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Hexamer
Selected AbstractsEntrapment of a Hexamer of Nitrobenzene Molecules between the Layers of (4,4)-Coordination Networks Containing Intra-,-Sheet Hydrogen BondsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 3 2006Madhushree Sarkar Abstract Two exo -bidentate pyridyl ligands containing diamides as spacers were shown to form non-interpenetrated 2D-coordination networks of (4,4)-geometry upon treatment with Cu(NO3)2 and NaSCN. The crystal structures reveal that both structures contain intralayer ,-sheet hydrogen bonds. In one of these structures nitrobenzene occupies 60,% of the crystal volume included between the coordination networks. The nitrobenzene molecules form a layer which has the hexameric C,H···O hydrogen bonded aggregate as a basic building block. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] ChemInform Abstract: Novel Polynuclear Nickel(II) Complex: Hydrazine, Sulfato, and Hydroxo Bridging in an Unusual Metal Hexamer.CHEMINFORM, Issue 35 2010Crystal Structure, Magnetic Properties of [Ni6(N2H4)6 (SO4)4(OH)2(H2O)8] (SO4) (H2O)10. Abstract The title compound is prepared by reaction of NiSO4 and hydrazine in aqueous solution (40 °C, 5 h; yield not given). [source] First Hexanuclear UIV and ThIV Formate Complexes , Structure and Stability Range in Aqueous SolutionEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 32 2009Shinobu Takao Abstract The actinide(IV) hexanuclear [M6(,3 -O)4(,3 -OH)4(HCOO)12(LT)6] complexes were prepared (LT = H2O or CH3OH). Their structures were investigated by single-crystal X-ray analysis and XAFS spectroscopy. HCOO, acts as a bridging ligand, which prevents the formation of polynuclear hydrolysis species like UIV hydrous oxide colloids at least up to pH = 3.25, and stabilizes the nanosized clusters in solution. The charge of the hexamer is balanced by the O/OH ratio of the ,3 -bridges.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Disulfide bond formation through Cys186 facilitates functionally relevant dimerization of trimeric hyaluronan-binding protein 1 (HABP1)/p32/gC1qRFEBS JOURNAL, Issue 1 2002Babal Kant Jha Hyaluronan-binding protein 1 (HABP1), a ubiquitous multifunctional protein, interacts with hyaluronan, globular head of complement component 1q (gC1q), and clustered mannose and has been shown to be involved in cell signalling. In vitro, this recombinant protein isolated from human fibroblast exists in different oligomeric forms, as is evident from the results of various independent techniques in near-physiological conditions. As shown by size-exclusion chromatography under various conditions and glutaraldehyde cross-linking, HABP1 exists as a noncovalently associated trimer in equilibrium with a small fraction of a covalently linked dimer of trimers, i.e. a hexamer. The formation of a covalently-linked hexamer of HABP1 through Cys186 as a dimer of trimers is achieved by thiol group oxidation, which can be blocked by modification of Cys186. The gradual structural transition caused by cysteine-mediated disulfide linkage is evident as the fluorescence intensity increases with increasing Hg2+ concentration until all the HABP1 trimer is converted into hexamer. In order to understand the functional implication of these transitions, we examined the affinity of the hexamer for different ligands. The hexamer shows enhanced affinity for hyaluronan, gC1q, and mannosylated BSA compared with the trimeric form. Our data, analyzed with reference to the HABP1/p32 crystal structure, suggest that the oligomerization state and the compactness of its structure are factors that regulate its function. [source] Mammalian Mcm2/4/6/7 complex forms a toroidal structureGENES TO CELLS, Issue 5 2003Norikazu Yabuta Background: The Mcm proteins are a family of six homologous proteins (Mcm2,7) that play an important role in DNA replication. They form Mcm4/6/7 and Mcm2/4/6/7 complexes, but their structures are not known. Results: We found that the human Mcm2/4/6/7 tetramer forms a toroidal structure, with a central cavity about 3,4 nm in diameter. Observations were made using electron microscopy, employing the image analysis of single particles. The most predominant averaged image displayed a toroid harbouring four bulges forming corners, one of which was larger than the others. This structure was very similar to the mouse Mcm2/4/6/7 tetramer that was independently prepared and analysed by electron microscopy. These toroidal structures are distinct from that of the Mcm4/6/7 hexamer, which was also examined by electron microscopy. GST(glutathione S-transferase)-pull down and two hybrid experiments suggest that a putative Mcm6-Mcm6 hinge contributes to the formation of the Mcm7/4/6/6/4/7 heterohexamer. Conclusions: The Mcm2/4/6/7 tetramer forms a toroidal structure that is distinct from that of the Mcm4/6/7 hexamer in size and shape. [source] Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculationsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2009Emilie-Laure Zins Abstract Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters. Copyright © 2009 John Wiley & Sons, Ltd. [source] Matrix-assisted laser desorption/ionization collision-induced dissociation of linear single oligomers of nylon-6JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 10 2001Renata Murgasova Abstract Matrix-assisted laser desorption/ionization, collision induced-dissociation (MALDI-CID) has been used to obtain structural information for linear single oligomers of nylon-6. The effects of matrix and cationization agent in MALDI-CID analysis have been investigated. Fragmentation mechanisms are proposed for the series of ions that are observed in the MALDI-CID spectra of the hexamer, octamer and dodecamer. Fragmentation processes observed in the MALDI-CID spectra include cleavage of the end groups followed by dissociation of the m/z 113 unit. Cleavage of the oligamide chain occurs at the amide linkage, as well as at adjacent bonds. For the four matrices and three cationization agents investigated, 2,5-dihydroxybenzoic acid and sodium chloride showed the best performance for MALDI-CID analysis of the dodecamer. In addition, yields of the fragment ions in MALDI-CID spectra were found to be dependent on the chain length distribution. Copyright © 2001 John Wiley & Sons, Ltd. [source] Electrospray and matrix-assisted laser desorption/ionization mass spectral characterization of linear single nylon-6 oligomersJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2001Lu Shan Abstract Synthetic nylon-6 single molecular mass oligomers were studied by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. These oligomers, considered as model compounds for the study of nylon-6 polymers, gave good mass spectrometric results using both MALDI and ESI. In spite of the gentle nature of both techniques, the MALDI and ESI spectra showed evidence of end-group cleavage from the oligomer chains. MALDI-MS was found to give similar fragmentation patterns for all of the oligomer samples. An increase in doubly charged ion signals with increasing oligomer mass was observed in the ESI mass spectra, as was end-group fragmentation. Signals from oligomer clusters were observed in ESI-MS for the dimer, tetramer and hexamer, most likely due to non-covalent bonding among the low-mass oligomer molecules. Copyright © 2001 John Wiley & Sons, Ltd. [source] Binding site on human immunoglobulin G for the affinity ligand HWRGWVJOURNAL OF MOLECULAR RECOGNITION, Issue 3 2010Haiou Yang Abstract Affinity ligand HWRGWV has demonstrated the ability to isolate human immunoglobulin G (hIgG) from mammalian cell culture media. The ligand specifically binds hIgG through its Fc portion. This work shows that deglycosylation of hIgG has no influence on its binding to the HWRGWV ligand and the ligand does not compete with Protein A or Protein G in binding hIgG. It is suggested by the mass spectrometry (MS) data and docking simulation that HWRGWV binds to the pFc portion of hIgG and interacts with the amino acids in the loop Ser383,Asn389 (SNGQPEN) located in the CH3 domain. Subsequent modeling has suggested a possible three-dimensional minimized solution structure for the interaction of hIgG and the HWRGWV ligand. The results support the fact that a peptide as small as a hexamer can have specific interactions with large proteins such as hIgG. Copyright © 2009 John Wiley & Sons, Ltd. [source] The synthesis of oligomers of oxetane-based dipeptide isosteres derived from L -rhamnose or D -xyloseJOURNAL OF PEPTIDE SCIENCE, Issue 6 2005Stephen W. Johnson Abstract Routes to oligomers (dimers, tetramers, hexamers) of five oxetane-based dipeptide isosteres have been established. Methyl 2,4-anhydro-5-azido-5-deoxy- L -rhamnonate ,monomer' led, by coupling the corresponding carboxylic acid and amine, to a ,dimer'. Reverse-aldol ring-opening occurred on attempted saponification of the dimer, so all further oligomerization was performed using TBDMS C-3 hydroxyl protection. The silyl protected L -rhamnonate monomer led in turn to the dimer (via the monomer acid and amine), the tetramer (via the dimer acid and amine) and finally the hexamer (via the tetramer acid and dimer amine). In each case the acids were obtained through saponification of the respective methyl esters and the amines were obtained by hydrogenation of the azides; coupling was TBTU-mediated. Essentially the same strategy was employed on equivalent D -lyxonate, 6-deoxy- L -altronate, 6-deoxy- D -gulonate and D -fuconate dipeptide isosteres to give the respective dimers, tetramers and hexamers. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] Prediction of the association state of insulin using spectral parametersJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 4 2003Vladimir N. Uversky Abstract Human insulin exists in different association states, from monomer to hexamer, depending on the conditions. In the presence of zinc the "normal" state is a hexamer. The structural properties of 20 variants of human insulin were studied by near-UV circular dichroism, fluorescence spectroscopy, and small-angle X-ray scattering (SAXS). The mutants showed different degrees of association (monomer, dimers, tetramers, and hexamers) at neutral pH. A correlation was shown between the accessibility of tyrosines to acrylamide quenching and the degree of association of the insulin mutants. The near-UV CD spectra of the insulins were affected by protein association and by mutation-induced structural perturbations. However, the shape and intensity of difference CD spectra, obtained by subtraction of the spectra measured in 20% acetic acid (where all insulin species were monomeric) from the corresponding spectra measured at neutral pH, correlate well with the degree of insulin association. In fact, the near-UV CD difference spectra for monomeric, dimeric, tetrameric, and hexameric insulin are very distinctive, both in terms of intensity and shape. The results show that the spectral properties of the insulins reflect their state of association, and can be used to predict their oligomeric state. © 2003 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 92:847,858, 2003 [source] Self-assembly of daisy chain oligomers from heteroditopic molecules containing secondary ammonium ion and crown ether moietiesJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 4 2010Harry W. Gibson Abstract MALDI-TOF MS of the heteroditopic compound 2 -(benzylammoniomethyl)dibenzo-24-crown-8 hexafluorophosphate (4) revealed oligomeric "daisy chain" species up to the hexamer. Similar results were obtained for 2-(6,-hydroxyhexylammoniomethyl)dibenzo-24-crown-8 hexafluorophosphate (8). The complexations of two substituted dibenzylammonium salts, 2,2,-dimethyldibenzylammonium hexaflurophosphate (9a) and 2,2,,5-trimethoxydibenzylammonium hexafluorophosphate (9b), with dibenzo-24-crown-8 were examined as models for slippage systems; association constants are reported for these systems. A crystal structure is reported for the new dimethylbenzylammonoium pseudorotaxane. The trimethoxy analog is shown to be capable of slippage formation of a rotaxane, albeit in low yield. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 975,985, 2010 [source] A RUNX/AML-binding motif residing in a novel 13-bp DNA palindrome may determine the expression of the proximal promoter of the human uPA geneJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 9 2005E. KOPF Summary., Urokinase-type plasminogen activator (uPA) is a multifunctional extracellular serine protease implicated in different events including fibrinolysis, tissue remodeling, and hematopoiesis. The human uPA gene contains a major promoter region at around 2000 bp upstream from the transcription start site (+1), and a second regulatory region spanning nucleotides ,90/+32 within the proximal promoter. Here, an inspection of this region revealed a novel 13-bp palindrome residing at position +8/+20. Interestingly, the palindrome contains the DNA consensus-binding hexamer for the RUNX/AML family of transcription factors that play a role in hematopoiesis, leukemia, and several developmental processes. Measuring the expression for promoter,reporter constructs after transfection revealed that deletion of the palindrome abrogated most of the proximal promoter activity in 293A cell. Additionally, electrophoretic mobility shift assays have shown that the palindrome could bind the RUNX1 component in nuclear extracts of myeloid cell lines exclusively through its RUNX motif. The palindrome was found in five additional human genes, two of which (MYH11 and MLLT1) have been linked to chromosomal rearrangements leading to leukemia. The data presented here have implicated, for the first time, RUNX/AML in the regulation of the uPA gene. The significance of the novel palindrome regarding gene regulation through the RUNX motif deserves further investigation. [source] Channel mutations in Hsp104 hexamer distinctively affect thermotolerance and prion-specific propagationMOLECULAR MICROBIOLOGY, Issue 6 2007Hiroshi Kurahashi Summary The yeast prion [PSI+] represents an aggregated state of the translation termination factor Sup35 resulting in the tendency of ribosomes to readthrough stop codons. In this study, we constructed an auxotrophic chromosomal marker, ura3-197 (nonsense allele), applicable to selection for loss of [PSI+] to [psi,]. Unlike [psi,] yeast strains, [PSI+] yeast strains exhibit nonsense suppression of the ura3-197 allele and are not viable in the presence of 5-fluoroorotic acid (5-FOA) that is converted to a toxic material by the readthrough product of Ura3. We selected 20 5-FOA-resistant, loss-of-[PSI+], mutants spontaneously or by transposon-mediated mutagenesis from ura3-197[PSI+] cells. All of the 20 [psi,] isolates were affected in Hsp104, a protein-remodelling factor. Although most of them were disabled in a normal Hsp104 function for thermotolerance, three single mutants, L462R, P557L and D704N, remained thermotolerant. Importantly, L462R and D704N also eliminate other yeast prions [URE3] and [PIN+], while P557L does not, suggesting that Hsp104 harbours a unique activity to prion propagation independent of its function in thermotolerance. The mutations that are specific to prion propagation are clustered around the lateral channel of the Hsp104 hexamer, suggesting a crucial and specific role of this channel for prion propagation. [source] Molecular analysis of tyrosine- and phenylalanine-mediated repression of the tyrB promoter by the TyrR protein of Escherichia coliMOLECULAR MICROBIOLOGY, Issue 5 2002Ji Yang Summary The mechanism of repression of the tyrB promoter by TyrR protein has been studied in vivo and in vitro. In tyrR+ strains, transcription of tyrB is repressed by either tyrosine or phenylalanine. Both of the TyrR binding sites (strong and weak TyrR boxes) lie downstream of the tyrB transcription start site and are required for tyrosine- or phenylalanine-mediated repression. Our results establish that the binding of the TyrR protein to the weak box, induced by cofactor tyrosine or phenylalanine, is critical for repression to occur. Neither the binding of the TyrR protein dimer formed in the presence of phenylalanine, nor the binding of the hexamer formed in the presence of tyrosine, blocks the binding of RNA polymerase to the promoter. Instead, open complex formation is inhibited in the presence of tyrosine whereas a step(s) following open complex formation is inhibited in the presence of phenylalanine. Moving the TyrR boxes 3 bp or more further away from the promoter affects tyrosine-mediated repression without affecting phenylalanine-mediated repression which remains unaltered until 6 bp are inserted between the TyrR boxes and the promoter. Analysis of deletion and insertion mutants fails to reveal any face of the helix specificity for either tyrosine- or phenylalanine-mediated repression. [source] Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based methodPROTEIN SCIENCE, Issue 4 2002Kendall D. Powell Abstract We recently reported on a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based technique, termed SUPREX, that removes several important limitations associated with measuring the thermodynamic stability of proteins. In contrast to conventional spectroscopy-based techniques for characterizing the equilibrium unfolding behavior of proteins, SUPREX is amenable to the thermodynamic analysis of both purified and unpurified proteins using mg to ng quantities of material. Here we report on the application of SUPREX to the analysis of multimeric protein systems. Included in this work are the SUPREX results we obtained in studies on six model multimeric proteins including the GCN4p1 dimer, the coil-VaLd trimer, the 4-oxalocrotonate tautomerase (4-OT) hexamer, the Trp repressor (TrpR) dimer, the Arc repressor (ArcR) dimer, and an ArcR mutant (the (DOA20)ArcR) dimer which contained two destabilizing mutations including an Asp to Ala mutation at position 20 and an amide to ester bond mutation between amino acid (aa) residues 19 and 20. As part of the work described here, we present a new method for the analysis of SUPREX data that is generally applicable to both monomeric and multimeric protein systems. Our results on the model proteins in this study indicate that this new method can be used to determine folding free energies for proteins with the accuracy and precision of conventional spectroscopy-based methods. [source] Determination of ,-helix N1 energies after addition of N1, N2, and N3 preferences to helix/coil theoryPROTEIN SCIENCE, Issue 4 2000Jia Ke Sun Abstract Surveys of protein crystal structures have revealed that amino acids show unique structural preferences for the N1, N2, and N3 positions in the first turn of the ,-helix. We have therefore extended helix-coil theory to include statistical weights for these locations. The helix content of a peptide in this model is a function of N-cap, C-cap, N1, N2, N3, C1, and helix interior (N4 to C2) preferences. The partition function for the system is calculated using a matrix incorporating the weights of the fourth residue in a hexamer of amino acids and is implemented using a FORTRAN program. We have applied the model to calculate the N1 preferences of Gln, Val, Ile, Ala, Met, Pro, Leu, Thr, Gly, Ser, and Asn, using our previous data on helix contents of peptides Ac-XAKAAAAKAAGY-CONH2. We find that Ala has the highest preference for the N1 position. Asn is the most unfavorable, destabilizing a helix at N1 by at least 1.4 kcal mol,1 compared to Ala. The remaining amino acids all have similar preferences, 0.5 kcal mol,1 less than Ala. Gln, Asn, and Ser, therefore, do not stabilize the helix when at N1. [source] An ice-like water hexamer with symmetry in the hydrogen-bonded structure of 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Huan Xu An ice-like hexameric water cluster, stabilized by the flexible bis-imidazolyl compound 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene (Fbix), is found in the trigonal R crystal structure of the title compound, C14H10F4N4·2H2O or Fbix·2H2O. The Fbix molecule lies about an inversion centre with one water molecule in the asymmetric unit in a general position. A cyclic chair-like hexameric water cluster with symmetry is generated with a hydrogen-bonded O...O distance within the hexamer of 2.786,(3),Å. The Fbix molecule adopts a trans conformation, where the imidazole ring makes a dihedral angle of 70.24,(11)° with the central tetrafluorinated aromatic ring. Each water hexamer is connected by six Fbix molecules through intermolecular O,H...N hydrogen bonds [N...O = 2.868,(3),Å] to yield a three-dimensional supramolecular network with primitive cubic (pcu) topology. Large voids in each single pcu network lead to fourfold interpenetrated aggregates of Fbix·2H2O. [source] A novel (3,4,10)-connected three-dimensional hydrogen-bonded supramolecular network containing a cyclic water hexamerACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009Yan Zhou The title compound, 4,4,-(1,1,1,3,3,3-hexafluoroisopropylidene)diphthalic acid hexahydrate, C19H10F6O8·6H2O, crystallizes in the centrosymmetric space group Pbcn, with half of the diphthalic acid residue and three water molecules in the asymmetric unit. The organic molecule is located on a crystallographic twofold axis. In the solid, cyclic water hexamers in chair conformations have crystallographically imposed inversion symmetry. Strong O,H...O hydrogen bonds between the hexamers and organic molecules result in a unique three-dimensional supramolecular network [O...O = 2.554,(2),2.913,(2),Å]. This compound represents the first example of a (3,4,4,10)-connected four-nodal supramolecular topology with the Schläfli symbol (43.5.6.7)2(43.52.7)2(43)2(46.56.62.78.814.99). [source] Synthesis, structure and biological activity of triorganotin 1H -tetrazolyl-1-acetates: cyclic hexamer and linkage coordination polymersAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 1 2010Yun-Fu Xie Abstract Reaction of 1H -tetrazolyl-1-acetic acid (CHN4CH2CO2H) with (R3Sn)2O or R3SnOH yields triorganotin 1H -tetrazolyl-1-acetates [CHN4CH2CO2SnR3, R = Ph (1), p -tolyl (2), cyclohexyl (3), n -Bu (4) and Et (5)]. 1H -tetrazolyl-1-acetates in these triorganotin derivatives display remarkably different coordination modes, depending on the properties of the organic substituents bonded to the tin atoms. Complex 1 displays a rare cyclohexameric structure by the assembly of the SnN coordination bond, while complex 2 forms a linkage coordination polymer through the intermolecular Sn···N interactions. The structure of complex 3 is similar to that of complex 2, but the intermolecular Sn···N interactions are weaker in the former. However, in complex 4, the tetrazolyl nitrogen atoms do not coordinate to the tin atoms. This complex forms a polymeric chain by the unsymmetric bridging carboxylate group. All these complexes exhibit good antifungal activities in vitro against Alternaria solani, Cercospora arachidicola, Gibberella zeae, Physalospora piricola and Botrytis cinerea. The corresponding EC50 values of these complexes were tested. Copyright © 2009 John Wiley & Sons, Ltd. [source] Unprecedented self-assembled cyclic hexamer of ferrocenyldimethylsilanol, [FcSiMe2OH]6 (Fc = (,5 -C5H5)Fe(,5 -C5H4)),,APPLIED ORGANOMETALLIC CHEMISTRY, Issue 4 2005Hemant K. Sharma Abstract Ferrocenyldimethylsilanol, FcSiMe2OH, Fc = (,5 -C5H5)Fe(,5 -C5H4), features a self-assembled (through intermolecular hydrogen bonding) cyclohexameric supermolecule with a chair conformation. Copyright © 2005 John Wiley & Sons, Ltd. [source] A neutron crystallographic analysis of T6 porcine insulin at 2.1,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2009Wakari Iwai Neutron diffraction data for T6 porcine insulin were collected to 2.1,Å resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essential to interpreting the charge balance and could be compared with the structure of a dried crystal of T6 human insulin at 100,K. Differences in the dynamic behaviour of the water molecules coordinating the upper and lower Zn ions were observed and interpreted. The hydrogen bonds in the insulin molecules, as well as those involving HisB10 and GluB13, are discussed. The hydrogen/deuterium (H/D) exchange ratios of the amide H atoms of T6 porcine insulin in crystals were obtained and showed that regions highly protected from H/D exchange are concentrated in the centre of a helical region of the B chains. From the viewpoint of soaking time versus H/D-exchange ratios, the amide H atoms can be classified into three categories. [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] Structure of an aliphatic amidase from Geobacillus pallidus RAPc8ACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2007Serah W. Kimani The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9,Å was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily ,-,-,-, fold. Association in the hexamer preserves the eight-layered ,-,-,-,:,-,-,-, structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity. [source] Structure of d -ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Eric L. Wise The crystal structure of d -ribulose 5-phosphate 3-epimerase (RPE) from the cyanobacterium Synechocystis was determined by X-ray crystallography to 1.6,Å resolution. The enzyme, which catalyzes the epimerization of d -ribulose 5-phosphate and d -xylulose 5-phosphate, assembles as a hexamer of (,/,)8 -barrels in the crystallographic asymmetric unit. The active site is highly similar to those of two previously reported RPEs and provides further evidence for essential catalytic roles for several active-site residues. [source] Purification, crystallization and preliminary X-ray analysis of uridine phosphorylase from Salmonella typhimuriumACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Mariya V. Dontsova The structural udp gene encoding uridine phosphorylase (UPh) was cloned from the Salmonella typhimurium chromosome and overexpressed in Escherichia coli cells. S. typhimurium UPh (StUPh) was purified to apparent homogeneity and crystallized. The primary structure of StUPh has high homology to the UPh from E. coli, but the enzymes differ substantially in substrate specificity and sensitivity to the polarity of the medium. Single crystals of StUPh were grown using hanging-drop vapor diffusion with PEG 8000 as the precipitant. X-ray diffraction data were collected to 2.9,Å resolution. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group P61(5), with unit-cell parameters a = 92.3, c = 267.5,Å. The solvent content is 37.7% assuming the presence of one StUPh hexamer per asymmetric unit. [source] Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilusACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2004Phosphopantetheine adenylyltransferase Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in bacteria that catalyzes the rate-limiting step in coenzyme A (CoA) biosynthesis by transferring an adenylyl group from ATP to 4,-phosphopantetheine (Ppant), yielding 3,-dephospho-CoA (dPCoA). The crystal structure of PPAT from Thermus thermophilus HB8 (Tt PPAT) complexed with Ppant has been determined by the molecular-replacement method at 1.5,Å resolution. The overall fold of the enzyme is almost the same as that of Escherichia coli PPAT, a hexamer having point group 32. The asymmetric unit of Tt PPAT contains a monomer and the crystallographic triad and dyad coincide with the threefold and twofold axes of the hexamer, respectively. Most of the important atoms surrounding the active site in E. coli PPAT are conserved in Tt PPAT, indicating similarities in their substrate binding and enzymatic reaction. The notable difference between E. coli PPAT and Tt PPAT is the simultaneous substrate recognition by all six subunits of Tt PPAT compared with substrate recognition by only three subunits in E. coli PPAT. Comparative analysis also revealed that the higher stability of Tt PPAT arises from stabilization of each subunit by hydrophobic effects, hydrogen bonds and entropic effects. [source] Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2002Mohammad W. Bhuiya Glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1, was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol (PEG) 400 as the precipitant. The crystals belong to the hexagonal space group P63, with unit-cell parameters a = b = 98.9, c = 394.8,Å, , = , = 90, , = 120°. The asymmetric unit contained one hexamer of the enzyme, giving a crystal volume per enzyme mass (VM) of 1.98,Å3,Da,1 and a solvent content of 37.3%. The X-ray diffraction data were collected to a resolution of 3.0,Å at the BL6B beamline in the Photon Factory with an overall Rsym of 13.8% and a completeness of 87.1%. [source] Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Kavyashree Manjunath The study of proteins involved in de novo biosynthesis of purine nucleotides is central in the development of antibiotics and anticancer drugs. In view of this, a protein from the hyperthermophile Pyrococcus horikoshii OT3 was isolated, purified and crystallized using the microbatch method. Its primary structure was found to be similar to that of SAICAR synthetase, which catalyses the seventh step of de novo purine biosynthesis. A diffraction-quality crystal was obtained using Hampton Research Crystal Screen II condition No. 34, consisting of 0.05,M cadmium sulfate hydrate, 0.1,M HEPES buffer pH 7.5 and 1.0,M sodium acetate trihydrate, with 40%(v/v) 1,4-butanediol as an additive. The crystal belonged to space group P31, with unit-cell parameters a = b = 95.62, c = 149.13,Å. Assuming the presence of a hexamer in the asymmetric unit resulted in a Matthews coefficient (VM) of 2.3,Å3,Da,1, corresponding to a solvent content of about 46%. A detailed study of this protein will yield insights into structural stability at high temperatures and should be highly relevant to the development of antibiotics and anticancer drugs targeting the biosynthesis of purine nucleotides. [source] Structure of hypothetical Mo-cofactor biosynthesis protein B (ST2315) from Sulfolobus tokodaiiACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Svetlana V. Antonyuk The structure of a probable Mo-cofactor biosynthesis protein B from Sulfolobus tokodaii, belonging to space group P6422 with unit-cell parameters a = b = 136.68, c = 210.52,Å, was solved by molecular replacement to a resolution of 1.9,Å and refined to an R factor and Rfree of 16.8% and 18.5%, respectively. The asymmetric unit contains a trimer, while the biologically significant oligomer is predicted to be a hexamer by size-exclusion chromatography. The subunit structure and fold of ST2315 are similar to those of other enzymes that are known to be involved in the molybdopterin- and molybdenum cofactor-biosynthesis pathways. [source] | |||||||||||||||||||||||||||||||||||||