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One Monomer (one + monomer)
Selected AbstractsEffect of stoichiometry on liquid crystalline supramolecular polymers formed with complementary nucleobase pair interactionsJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 17 2006Kelly A. Burke Abstract We report herein studies on the liquid crystalline behavior of a series of supramolecular materials that contain different ratios of two complementary symmetrically-substituted alkoxy-bis(phenylethynyl)benzene AA- and BB-type monomers. One monomer has thymine units placed at either end of the rigid mesogenic core, while the other has N6 -(4-methoxybenzoyl)-adenine units placed on the ends. Differential scanning calorimetric and polarized optical microscopy studies have been carried out on these systems. These studies show that the material's behavior is strongly dependent on its thermal history. As a result, the materials can exhibit, on heating, either a liquid crystalline phase, a crystalline phase, or the coexistence of crystalline and liquid crystalline regions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5049,5059, 2006 [source] Purification, crystallization and preliminary X-ray analysis of a deletion mutant of a major buckwheat allergenACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Yuichiro Kezuka A 16,kDa buckwheat protein (BWp16) is a major allergen responsible for immediate hypersensitivity reactions including anaphylaxis. A deletion mutant of BWp16 (rBWp16,N) was overproduced and purified and was shown to be immunologically active. A three-wavelength MAD data set was collected from a crystal of selenomethionine-labelled rBWp16,N. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 28.39, b = 31.54, c = 32.20,Å, , = 111.92, , = 108.91, , = 98.74°. One monomer was expected to be present in the asymmetric unit based on the calculated Matthews coefficient of 1.76,Å3,Da,1. [source] Surprises from the crystal structure of the hepatitis C virus NS2-3 protease,HEPATOLOGY, Issue 6 2006Jerome Gouttenoire Ph.D. Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes 2 proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at 4 downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here, we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 Å resolution. The structure reveals a dimeric cysteine protease with 2 composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the 2 active sites, predicting an inactive postcleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design. [source] Nanostructured Organic,Inorganic Composite Materials by Twin Polymerization of Hybrid MonomersADVANCED MATERIALS, Issue 20 2009Stefan Spange Abstract Forming two structurally different but associated polymer structures in a single step is a possible route for the production of nanostructured materials. By means of twin polymerization of specially constructed monomers consisting of two different covalently bonded building blocks (hybrid monomers), this route is realized. What is important is that two different macromolecular structures are formed from one monomer in a single process. The two polymers formed can be linear, branched, or cross-linked structures. The molecular composition of the hybrid monomer defines the degree of cross-linking of the corresponding macromolecular structures that is theoretically possible. [source] PVC modification through polymerization of a monomer absorbed in porous suspension-type PVC particlesJOURNAL OF VINYL & ADDITIVE TECHNOLOGY, Issue 3 2004M. Narkis In-situ polymerization is the polymerization of one monomer in the presence of another polymer. It can be performed by sequential emulsion polymerization, or by reactions in the melt, in the solid phase, or in solution. The current report describes two methods to obtain poly(vinyl chloride) (PVC) modification through polymerization of a monomer absorbed in commercial porous suspension-type PVC particles. The generated modified PVC products differ significantly in their structure and properties. The first approach includes absorption of a monomer/peroxide solution within porous suspension-type PVC particles, followed by polymerization/crosslinking in the solid state at 80°C in an aqueous stabilizer-free dispersion. The monomer/crosslinker pairs selected are styrene/DVB (divinyl benzene), methylmethacrylate/EGDMA (ethylene glycol dimethacrylate), butyl acrylate/EGDMA, and ethylhexyl acrylate/EGDMA. The influence of composition and nature of the polymerizing/crosslinking constituents on the modified PVC particle structure was studied by microscopy methods, porosity measurements, and dynamic mechanical behavior (DMTA). The level of molecular grafting between PVC and the modifying polymer was determined by solvent extraction experiments. This work shows that the different monomers used represent distinct courses of monomer transport through the PVC particles. The characteristics of the modified PVC particle indicate that the polymerization/crosslinking process occurs in both the PVC bulk, i.e., within the walls constituting a particle, and in the PVC pores. No indication of chemical intermolecular interaction within the modified PVC particles was found. In the second approach, a solution of monomer, initiator, and a crosslinking agent is absorbed in commercial suspension-type porous PVC particles, thus forming a dry blend. This dry blend is subsequently reactively polymerized in a twin-screw extruder at an elevated temperature, 180°C, in the molten state. The properties of the reactively extruded PVC/PMMA blends are compared with those of physical blends at similar compositions. Owing to the high polymerization temperature, short-chain polymers are formed in the reactive polymerization process. Reactively extruded PVC/PMMA blends are transparent, form single-phase morphology, have a single Tg, and show mechanical properties comparable with those of the neat PVC. The resulting reactively extruded PVC/PMMA blends have high compatibility. J. Vinyl Addit. Technol. 10:109,120, 2004. © 2004 Society of Plastics Engineers. [source] Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimerPROTEIN SCIENCE, Issue 11 2003Terence C. Flynn Abstract The crystal structures of lactose repressor protein (LacI) provide static endpoint views of the allosteric transition between DNA- and IPTG-bound states. To obtain an atom-by-atom description of the pathway between these two conformations, motions were simulated with targeted molecular dynamics (TMD). Strikingly, this homodimer exhibited asymmetric dynamics. All asymmetries observed in this simulation are reproducible and can begin on either of the two monomers. Asymmetry in the simulation originates around D149 and was traced back to the pre-TMD equilibrations of both conformations. In particular, hydrogen bonds between D149 and S193 adopt a variety of configurations during repetitions of this process. Changes in this region propagate through the structure via noncovalent interactions of three interconnected pathways. The changes of pathway 1 occur first on one monomer. Alterations move from the inducer-binding pocket, through the N-subdomain ,-sheet, to a hydrophobic cluster at the top of this region and then to the same cluster on the second monomer. These motions result in changes at (1) side chains that form an interface with the DNA-binding domains and (2) K84 and K84', which participate in the monomer,monomer interface. Pathway 2 reflects consequent reorganization across this subunit interface, most notably formation of a H74-H74rsquo; ,-stacking intermediate. Pathway 3 extends from the rear of the inducer-binding pocket, across a hydrogen-bond network at the bottom of the pocket, and transverses the monomer,monomer interface via changes in H74 and H74rsquo;. In general, intermediates detected in this study are not apparent in the crystal structures. Observations from the simulations are in good agreement with biochemical data and provide a spatial and sequential framework for interpreting existing genetic data. [source] A case of structure determination using pseudosymmetryACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Sergei Radaev Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: am = bo,co, bm = ao and cm = ,2co,bo. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement. [source] A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Bret D. Freudenthal Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form of the protein. In this nontrimeric form, domain A of one PCNA monomer interacts with domain A of a neighboring monomer, while domain B of this monomer interacts with domain B of a different neighboring monomer. The B,B interface is stabilized by an antiparallel ,-sheet and appears to be structurally similar to the A,B interface observed in the trimeric form of PCNA. The A,A interface, in contrast, is primarily stabilized by hydrophobic interactions. Because the E113G substitution is located on this hydrophobic surface, the A,A interface should be less favorable in the case of the wild-type protein. This suggests that the side chain of Glu113 promotes trimer formation by destabilizing these possible alternate subunit interactions. [source] Structural asymmetry and intersubunit communication in muscle creatine kinaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2007Jeffrey F. Ohren The structure of a transition-state analog complex of a highly soluble mutant (R134K) of rabbit muscle creatine kinase (rmCK) has been determined to 1.65,Å resolution in order to elucidate the structural changes that are required to support and regulate catalysis. Significant structural asymmetry is seen within the functional homodimer of rmCK, with one monomer found in a closed conformation with the active site occupied by the transition-state analog components creatine, MgADP and nitrate. The other monomer has the two loops that control access to the active site in an open conformation and only MgADP is bound. The N-terminal region of each monomer makes a substantial contribution to the dimer interface; however, the conformation of this region is dramatically different in each subunit. Based on this structural evidence, two mutational modifications of rmCK were conducted in order to better understand the role of the amino-terminus in controlling creatine kinase activity. The deletion of the first 15 residues of rmCK and a single point mutant (P20G) both disrupt subunit cohesion, causing the dissociation of the functional homodimer into monomers with reduced catalytic activity. This study provides support for a structural role for the amino-terminus in subunit association and a mechanistic role in active-site communication and catalytic regulation. [source] Crystallization and preliminary X-ray crystallographic analysis of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosaACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2004Hye-Lee Kim The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an adenyl group from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. NaMN AT from Pseudomonas aeruginosa was overexpressed in Escherichia coli and crystallized at 291,K using 100,mM bis,Tris propane pH 7.0, 700,mM trisodium citrate and 15%(v/v) glycerol. X-ray diffraction data have been collected to 1.70,Å. The crystals are tetragonal, belonging to space group P4122 (or P4322), with unit-cell parameters a = b = 65.02, c = 109.80,Å. The presence of one monomer in the asymmetric unit gives a reasonable VM of 2.15,Å3,Da,1, with a solvent content of 42.7%. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray analysis of a female-specific lipocalin (FLP) expressed in the lacrimal glands of Syrian hamstersACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Ved Prakash Dubey Proteins belonging to the lipocalin superfamily are usually secretory proteins of molecular mass ,20,kDa with a hydrophobic pocket for the binding and transport of diverse small ligands. Various lipocalins have been associated with many biological processes, e.g. immunomodulation, odorant transport, pheromonal activity, retinoid transport, cancer-cell interactions etc. However, the exact functions of many lipocalins and the ligands bound by them are unclear. Previously, the cDNA of a 20,kDa lipocalin (FLP) which is female-specifically expressed in the lacrimal glands of Syrian (golden) hamsters and secreted in the tears of females has been identified and cloned. His-tagged recombinant FLP (rFLP) has now been cloned, overexpressed in Escherichia coli as a soluble protein and purified to homogeneity using Ni-affinity followed by size-exclusion chromatography. Purified rFLP was crystallized using the sitting-drop vapour-diffusion method. The crystals tested belonged to space group P212121 and diffracted to beyond 1.86,Å resolution. Solvent-content analysis indicated the presence of one monomer in the asymmetric unit. [source] Cloning, purification, crystallization and X-ray crystallographic analysis of Ignicoccus hospitalis neelaredoxinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Filipa G. Pinho Superoxide reductases (SORs) are metalloproteins which constitute the most recently identified oxygen-detoxification system in anaerobic and microaerobic bacteria and archaea. SORs are involved in scavenging superoxide radicals from the cell by catalyzing the reduction of superoxide () to hydrogen peroxide and are characterized by a catalytic nonhaem iron centre coordinated by four histidine ligands and one cysteine ligand. Ignicoccus hospitalis, a hyperthermophilic crenarchaeon, is known to have a neelaredoxin-type SOR that keeps toxic oxygen species levels under control. Blue crystals of recombinant I. hospitalis oxidized neelaredoxin (14.1,kDa, 124 residues) were obtained. These crystals diffracted to 2.4,Å resolution in-house at room temperature and belonged to the hexagonal space group P6222 or P6422, with unit-cell parameters a = b = 108, c = 64,Å. Cell-content analysis indicated the presence of one monomer in the asymmetric unit. [source] Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal formACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2007Mihwa Lee Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l -dihydroorotate (l -DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989,6997; Lee et al. (2005), J. Mol. Biol.348, 523,533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N -carbamyl- l -aspartate (l -CA-asp) and the active site of the other monomer contains the product of the reaction, l -DHO. In the subunit with l -DHO in the active site, a surface loop (residues 105,115) is `open'. In the other subunit, with l -CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l -CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l -DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1,Å. The structure has been refined to R and Rfree values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the `open' conformation, which is consistent with FOA, like l -DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l -DHO is explained by initial binding of l -DHO to both subunits, followed by slow conversion to l -CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l -DHO and l -CA-asp. [source] Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioidesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2005Marcos Vicente de A. S. Navarro A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293,K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87,Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P212121, with unit-cell parameters a = 46.70, b = 64.14, c = 59.24,Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (VM = 2.5,Å3,Da,1). Iodinated crystals were prepared and a derivative data set was also collected at 2.1,Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5,M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method. [source] Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline stateACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005Olga K. Molchan Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C,N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5,Å resolution and refined to an R factor of 22.1% and an Rfree of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh). [source] | |||||||||||||