylene PolymerizationMACROMOLECULAR RAPID COMMUNICATIONS, Issue 21 2008Rubin Huang Abstract The ability of a MgCl2 support to activate a transition metal catalyst has been found to depend both on the crystallographic structure of the support and on the nature of the catalyst. A high degree of crystallographic disorder can be very effective for the immobilization and activation of titanium and vanadium complexes, but is not necessarily effective for zirconocene activation. A highly disordered support prepared by the reaction of MgBu2 with HCl gave high activity with TiCl4 but low activity with (n -PrCp)2ZrCl2. High polymerization activities with the zirconocene were only obtained with supports of type MgCl2/AlRn(OEt)3,n prepared from the reaction of AlR3 with MgCl2,·,1.1EtOH. These supports are characterized by additional peaks in the X-ray diffraction pattern, indicating the presence of a crystalline structure which is absent in the other supports and contains highly Lewis acidic sites able to generate the active metallocenium species. [source] Bis-Tetrahydrofuran: a Privileged Ligand for Darunavir and a New Generation of HIV Protease Inhibitors That Combat Drug ResistanceCHEMMEDCHEM, Issue 9 2006Two inhibitors that incorporate bis-THF as an effective high-affinity P2 ligand for the HIV-1 protease substrate binding site maintain impressive potency against mutant strains resistant to currently approved protease inhibitors. Crystallographic structures of protein,ligand complexes help to explain the superior antiviral property of these inhibitors and their potency against a wide spectrum of HIV-1 strains. [source] Mutagenesis of ,-tubulin cysteine residues in Saccharomyces cerevisiae: Mutation of cysteine 354 results in cold-stable microtubulesCYTOSKELETON, Issue 2 2001Mohan L. Gupta Jr. Abstract Cysteine residues play important roles in the control of tubulin function. To determine which of the six cysteine residues in ,-tubulin are critical to tubulin function, we mutated the cysteines in Saccharomyces cerevisiae ,-tubulin individually to alanine and serine residues. Of the twelve mutations, only three produced significant effects: C12S, C354A, and C354S. The C12S mutation was lethal in the haploid, but the C12A mutation had no observable phenotype. Based on interactive views of the electron crystallographic structure of tubulin, we suggest that substitution of serine for cysteine at this position has a destabilizing effect on the interaction of tubulin with the exchangeable GTP. The two C354 mutations, although not lethal, produced dramatic effects on microtubules and cellular processes that require microtubules. The C354 mutant cells had decreased growth rates, a slowed mitosis, increased resistance to benomyl, and impaired nuclear migration and spindle assembly. The C354A mutation produced a more severe phenotype than the C354S mutation: the haploid cells had chromosome segregation defects, only 50% of cells in a culture were viable, and a significant percentage of the cells were misshapened. Cytoplasmic microtubules in the C354S and C354A cells were longer than in the control strain and spindle structures appeared shorter and thicker. Both cytoplasmic and spindle microtubules in the two C354 mutants were extremely stable to cold temperature. After 24 h at 4°C, the microtubules were still present and, in fact, very long and thick tubulin polymers had formed. Evidence exists to indicate that the C354 residue in mammalian tubulin is near the colchicine binding site and the electron crystal structure of tubulin places the residue at the interface between the ,- and ,-subunits. The sulfhydryl group is situated in a polar environment, which may explain why the alanine mutation is more severe than the serine mutation. When the C12S and the two C354 mutations were made in a diploid strain, the mutated tubulin was incorporated into microtubules and the resulting heterozygotes had phenotypes that were intermediate between those of the mutated haploids and the wild-type strains. The results suggest that the C12 and C354 residues play important roles in the structure and function of tubulin. Cell Motil. Cytoskeleton 49:67,77, 2001. © 2001 Wiley-Liss, Inc. [source] Direct Access to Furanosidic Eight-Membered Ulosonic Esters from cis -,,,-Epoxy AldehydesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2003Claudia H. Sugisaki Abstract Direct access to bicyclic precursors of octulosonic acids is achieved by treatment of differentially (or not) protected ,,,-bis(silyloxy) cis -,,,-epoxy aldehydes with ethyl 2-(trimethylsilyloxy)-2-propenoate in the presence of boron trifluoride,diethyl ether. An X-ray crystallographic structure of a bicycle (compound 33a) was obtained and used to determine the absolute configurations of the different stereogenic centers and thus the diastereoselective preference of the aldol reaction (syn) and the regioselectivity of the epoxide ring-opening (C-6 atom). Functionalization and opening of the bicyclic compound to afford octulosonic analogues in their furanoside forms was studied. An octulosonic 8-phosphate analogue has been synthesized. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] From the Atomic Jump Frequencies to the Phenomenological Transport Coefficients,ADVANCED ENGINEERING MATERIALS, Issue 12 2006M. Nastar The SCMF theory based on an atomic model of atom-vacancy exchange frequencies yields general expressions of the phenomenological coefficients Lij of a multi-component alloy with any crystallographic structure. The limitations and future improvements of the Self-Consistent Mean-Field (SCMF) approach are easily related to the statistical approximation of the thermodynamic correlations and to the time-dependent effective interactions used to describe the kinetic correlations induced by the vacancy diffusion mechanism. [source] X-ray crystallography and structural stability of digestive lysozyme from cow stomachFEBS JOURNAL, Issue 8 2009Yasuhiro Nonaka In ruminants, some leaf-eating animals, and some insects, defensive lysozymes have been adapted to become digestive enzymes, in order to digest bacteria in the stomach. Digestive lysozyme has been reported to be resistant to protease and to have optimal activity at acidic pH. The structural basis of the adaptation providing persistence of lytic activity under severe gastric conditions remains unclear. In this investigation, we obtained the crystallographic structure of recombinant bovine stomach lysozyme 2 (BSL2). Our denaturant and thermal unfolding experiments revealed that BSL2 has high conformational stability at acidic pH. The high stability in acidic solution could be related to pepsin resistance, which has been previously reported for BSL2. The crystal structure of BSL2 suggested that negatively charged surfaces, a shortened loop and salt bridges could provide structural stability, and thus resistance to pepsin. It is likely that BSL2 loses lytic activity at neutral pH because of adaptations to resist pepsin. [source] Interflavin electron transfer in human cytochrome P450 reductase is enhanced by coenzyme bindingFEBS JOURNAL, Issue 12 2003Relaxation kinetic studies with coenzyme analogues The role of coenzyme binding in regulating interflavin electron transfer in human cytochrome P450 reductase (CPR) has been studied using temperature-jump spectroscopy. Previous studies [Gutierrez, A., Paine, M., Wolf, C.R., Scrutton, N.S., & Roberts, G.C.K. Biochemistry (2002) 41, 4626,4637] have shown that the observed rate, 1/,, of interflavin electron transfer (FADsq , FMNsq,FADox , FMNhq) in CPR reduced at the two-electron level with NADPH is 55 ± 2 s,1, whereas with dithionite-reduced enzyme the observed rate is 11 ± 0.5 s,1, suggesting that NADPH (or NADP+) binding has an important role in controlling the rate of internal electron transfer. In relaxation experiments performed with CPR reduced at the two-electron level with NADH, the observed rate of internal electron transfer (1/, = 18 ± 0.7 s,1) is intermediate in value between those seen with dithionite-reduced and NADPH-reduced enzyme, indicating that the presence of the 2,-phosphate is important for enhancing internal electron transfer. To investigate this further, temperature jump experiments were performed with dithionite-reduced enzyme in the presence of 2,,5,-ADP and 2,-AMP. These two ligands increase the observed rate of interflavin electron transfer in two-electron reduced CPR from 1/, = 11 s,1 to 35 ± 0.2 s,1 and 32 ± 0.6 s,1, respectively. Reduction of CPR at the two-electron level by NADPH, NADH or dithionite generates the same spectral species, consistent with an electron distribution that is equivalent regardless of reductant at the initiation of the temperature jump. Spectroelectrochemical experiments establish that the redox potentials of the flavins of CPR are unchanged on binding 2,,5,-ADP, supporting the view that enhanced rates of interdomain electron transfer have their origin in a conformational change produced by binding NADPH or its fragments. Addition of 2,,5,-ADP either to the isolated FAD-domain or to full-length CPR (in their oxidized and reduced forms) leads to perturbation of the optical spectra of both the flavins, consistent with a conformational change that alters the environment of these redox cofactors. The binding of 2,,5,-ADP eliminates the unusual dependence of the observed flavin reduction rate on NADPH concentration (i.e. enhanced at low coenzyme concentration) observed in stopped-flow studies. The data are discussed in the context of previous kinetic studies and of the crystallographic structure of rat CPR. [source] Potential active-site residues in polyneuridine aldehyde esterase, a central enzyme of indole alkaloid biosynthesis, by modelling and site-directed mutagenesisFEBS JOURNAL, Issue 12 2002Emine Mattern-Dogru In the biosynthesis of the antiarrhythmic alkaloid ajmaline, polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. The PNAE cDNA was previously heterologously expressed in E. coli. Sequence alignments indicated that PNAE has a 43% identity to a hydroxynitrile lyase from Hevea brasiliensis, which is a member of the ,/, hydrolase superfamily. The catalytic triad, which is typical for this family, is conserved. By site-directed mutagenesis, the members of the catalytic triad were identified. For further detection of the active residues, a model of PNAE was constructed based on the X-ray crystallographic structure of hydroxynitrile lyase. The potential active site residues were selected on this model, and were mutated in order to better understand the relationship of PNAE with the ,/, hydrolases, and as well its mechanism of action. The results showed that PNAE is a novel member of the ,/, hydrolase enzyme superfamily. [source] Molecular dynamics simulations of polarizable DNA in crystal environmentINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2006Volodymyr Babin Abstract We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the "right" distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Etiopathogenic role of HLA-B27 alleles in ankylosing spondylitisINTERNATIONAL JOURNAL OF RHEUMATIC DISEASES, Issue 3 2005Nurullah AKKOC Abstract HLA-B27 is the major genetic susceptibility factor for ankylosing spondylitis (AS). However, its precise role in the pathogenesis of AS still remains unclear, even though its gene has been cloned and sequenced, and its crystallographic structure has been defined. Arthritogenic peptide and molecular mimicry hypotheses propose mechanisms related to an antigen-presenting function of HLA-B27 to be responsible for disease development. However, peculiar aspects of its immunobiology, such as its misfolding and heavy chain dimerization raise the possibility of involvement of pathogenic mechanisms unrelated to its physiological function. Moreover, HLA-B27 is not a single allele, but a family of 31 different alleles, named HLA-B*2701 to HLA-B*2727. Studies worldwide indicate that the relatively common alleles (subtypes) HLA-B*2705, B*2704, and B*2702 are strongly associated with AS, whereas HLA-B*2706 which is prevalent in South-east Asia and HLA-B*2709 which is prevalent on the Italian island of Sardinia, seem to lack such an association. The distinction between the disease-associated subtypes and those that are not associated, may provide clues to the actual role of HLA-B27 in disease pathogenesis. B*2706 differs from B*2704 by only two residues, and B*2709 differs from B*2705 by only one residue. Moreover, both B*2706 and B*2709 bind an endogenous peptide (derived from vasoactive intestinal peptide type 1 receptor) and also an exogenous peptide (latent membrane protein 2 of Epstein-Barr virus) but in two drastically diverse conformations. These recent X-ray diffraction studies of individual peptides in the context of different HLA-B27 alleles broaden our perception of the possible pathogenetic role of this molecule in the development of AS and related spondyloarthopathies. In summary, the pathogenetic role of HLA-B27 in AS seem to be quite heterogenous, and cannot be explained by a single mechanism, and new ideas have been raised based on the aberrant immunobiologic features of HLA-B27. [source] Effects of MgCl2 Crystallographic Structure on Active Centre Formation in Immobilized Single-Centre and Ziegler,Natta Catalysts for Ethylene PolymerizationMACROMOLECULAR RAPID COMMUNICATIONS, Issue 21 2008Rubin Huang Abstract The ability of a MgCl2 support to activate a transition metal catalyst has been found to depend both on the crystallographic structure of the support and on the nature of the catalyst. A high degree of crystallographic disorder can be very effective for the immobilization and activation of titanium and vanadium complexes, but is not necessarily effective for zirconocene activation. A highly disordered support prepared by the reaction of MgBu2 with HCl gave high activity with TiCl4 but low activity with (n -PrCp)2ZrCl2. High polymerization activities with the zirconocene were only obtained with supports of type MgCl2/AlRn(OEt)3,n prepared from the reaction of AlR3 with MgCl2,·,1.1EtOH. These supports are characterized by additional peaks in the X-ray diffraction pattern, indicating the presence of a crystalline structure which is absent in the other supports and contains highly Lewis acidic sites able to generate the active metallocenium species. [source] Composition and formation mechanism of zirconium oxynitride films produced by reactive direct current magnetron sputteringPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 5 2004J. M. Ngaruiya Abstract Direct current magnetron sputtered zirconium oxynitride films show an improvement in both deposition rate and physical properties compared to zirconium oxide. Here we seek to understand these beneficial effects and report on the film composition and crystallographic structure. Based on a thermochemical description together with a modeling of formation kinetics we propose a film formation mechanism, which explains many of the observations. Rutherford backscattering spectroscopy (RBS) shows early nitrogen incorporation at 64% N2 flow in disagreement with the predictions of thermochemistry. The stoichiometry is only successfully simulated with the use of an expanded Berg,Larsson model with a low replacement coefficient of about 0.1 of nitrogen by oxygen after metal-nitrogen bond formation. The deviation from complete replacement as predicted by thermodynamics illustrates the importance of kinetics in film formation. The model further successfully predicts the variation of the mass deposition rate. The X-ray diffraction analyses suggest that, within the crystalline phase, nitrogen atoms occupy oxygen sites, resulting in an unchanged zirconium oxide structure. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Influence of substrate and temperature on the shape of deposited Fe, Co, and FeCo nanoparticlesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 5 2010Wolfgang Rosellen Abstract In situ scanning tunneling measurements have been carried out on mass-filtered supported Fe, Co, and FeCo alloy nanoparticles with diameters between 4 and 14,nm. These nanoparticles are prepared from the gas phase using a continuously working cluster source and are subsequently deposited on bare W(110) and Ni(111)/W(110) surfaces. The size and the crystallographic structure before deposition are determined by high resolution transmission electron microscopy (HRTEM), the height of the nanoparticles on the substrate by scanning tunneling microscopy (STM). Depending on the substrate the particles do not maintain their spherical shape after deposition. The melting at elevated temperatures results in an anisotropic elongation along the [001] direction of the W(110) substrate. STM illustration of large Co nanoparticles deposited on an atomically flat W(110)-surface. [source] Modelling of magneto-mechanical hysteresis loops in Ni-Mn-Ga shape memory alloysPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 12 2004Laurent HirsingerArticle first published online: 17 DEC 200 Abstract A predictive model of field-induced strain in Ni-Mn-Ga ferromagnetic shape memory alloys is proposed. In this study, magnetocrystalline anisotropy K1 is introduced to permit magnetisation rotation in martensite platelets. The demagnetisation field induced by the shape of platelets is investigated. The proposed model is identified on experiments performed by Straka et al. This identification shows that observed macroscopic hysteresis loops, i.e. magnetisation and detwinning strain versus applied magnetic field, correspond exactly to a successive activation of three mechanisms: Movement of 180° domain walls, rotation of magnetisation and martensite detwinning. As expected, magnetization and strain -induced by magnetic field- in a single crystal are mainly given by the mobility of twin boundaries and magnetic anisotropies (due to the martensite crystallographic structure and to the shape of platelets). (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Integrity of thermus thermophilus cytochrome c552 Synthesized by escherichia coli cells expressing the host-specific cytochrome c maturation genes, ccmABCDEFGH: Biochemical, spectral, and structural characterization of the recombinant proteinPROTEIN SCIENCE, Issue 11 2000James A. Fee Abstract We describe the design of Escherichia coli cells that synthesize a structurally perfect, recombinant cytochrome c from the Thermus thermophilus cytochrome c552 gene. Key features are (1) construction of a plasmid-borne, chimeric cycA gene encoding an Escherichia coli -compatible, N-terminal signal sequence (MetLysIleSerIleTyrAlaThrLeu AlaAlaLeuSerLeuAlaLeuProAlaGlyAla) followed by the amino acid sequence of mature Thermus cytochrome c552; and (2) coexpression of the chimeric cycA gene with plasmid-borne, host-specific cytochrome c maturation genes (ccmABCDEFGH). Approximately 1 mg of purified protein is obtained from 1 L of culture medium. The recombinant protein, cytochrome rsC552, and native cytochrome c552 have identical redox potentials and are equally active as electron transfer substrates toward cytochrome ba3, a Thermus heme-copper oxidase. Native and recombinant cytochromes c were compared and found to be identical using circular dichroism, optical absorption, resonance Raman, and 500 MHz 1H-NMR spectroscopies. The 1.7 Å resolution X-ray crystallographic structure of the recombinant protein was determined and is indistinguishable from that reported for the native protein (Than, ME, Hof P, Huber R, Bourenkov GP, Bartunik HD, Buse G, Soulimane T, 1997, J Mol Biol 271:629,644). This approach may be generally useful for expression of alien cytochrome c genes in E. coli. [source] Tryptophanyl fluorescence lifetime distribution of hyperthermophilic ,-glycosidase from molecular dynamics simulation: A comparison with the experimental dataPROTEIN SCIENCE, Issue 9 2000Ettore Bismuto Abstract A molecular dynamics simulation approach has been utilized to understand the unusual fluorescence emission decay observed for ,-glycosidase from the hyperthermophilic bacterium Solfolobus sulfataricus (S,gly), a tetrameric enzyme containing 17 tryptophanyl residues for each subunit. The tryptophanyl emission decay of (S,gly) results from a bimodal distribution of fluorescence lifetimes with a short-lived component centered at 2.5 ns and a long-lived one at 7.4 ns Bismuto E, Nucci R, Rossi M, Irace G, 1999, Proteins 27:71,79). From the examination of the trajectories of the side chains capable of causing intramolecular quenching for each tryptophan microenvironment and using a modified Stern,Volmer model for the emission quenching processes, we calculated the fluorescence lifetime for each tryptophanyl residue of S,gly at two different temperatures, i.e., 300 and 365 K. The highest temperature was chosen because in this condition S,lgy evidences a maximum in its catalytic activity and is stable for a very long time. The calculated lifetime distributions overlap those experimentally determined. Moreover, the majority of trytptophanyl residues having longer lifetimes correspond to those originally identified by inspection of the crystallographic structure. The tryptophanyl lifetimes appear to be a complex function of several variables, such as microenvironment viscosity, solvent accessibility, the chemical structure of quencher side chains, and side-chain dynamics. The lifetime calculation by MD simulation can be used to validate a predicted structure by comparing the theoretical data with the experimental fluorescence decay results. [source] Structure of NS1A effector domain from the influenza A/Udorn/72 virusACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009Shuangluo Xia The nonstructural protein NS1A from influenza virus is a multifunctional virulence factor and a potent inhibitor of host immunity. It has two functional domains: an N-terminal 73-amino-acid RNA-binding domain and a C-terminal effector domain. Here, the crystallographic structure of the NS1A effector domain of influenza A/Udorn/72 virus is presented. Structure comparison with the NS1 effector domain from mouse-adapted influenza A/Puerto Rico/8/34 (PR8) virus strain reveals a similar monomer conformation but a different dimer interface. Further analysis and evaluation shows that the dimer interface observed in the structure of the PR8 NS1 effector domain is likely to be a crystallographic packing effect. A hypothetical model of the intact NS1 dimer is presented. [source] Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphateACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2008Anil Kumar A1A0 ATP synthases are the major energy producers in archaea. Like the related prokaryotic and eukaryotic F1F0 ATP synthases, they are responsible for most of the synthesis of adenosine triphosphate. The catalytic events of A1A0 ATP synthases take place inside the A3B3 hexamer of the A1 domain. Recently, the crystallographic structure of the nucleotide-free subunit B of Methanosarcina mazei Gö1 A1A0 ATP synthase has been determined at 1.5,Å resolution. To understand more about the nucleotide-binding mechanism, a protocol has been developed to crystallize the subunit B,ADP complex. The crystallographic structure of this complex has been solved at 2.7,Å resolution. The ADP occupies a position between the essential phosphate-binding loop and amino-acid residue Phe149, which are involved in the binding of the antibiotic efrapeptin in the related F1F0 ATP synthases. This trapped ADP location is about 13,Å distant from its final binding site and is therefore called the transition ADP-binding position. In the trapped ADP position the structure of subunit B adopts a different conformation, mainly in its C-terminal domain and also in the final nucleotide-binding site of the central ,,-domain. This atomic model provides insight into how the substrate enters into the nucleotide-binding protein and thereby into the catalytic A3B3 domain. [source] Crystallization and preliminary X-ray analysis of the glycogen synthase from Pyrococcus abyssiACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Cristina Horcajada Glycogen synthase catalyzes the transfer of glucosyl residues from ADP- or UDP-glucose to the non-reducing end of a growing ,-1,4-glucan chain. To date, no crystallographic structure of an animal/fungal glycogen synthase (family 3 of the glycosyl transferases) or a bacterial/plant glycogen/starch synthase (family 5) has been reported. This paper describes the recombinant expression, crystallization and preliminary X-ray analysis of the glycogen synthase from the hyperthermophilic archaeon Pyrococcus abyssi, the smallest enzyme of the members of families 3 and 5 of the glycosyl transferases. Crystals from this protein and from its selenomethionyl variant were grown in 100,mM sodium citrate pH 5.6 containing 20% PEG and 20% dioxane by the hanging-drop vapour-diffusion method at 293,K. The crystals, which grew as thin needles, diffracted to 3.5,Å resolution and belong to space group C2, with unit-cell parameters a = 202, b = 73, c = 149,Å, , = 131°. The crystallographic and biochemical data are consistent with either a dimer or a tetramer in the crystal asymmetric unit and a volume solvent content of 70 or 39%, respectively. [source] Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002E. Rudiño-Piñera A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role. The T conformer's external zone [Horjales et al. (1999), Structure, 7, 527,536] presents higher B values than in the R conformers. The ligand-free enzyme (T conformer) undergoes an allosteric transition to the free active-site R conformer upon binding of the allosteric activator. This structure shows three alternate conformations of the mobile section of the active-site lid (residues 163,182), in comparison to the high B values for the unique conformation of the T conformer. One of these alternate R conformations corresponds to the active-site lid found when the substrate is bound. The disorder associated with the three alternate conformations can be related to the biological regulation of the Km of the enzyme for the reaction, which is metabolically required to maintain adequate concentrations of the activator, which holds the enzyme in its R state. Seven alternate conformations for the active-site lid and three for the C-terminus were refined for the T structure using isotropic B factors. Some of these conformers approach that of the R conformer in geometry. Furthermore, the direction of the atomic vibrations obtained with anisotropic B refinement supports the hypothesis of an oscillating rather than a tense T state. The concerted character of the allosteric transition is also analysed in view of the apparent dynamics of the conformers. [source] The X-ray structure of a recombinant major urinary protein at 1.75,Å resolution.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2001A comparative study of X-ray, NMR-derived structures Major urinary proteins belong to the lipocalin family and are present in the urine of rodents as an ensemble of isoforms with pheromonal activity. The crystal structure of a recombinant mouse MUP (rMUP) was solved by the molecular-replacement technique and refined to an R factor and Rfree of 20 and 26.5%, respectively, at 1.75,Å resolution. The structure was compared with an NMR model and with a crystallographic structure of the wild-type form of the protein. The crystal structures determined in different space groups present significantly smaller conformational differences amongst themselves than in comparison with NMR models. Some, but not all, of the conformational differences between the crystal and solution structures can be explained by the influence of crystallographic contacts. Most of the differences between the NMR and X-ray structures were found in the N-terminus and loop regions. A number of side chains lining the hydrophobic pocket of the molecule are more tightly packed in the NMR structure than in the crystallographic model. Surprisingly, clear and continuous electron density for a ligand was observed inside the hydrophobic pocket of this recombinant protein. Conformation of the ligand modelled inside the density is coherent with the results of recent NMR experiments. [source] Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalisACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2000Christopher J. Bond The gene encoding the iron-dependent superoxide dismutase from Pseudomonas ovalis was cloned from a genomic library and sequenced. The ORF differs from the previously published protein sequence, which was used for the original structure determination, at 16 positions. The differences include three additional inserted residues, one deleted residue and 12 point substitutions. The gene was subcloned and the recombinant protein overexpressed, purified and crystallized in a trigonal space group. The structure was determined by molecular replacement and was refined to 2.1,Å resolution. [source] Crystallization and preliminary X-ray diffraction analysis of a rat biliverdin reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2000Danyu Sun Biliverdin reductase (BVR) catalyzes the final step of haem degradation and converts biliverdin to bilirubin using NAD(P)H as an electron donor. This paper deals with the first crystallization and preliminary crystallographic study of recombinant rat BVR expressed in Escherichia coli. Crystals of BVR were obtained by the sitting-drop vapour-diffusion method. Using synchrotron radiation at station BL44B2 of SPring-8, Japan, BVR diffraction data were collected to 1.6,Å resolution. Crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 58.89, b = 70.41, c = 87.76,Å. The complete determination of the crystallographic structure is currently in progress using MAD (multiwavelength anomalous diffraction) data from an Ir-derivative crystal. [source] Crystallization and preliminary crystallographic characterization of glutamine synthetase from Medicago truncatulaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Ana Rita Seabra The condensation of ammonium and glutamate into glutamine catalyzed by glutamine synthetase (GS) is a fundamental step in nitrogen metabolism in all kingdoms of life. In plants, this is preceded by the reduction of inorganic nitrogen to an ammonium ion and therefore effectively articulates nitrogen fixation and metabolism. Although the three-dimensional structure of the dodecameric bacterial GS was determined quite some time ago, the quaternary architecture of the plant enzyme has long been assumed to be octameric, mostly on the basis of low-resolution electron-microscopy studies. Recently, the crystallographic structure of a monocotyledonous plant GS was reported that revealed a homodecameric organization. In order to unambiguously establish the quaternary architecture of GS from dicotyledonous plants, GS1a from the model legume Medicago truncatula was overexpressed, purified and crystallized. The collection of synchrotron diffraction data to 2.35,Å resolution allowed the determination of the three-dimensional structure of this enzyme by molecular replacement. [source] Overexpression, crystallization and preliminary X-ray crystallographic analysis of d -ribose-5-phosphate isomerase from Clostridium thermocellumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Junho Jung Rare sugars are used for many industrial and medical purposes and are produced by the interconversion between aldoses and ketoses catalyzed by sugar and sugar-phosphate isomerases. Recently, Clostridium thermocellumd -ribose-5-phosphate isomerase (CTRPI), an aldose,ketose isomerase, was cloned in order to synthesize d -allose and its substrate specificity was further characterized for industrial usage. CTRPI has a novel substrate specificity that differs from those of other isomerases, which have broad substrate specificities. CTRPI prefers aldose substrates such as l -talose, d -ribose and d -allose. CTRPI was purified and crystallized in order to determine its three-dimensional structure and thus to elucidate its enzymatic reaction mechanism and understand its substrate specificity. The crystal belonged to the trigonal space group P3221, with unit-cell parameters a = b = 69.5, c = 154.4,Å, and diffracted to 1.9,Å resolution. According to Matthews coefficient calculations, the crystallographic structure consists of a dimer in the asymmetric unit, with a VM of 3.2,Å3,Da,1 and a solvent content of 61.7%. [source] X-ray Crystal Structure Study of Sterically Congested DiphenyldiazomethanesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 14 2004Takashi Iikubo Abstract X-ray crystallographic structures were determined for five diphenyldiazomethanes (DDMs) with various ortho substituents, namely, bis(2,4,6-trichlorophenyl)diazomethane, bis(2,4,6-tribromophenyl)diazomethane, bis(4- tert -butyl-2,6-dibromophenyl)diazomethane, (4- tert -butyl-2,6-dimethylphenyl)(2,4,6-tribromophenyl)diazomethane, and [4- tert -butyl-2,6-bis(trifluoromethyl)phenyl](4- tert -butyl-2,6-dibromophenyl)diazomethane, and for bis(4-bromophenyl)diazomethane, a DDM with no ortho substituents. The correlation between the structural parameters, the ESR zero-field splitting (ZFS) parameters and the lifetimes of the triplet diphenylcarbenes (DPCs) generated from these diazo compounds was examined. It is noted that as ortho substituents are introduced onto the phenyl rings of the DDMs, the interplanar angle between the two phenyl rings increases, while the angle of the diazo carbon changes very little. DDM 6 -N2, from which the longest-lived triplet carbene is generated, is shown to have the largest interplanar angle of the DDMs examined. The bond distances between the aromatic carbons and the ortho substituents as well as the van der Waals radii of the substituents were also examined. These studies do not provide a quantitative correlation between the structural parameters of the precursor DDMs and the ZFS parameters and lifetimes of their photoproducts, triplet DPCs, but show how steric shielding of the ortho substituents affects the structures and stabilities of triplet DPCs. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Ab Initio Structure/Reactivity Investigations of Illudin-Based Antitumor Agents: A Model for Reaction in vivoHELVETICA CHIMICA ACTA, Issue 12 2003Laura (Hydroxymethyl)acylfulvene (HMAF, irofulven; 4), a third-generation derivative of a natural product extracted from the mushroom Omphalotus illudens, is selectively toxic towards certain forms of malignant tumors. Conversion of HMAF and cognates to stable aromatic derivatives is triggered by thiol attack in vitro and in vivo. Quantum-chemical methods predict well the structure for several functionalized derivatives of irofulven as compared to known X-ray crystallographic structures. Computational reaction profiles for thiol attack and aromatic rearrangement of irofulven and illudin S, a toxin from which irofulven is derived, provide insight into HMAF's selectivity and toxicity. Methods used include hybrid density-functional theory (HDFT), HartreeFock (HF), and MøllerPlesset second-order perturbation theory (MP2). Solvent effects have been explored by means of the new continuum-solvation method, COSab, presented in an accompanying paper. [source] A DFT study of two diiron (II) synthetic model compounds and their diiron(III) peroxide oxygenation productsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009R. C. Binning Jr. Abstract Unrestricted density functional theory calculations have been conducted on two diiron(II) synthetic model compounds. Calculations employed the BPW91 and BOP density functionals with both high-spin and broken symmetry low-spin representations of weakly coupled high-spin irons. Comparison of the calculated and crystallographic structures is made, and good agreement is found with both spin representations. Raman spectral data are available for the diiron(III) product of the reaction with O2 to form a bridged peroxide. Calculated harmonic frequencies confirm the experimental assignments. Small geometry differences between the high spin and broken symmetry results are seen in bond lengths, angles, Raman frequencies, and spin densities associated with oxo and peroxo bridges in the diiron(III) oxidation products. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Electron crystallography of aquaporinsIUBMB LIFE, Issue 7 2008Simeon Andrews Abstract Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions. © 2008 IUBMB IUBMB Life, 60(7): 430,436, 2008 [source] Toward accurate relative energy predictions of the bioactive conformation of drugsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Keith T. Butler Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] |