Characterization of the DNA-binding domain of beta protein, a component of phage lambda Red-pathway by UV catalyzed cross-linking

beta protein, a key component of Red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of Escherichia coli. To facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. A chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. A 67-kDa band, corresponding to homodimer, was identified after separation by SDS-polyacrylamide gel electrophoresis. Stoichiometric measurements indicated a site-size of 1 monomer of beta protein/5 nucleotide residues. Electrophoretic gel mobility shift assays suggested that beta protein formed stable nucleoprotein complexes with 36-mer, but not with 27- or 17-mer DNA. Interestingly, the interaction of beta protein with DNA and the stability of nucleoprotein complexes was dependent on the presence of MgCl2, and the binding was abolished by 250 mM NaCl. The K-d of beta protein binding to 36-mer DNA was on the order of 1.8 x 10(-6) M. Photochemical cross-linking of native beta protein or its fragments, generated by chymotrypsin, to 36-mer DNA was performed to identify its DNA-binding domain. Characterization of the cross-linked peptide disclosed that amino acids required for DNA-binding specificity resided within a 20-kDa peptide at the N-terminal end. These findings provide a basis for further understanding oi the structure and function of beta protein.

Molecular dynamic simulations of elastomer structure and its influence on anisotropic stress under time-varying strain

We investigate the evolution of polymer structure and its influence on uniaxial anisotropic stress under time-varying uniaxial strain, and the role of external control variables such as temperature, strain rate, chain length, and density, using molecular dynamics simulation. At temperatures higher than glass transition, stress anisotropy in the system is reduced even though the bond stretch is greater at higher temperatures. There is a significant increase in the stress level with increasing density. At higher densities, the uncoiling of the chains is suppressed and the major contribution to the deformation is by internal deformation of the chains. At faster rates of loading stress anisotropy increases. The deformation mechanism is mostly due to bond stretch and bond bending rather than overall shape and size. Stress levels increase with longer chain length. There is a critical value of the functionality of the cross-linkers beyond which the uniaxial stress developed increases caused primarily by bond stretching due to increased constraint on the motion of the monomers. Stacking of the chains in the system also plays a dominant role in the behaviour in terms of excluded volume interactions. Low density, high temperature, low values of functionality of cross-linkers, and short chain length facilitate chain uncoiling and chain slipping in cross-linked polymers.

Three-dimensional plotted hydroxyapatite scaffolds with predefined architecture: comparison of stabilization by alginate cross-linking versus sintering

Scaffolds for bone tissue engineering are essentially characterized by porous three-dimensional structures with interconnected pores to facilitate the exchange of nutrients and removal of waste products from cells, thereby promoting cell proliferation in such engineered scaffolds. Although hydroxyapatite is widely being considered for bone tissue engineering applications due to its occurrence in the natural extracellular matrix of this tissue, limited reports are available on additive manufacturing of hydroxyapatite-based materials. In this perspective, hydroxyapatite-based three-dimensional porous scaffolds with two different binders (maltodextrin and sodium alginate) were fabricated using the extrusion method of three-dimensional plotting and the results were compared in reference to the structural properties of scaffolds processed via chemical stabilization and sintering routes, respectively. With the optimal processing conditions regarding to pH and viscosity of binder-loaded hydroxyapatite pastes, scaffolds with parallelepiped porous architecture having up to 74% porosity were fabricated. Interestingly, sintering of the as-plotted hydroxyapatite-sodium alginate (cross-linked with CaCl2 solution) scaffolds led to the formation of chlorapatite (Ca9.54P5.98O23.8Cl1.60(OH)(2.74)). Both the sintered scaffolds displayed progressive deformation and delayed fracture under compressive loading, with hydroxyapatite-alginate scaffolds exhibiting a higher compressive strength (9.5 +/- 0.5MPa) than hydroxyapatite-maltodextrin scaffolds (7.0 +/- 0.6MPa). The difference in properties is explained in terms of the phase assemblage and microstructure.

Role of transglutaminase-mediated cross-linking of protein in the temperature-dependent setting of Alaska pollack surimi

During the low temperature setting of fish paste, myosin heavy chain (MHC) is polymerized to cross-linked myosin heavy chain (CMHC), which is considered to occur by the action of endogenous transglutaminase (TGase). In this study the contribution of TGase on the setting of Alaska pollack surimi at different temperatures was studied. Alaska pollack surimi was ground with 3% NaCl, 30% h2o and with or without ethylene glycol bis (β-aminoethylether) N, N, N¹,N¹- tetra acetic acid (EGTA), an inhibitor of TGase. Among the pastes without EGTA, highest TGase activity was observed at 25°C but breaking force of the gel set at 25°C was lower than that set at 30°, 35°, and 40°C. Addition of EGTA (5m mol/kg) to the paste suppressed TGase activity at all setting temperatures from 20° to 40°C. Gelation of the pastes and cross-linking of MHC on addition of EGTA were suppressed completely at 20° and 25°C, partially at 30° and 35°C, and not at all at 40°C. The findings suggested that during the setting of Alaska pollack surimi TGase mediated cross-linking of MHC was strong at around 25°C but the thermal aggregation of MHC by non-covalent bonds was strong at above 35°C. Setting of surimi at 40°C and cross-linking of its MHC did not involve TGase.

Using mesoscopic models to design strong and tough biomimetic polymer networks

Using computational modeling, we investigate the mechanical properties of polymeric materials composed of coiled chains, or "globules", which encompass a folded secondary structure and are cross-linked by labile bonds to form a macroscopic network. In the presence of an applied force, the globules can unfold into linear chains and thereby dissipate energy as the network is deformed; the latter attribute can contribute to the toughness of the material. Our goal is to determine how to tailor the labile intra- and intermolecular bonds within the network to produce material exhibiting both toughness and strength. Herein, we use the lattice spring model (LSM) to simulate the globules and the cross-linked network. We also utilize our modified Hierarchical Bell model (MHBM) to simulate the rupture and reforming of N parallel bonds. By applying a tensile deformation, we demonstrate that the mechanical properties of the system are sensitive to the values of N in and N out, the respective values of N for the intra- and intermolecular bonds. We find that the strength of the material is mainly controlled by the value of N out, with the higher value of N out providing a stronger material. We also find that, if N in is smaller than N out, the globules can unfold under the tensile load before the sample fractures and, in this manner, can increase the ductility of the sample. Our results provide effective strategies for exploiting relatively weak, labile interactions (e.g., hydrogen bonding or the thiol/disulfide exchange reaction) in both the intra- and intermolecular bonds to tailor the macroscopic performance of the materials. © 2011 American Chemical Society.

Polyamide thin film composite membranes prepared from 3,4',5-biphenyl triacyl chloride, 3,3',5,5'-biphenyl tetraacyl chloride and m-phenylenediamine

Two novel of tri- and tetra-functional biphenyl acid chloride: 3,4',5-biphenyl triacyl chloride (BTRC) and 3,3',5,5'-biphenyl tetraacyl chloride (BTEC), were synthesized, and used as new monomers for the preparations of the thin film composite (TFC) reverse osmosis (RO) membranes. The TFC RO membranes were prepared on a polysulfone supporting film through interfacial polymerization with the two new monomers and m-phenylenediamine (MPD). The membranes were characterized for the permeation properties, chemical composition, d-space between polymer chains, hydrophilicity, membrane morphology including top surface and cross-section. Permeation experiment was employed to evaluate the membranes performance including salt rejection and water flux. The surface structure and chemical composition of membranes were analyzed by attenuated total reflectance infrared (ATR-IR) and X-ray photoelectronic spectroscopy (XPS). The results revealed that the active layer of membranes was composed of highly cross-linked aromatic polyamide with the functional acylamide (-CONH-) bonds. The TFC membranes prepared from biphenyl acid chloride exhibit higher salt rejection compared with that prepared from trimesoyl chloride (TMC) at the expanse of some flux.

A stable PEO-tethered PDMS surface having controllable wetting property by a swelling-deswelling process

A PEO-tethered layer on a PDMS (polydimethylsiloxane) cross-linked network has been prepared by a swelling-deswelling process. During swelling, the PDMS block of a PDMS-b-PEO diblock copolymer penetrates into the PDMS substrate and interacts with PDMS chains because of the van der Waals force and hydrophobic interaction between them. Upon deswelling, the PDMS block is trapped in the PDMS matrix while the PEO, as a hydrophilic block, is tethered to the surface. The PEO-tethered layer showed stability when treated in water for 16 h. The surface fraction of PEO and the wetting property of the PEO-tethered PDMS surface can be controlled by the cross linking density of the PDMS matrix. A patterned PEO-tethered layer on a PDMS network was also created by microcontact printing and water condensation figures (CFs) were used to study the patterned surface with different wetting properties.

Anion coordination and molecular assembly in C2-substituted thiamine-anion systems: effects of the anion and molecular conformation

The compounds (het)(PtCl6)2H(2)O 1, (het)(HgI4).H2O 2 (het = 2-(alpha-hydroxyethyl)thiamine) and (hpt)(Hg2Br6) 3 (hpt = 2-(alpha-hydroxypropyl)thiamine) have been prepared and structurally characterized by X-ray crystallography in order to study the influence of the anion and molecular conformation on the formation of supramolecular architectures that adsorb anionic species. Both het and hpt molecules adopt the usual S conformation for C2-substituted thiamine but differ from the F conformation for C2-free thiamine derivatives. Two types of characteristic ligand-anion complexation are observed, being of the forms C(6')-H...anion...thiazolium-ring (in 1 and 2) and N(4'1)-H...anion...thiazolium-ring (in 3). The reaction of het with PtCl62- or HgI42- gives a 1-D double-chain in 1, consisting of two hydrogen-bonded het chains, which are cross-linked by anions through hydrogen bonding and anion...aromatic-ring interactions, or a cationic 3-D framework in 2 formed by the stacking of hydrogen-bonded sheets with anion-and-water-filled channels. In the case of 3, hydrogen-bonded hpt dimers and HgBr62- anions form alternate cation-anion columns. A comparison with the cases of C2-free thiamine-anion complexes indicates that the change in molecular conformation results in novel supramolecular assemblies in 1 and 2 and an analogous architecture in 3, which also depends on the nature of the anions.

Advanced research work on radiation cross-linking of polymers in CIAC

Recent research carried out at the Chinese Institute of Applied Chemistry has contributed significantly to the understanding of the radiation chemistry of polymers. High energy radiation has been successfully used to cross-link fluoropolymers and polyimides. Here chain flexibility has been shown to play an important role, and T-type structures were found to exist in the cross-linked fluoropolymers. A modified Charlesby-Pinner equation, based upon the importance of chain flexibility, was developed to account for the sol-radiation dose relationship in systems of this type. An XPS method has been developed to measure the cross-linking yields in aromatic polymers and fluoropolymers, based upon the dose dependence of the aromatic shake-up peaks and the F/C ratios, respectively. Methods for radiation cross-linking degrading polymers in polymer blends have also been developed, as have methods for improving the radiation resistance of polymers through radiation cross-linking.

Lanthanide coordination polymers with dicarboxylate-like ligands: crystal structures of polymeric lanthanum(III) and terbium(III) complexes with flexible double betaines

Four novel polymeric lanthanide(III) complexes of two new double betaine derivatives have been synthesized and structurally determined. In [{La-2(L-1)(2)(H2O)(9)}(n)]Cl-6n. 2nH(2)O (1) and [{Tb(L-1)(H2O)(4)}(n)]Cl-3n. nH(2)O (2) (L-1 =4,4'-trimethylenedipyridinio-N,N'-diacetate), the lanthanide(III) ions form a two-dimensional layer in which each pair of lanthanide(III) ions is bridged by two syn-anti mu-carboxylato-O,O' groups. Adjacent layers are cross-linked through hydrogen bonds among aqua ligands, lattice water molecules and chloride ions, to form a three-dimensional network. Isomorphous [{Ln(L-1)(H2O)(4)}(n)]Cl-3n. 5nH(2)O (Ln=La, 3; Ln=Tb, 4; L-2=1,3 bis(pyridinio-4-carboxylato)-propane) each contain a centrosymmetric paddle-wheel-like dimeric unit in which each pair of adjacent metal atoms is bridged by four syn-syn mu-carboxylato-O,O' groups that are oriented nearly perpendicular to each other about the metal-metal axis. Neighboring dimeric subunits are bridged by a pair of flexible LL ligands into a polymeric chain. Adjacent chains are inter-linked by hydrogen bonds among aqua ligands, lattice water molecules and chloride ions into a three-dimensional network. (C) 1999 Elsevier Science Ltd. All rights reserved.

Synthesis, crystal structure and luminescence studies of a lanthanide coordination polymer with a new double betaine ligand

A novel europium(III) coordination polymer with a new double betaine derivative, {[Eu(L')(NO3)(H2O)(3)](NO3)(2). 3.5H(2)O}(n) (L-1 = 1,3-bis(pyridinio-4-carboxylato)-propane) has been synthesized and its structure determined. Its luminescence properties have also been studied. The title metal carboxylate coordination polymer contains centrosymmetric dimeric units in which each pair of metal ions is linked by a pair of syn-anti carboxylato-O,O' groups, and each pair of such dimeric units is bridged by the backbones of L-1 ligands to form infinite double chains in the b direction. These metal carboxylate chains are further cross-linked by hydrogen bonds among both coordinated and discrete nitrate anions, aqua ligands and lattice water molecules to form a three-dimensional network. Luminescent data show that the L-1 ligand is a good energy donor and the complex has a relatively long luminescent lifetime.

Structural characterization and luminescence studies of new lanthanide(III) complexes with nicotinic and isonicotinic acid N-oxides

Four new polymeric lanthanide(III) complexes of nicotinic acid N-oxide and isonicotinic acid N-oxide have been synthesized and structurally determined. In the isomorphous compounds [(Ln(L-1)(3) (H2O)(2))(n)]. 4nH(2)O(HL1 = nicotinic acid N-oxide; Ln = Eu, 1; Ln = Er, 2) the lanthanide(III) ions form infinite double chains along the b direction through the coordination of bridging carboxylate and N-oxide groups. The chains are cross-linked through hydrogen bonds between aqua ligands and uncoordinated N-oxide groups and between aqua ligands and lattice water molecules, to form a three-dimensional network. [(Eu(L-2)(2)-(H2O)(4))(n)](NO3)(n). nH(2)O (HL2 = isonicotinic acid N-oxide, 3) has a polymeric structure in which the europium (III) ions are connected into infinite chains by pairs of syn-syn carboxylate groups. Adjacent chains are interlinked by hydrogen bonds between aqua ligands and N-oxide groups to form a layer parallel to the (100) plane, and such layers are connected by hydrogen bonds between nitrate anions and aqua ligands, and between oxide groups and lattice water molecules, into a three-dimensional network. In [(Er-2(L-2)(4)(H2O)(10))](NO3)(2). H2O, 4, dinuclear units are inter-linked into a three-dimensional network through hydrogen bonding between aqua ligands and N-oxide groups of both bidentate bridging and unidentate L-2 ligands. Factors affecting the formation of coordination chains and dinuclear units are discussed. Luminescence properties of 1 and 3 have also been studied. (C) 1998 Elsevier Science Ltd. All rights reserved.

Synthesis and crystal structure of a polymeric erbium(III)-sodium(I) coordination complex of picolinic acid N-oxide

A new Er(III)-Na(I) coordination polymer of stoichiometry [NaEr2L5(H2O)(6)(NO3)](NO3). 3.5H(2)O (HL = picolinic acid N-oxide) has been synthesized and characterized by single-crystal X-ray analysis. Crystals are triclinic, P (1) over bar with a = 9.823(2), b = 12.453(2), c = 20.643(4) Angstrom; alpha = 98.49(3), beta = 101.40(3), gamma = 108.69(3)degrees; V = 2284(1) Angstrom(3); Z = 2. Of the two independent eight-coordinate erbium(III) ions in this complex, one is surrounded by four bidentate chelating L ligands, and the other by one bidentate chelating L ligand, four aqua ligands and two anti-carboxylate oxygen atoms from two neighboring [ErL4] units. The sodium(I) ion is in a distorted octahedral environment, being coordinated by a unidentate nitrate anion, three aqua ligands and two anti-carboxylate oxygen atoms from two adjacent [ErL4] units. The complex is built from zigzag chains of syn-anti carboxylate-bridged erbium(III) moieties directed in the a direction, which are cross-linked pairwise by aqua-bridged dimeric sodium(I) units. The resulting composite polymeric chains are further connected by hydrogen bonds to form a three-dimensional network.

Synthesis and structural characterization of a novel polymeric praseodymium(III) complex with a new flexible double betaine

A novel polymeric Pr(III) complex with a new double betaine, namely [{Pr(L-1)(1.5)(H2O)(2)}(n)] [ClOli4]3(n). nH(2)O (1) (L-1= 1,4-diazoniobicyclo[2,2,2]octane- 1,4-dipropionate), has been synthesized and characterized by X-ray analysis. In the title complex, the Pr(III) atom is nine-coordinated by seven oxygen atoms from five L-1 ligands and two aqua ligands. Each pair of adjacent praseodymium(III) atoms is linked by a pair of mu(3) chelating and bridging carboxylate groups, thus forming an infinite metal metal chain running parallel to the a direction, and such chains are cross-linked by flexible backbones of L-1 ligands into a three-dimensional network with the perchlorate anions and lattice water molecules accommodated in the interstitial space. The title complex crystallizes in the monoclinic space group P2(1)/n with a = 8.085(2), b = 14.316(3), c = 29.775(6) Angstrom, beta = 103.04(3)degrees and Z = 4.

Numerically Investigating the Effects of Cross-Links in Scaled Microchannel Heat Sinks

Thermal management as a method of heightening performance in miniaturized electronic devices using microchannel heat sinks has recently become of interest to researchers and the industry. One of the current challenges is to design heat sinks with uniform flow distribution. A number of experimental studies have been conducted to seek appropriate designs for microchannel heat sinks. However, pursuing this goal experimentally can be an expensive endeavor. The present work investigates the effect of cross-links on adiabatic two-phase flow in an array of parallel channels. It is carried out using the three dimensional mixture model from the computational fluid dynamics software, FLUENT 6.3. A straight channel and two cross-linked channel models were simulated. The cross-links were located at 1/3 and 2/3 of the channel length, and their widths were one and two times larger than the channel width. All test models had 45 parallel rectangular channels, with a hydraulic diameter of 1.59 mm. The results showed that the trend of flow distribution agrees with experimental results. A new design, with cross-links incorporated, was proposed and the results showed a significant improvement of up to 55% on flow distribution compared with the standard straight channel configuration without a penalty in the pressure drop. Further discussion about the effect of cross-links on flow distribution, flow structure, and pressure drop was also documented.