Pulsed EPR studies of a bacterial sulfite-oxidizing enzyme with pH-invariant hyperfine interactions from exchangeable protons

Variable-frequency pulsed electron paramagnetic resonance studies of the molybdenum(V) center of sulfite dehydrogenase (SDH) clearly show couplings from nearby exchangeable protons that are assigned to a (MoOHn)-O-v group. The hyperfine parameters for these exchangeable protons of SDH are the same at both low and high pH and similar to those for the high-pH forms of sulfite oxidases (SOs) from eukaryotes. The SDH proton parameters are distinctly different from the low-pH forms of chicken and human so.

Site-directed mutagenesis and kinetic studies of the West Nile virus NS3 protease identify key enzyme-substrate interactions

The flavivirus West Nile virus (WNV) has spread rapidly throughout the world in recent years causing fever, meningitis, encephalitis, and fatalities. Because the viral protease NS2B/NS3 is essential for replication, it is attracting attention as a potential therapeutic target, although there are currently no antiviral inhibitors for any flavivirus. This paper focuses on elucidating interactions between a hexapeptide substrate (Ae-KPGLKR-p-nitroanilide) and residues at S1 and S2 in the active site of WNV protease by comparing the catalytic activities of selected mutant recombinant proteases in vitro. Homology modeling enabled the predictions of key mutations in VWNV NS3 protease at S1 (V115A/F, D129A/ E/N, S135A, Y150A/F, S160A, and S163A) and S2 (N152A) that might influence substrate recognition and catalytic efficiency. Key conclusions are that the substrate P1 Arg strongly interacts with S1 residues Asp-129, Tyr-150, and Ser-163 and, to a lesser extent, Ser-160, and P2 Lys makes an essential interaction with Asn-152 at S2. The inferred substrate-enzyme interactions provide a basis for rational protease inhibitor design and optimization. High sequence conservation within flavivirus proteases means that this study may also be relevant to design of protease inhibitors for other flavivirus proteases.

Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dynamics. Taking lipid rafts as representative microdomains, we show that reduced protein mobility in rafts segregates dynamically partitioning proteins, but the equilibrium concentration is largely independent of raft size and mobility. Rafts weakly impede small-scale protein diffusion but more strongly impede long-range protein mobility. The long-range mobility of raft-partitioning and raft-excluded proteins, however, is reduced to a similar extent. Dynamic partitioning into rafts increases specific interprotein collision rates, but to maximize this critical, biologically relevant function, rafts must be small (diameter, 6 to 14 nm) and mobile. Intermolecular collisions can also be favored by the selective capture and exclusion of proteins by rafts, although this mechanism is generally less efficient than simple dynamic partitioning. Generalizing these results, we conclude that microdomains can readily operate as protein concentrators or isolators but there appear to be significant constraints on size and mobility if microdomains are also required to function as reaction chambers that facilitate nanoscale protein-protein interactions. These results may have significant implications for the many signaling cascades that are scaffolded or assembled in plasma membrane microdomains.

Interfacial interactions and structure of polyurethane intercalated nanocomposite

Understanding the interfacial interactions between the nanofiller and polymer matrix is important to improve the design and manufacture of polymer nanocomposites. This paper reports a molecular dynamic Study on the interfacial interactions and structure of a clay-based polyurethane intercalated nanocomposite. The results show that the intercalation of surfactant (i.e. dioctadecyldlmethyl ammonium) and polyurethane (PU) into the nanoconfined gallery of clay leads to the multilayer structure for both surfactant and PU, and the absence of phase separation for PU chains. Such structural characteristics are attributed to the result of competitive interactions among the surfactant, PU and the clay surface, including van der Waals, electrostatic and hydrogen bonding.

Comparative proteomic analysis to study molecular events during gonad development in mice

Sex determination represents a critical bifurcation in the road of embryonic development. It is based on a finely regulated network of gene activity, as well as protein-protein interactions and activation or silencing of signaling pathways. Despite the identification of a number of critical genes, many aspects of the molecular cascade that drives the differentiation of the embryonic gonad into either a testis or an ovary remain poorly understood. To identify new proteins involved in this cascade, we employed two-dimensional gel electrophoresis and mass spectrometry to compare the protein expression profiles of fetal mouse testes and ovaries. Three proteins, hnRPA1, TRA1, and HSC71, were found to be expressed in a male-specific manner and this expression was confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) and in situ hybridization. Moreover, HSC71 was found to be hyperphosphorylated in male compared to female gonads, emphasizing the advantage of the proteomic approach in allowing the detection of posttranslational modifications.

Effects of structural variation in xyloglucan polymers on interactions with bacterial cellulose

A cellulose/xyloglucan framework is considered to form the basis for the mechanical properties of primary plant cell walls and hence to have a major influence on the biomechanical properties of growing, fleshy plant tissues. In this study, structural variants of xyloglucan have been investigated as components of composites with bacterial cellulose as a simplified model for the cellulose/xyloglucan framework of primary plant cell walls. Evidence for molecular binding to cellulose with perturbation of cellulose crystallinity was found for all xyloglucan types. High molecular mass samples gave homogeneous centimeter-scale composites with extensive cross-linking of cellulose with xyloglucan. Lower molecular mass xyloglucans gave heterogeneous composites having a range of microscopic structures with little, if any, cross-linking. Xyloglucans with reduced levels of galactose substitution had evidence of self-association, competitive with cellulose binding. At comparable molecular mass, fucose substitution resulted in a modest promotion of microscopic features characteristic of primary cell walls. Taken together, the data are evidence that galactose substitution of the xyloglucan core structure is a major determinant of cellulose composite formation and properties, with additional fucose substitution acting as a secondary modulator. These conclusions are consistent with reported structural and mechanical properties of Arabidopsis mutants lacking specific facose and/or galactose residues.

First-principles quantum simulations of dissociation of molecular condensates: Atom correlations in momentum space

We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the molecules and atoms are simulated from first principles in three dimensions using the positive-P representation method. This allows us to provide an exact treatment of the molecular field depletion and s-wave scattering interactions between the particles, as well as to extend the analysis to nonuniform systems. In the simplest uniform case, we find that the major source of atom-atom decorrelation is atom-atom recombination which produces molecules outside the initially occupied condensate mode. The unwanted molecules are formed from dissociated atom pairs with nonopposite momenta. The net effect of this process-which becomes increasingly significant for dissociation durations corresponding to more than about 40% conversion-is to reduce the atom-atom correlations. In addition, for nonuniform systems we find that mode mixing due to inhomogeneity can result in further degradation of the correlation signal. We characterize the correlation strength via the degree of squeezing of particle number-difference fluctuations in a certain momentum-space volume and show that the correlation strength can be increased if the signals are binned into larger counting volumes.

Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 x 10(11) possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 angstrom r.m.s. deviation of C alpha atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes.

Molecular crowding effects of linear polymers in protein solutions

Measurement of protein-polymer second virial coefficients (B-AP) by sedimentation equilibrium studies of carbonic anhydrase and cytochrome c in the presence of dextrans (T10-T80) has revealed an inverse dependence of B-AP upon dextran molecular mass that conforms well with the behaviour predicted for the excluded-volume interaction between a spherical protein solute A and a random-flight representation of the polymeric cosolute P. That model of the protein-polymer interaction is also shown to provide a reasonable description of published gel chromatographic and equilibrium dialysis data on the effect of polymer molecular mass on BAP for human serum albumin in the presence of polyethylene glycols, a contrary finding from analysis of albumin solubility measurements being rejected on theoretical grounds. Inverse dependence upon polymer chainlength is also the predicted excluded-volume effect on the strength of several types of macromolecular equilibria-protein isomerization, protein dimerization, and 1 : 1 complex formation between dissimilar protein reactants. It is therefore concluded that published experimental observations of the reverse dependence, preferential reaction enhancement within DNA replication complexes by larger polyethylene glycols, must reflect the consequences of cosolute chemical interactions that outweigh those of thermodynamic nonideality arising from excluded-volume effects. (c) 2005 Elsevier B.V. All rights reserved.

Quantum gate based on Stark tunable nanocrystal interactions with ultrahigh-Q/V field modes in fused silica microcavities

We investigate the use of nanocrystal quantum dots as a quantum bus element for preparing various quantum resources for use in photonic quantum technologies. Using the Stark-tuning property of nanocrystal quantum dots as well as the biexciton transition, we demonstrate a photonic controlled-NOT (CNOT) interaction between two logical photonic qubits comprising two cavity field modes each. We find the CNOT interaction to be a robust generator of photonic Bell states, even with relatively large biexciton losses. These results are discussed in light of the current state of the art of both microcavity fabrication and recent advances in nanocrystal quantum dot technology. Overall, we find that such a scheme should be feasible in the near future with appropriate refinements to both nanocrystal fabrication technology and microcavity design. Such a gate could serve as an active element in photonic-based quantum technologies.

Venom proteins from polydnavirus-producing endoparasitoids: Their role in host-parasite interactions

Endoporasitoid wasps have evolved various mechanisms to ensure successful development of their progeny, including co-injection of a cocktail of maternal secretions into the host hemocoel, including venom, calyx fluid, and polydnoviruses. The components of each type of secretion may influence host physiology and development independently or in a synergistic fashion. For example, venom fluid consists of several peptides and proteins that promote expression of polydnavirus genes in addition to other activities, such as inhibition of prophenoloxidase activation, inhibition of hemocytes spreading and aggregation, and inhibition of development. This review provides a brief overview of advances and prospects in the study of venom proteins from polydnavirus-producing endoparositoid wasps with a special emphasis on the role of C. rubecula venom proteins in host-parositoid interactions.

Drop formation and breakup of low viscosity elastic fluids: Effects of molecular weight and concentration

The dynamics of drop formation and pinch-off have been investigated for a series of low viscosity elastic fluids possessing similar shear viscosities, but differing substantially in elastic properties. On initial approach to the pinch region, the viscoelastic fluids all exhibit the same global necking behavior that is observed for a Newtonian fluid of equivalent shear viscosity. For these low viscosity dilute polymer solutions, inertial and capillary forces form the dominant balance in this potential flow regime, with the viscous force being negligible. The approach to the pinch point, which corresponds to the point of rupture for a Newtonian fluid, is extremely rapid in such solutions, with the sudden increase in curvature producing very large extension rates at this location. In this region the polymer molecules are significantly extended, causing a localized increase in the elastic stresses, which grow to balance the capillary pressure. This prevents the necked fluid from breaking off, as would occur in the equivalent Newtonian fluid. Alternatively, a cylindrical filament forms in which elastic stresses and capillary pressure balance, and the radius decreases exponentially with time. A (0+1)-dimensional finitely extensible nonlinear elastic dumbbell theory incorporating inertial, capillary, and elastic stresses is able to capture the basic features of the experimental observations. Before the critical "pinch time" t(p), an inertial-capillary balance leads to the expected 2/3-power scaling of the minimum radius with time: R-min similar to(t(p)-t)(2/3). However, the diverging deformation rate results in large molecular deformations and rapid crossover to an elastocapillary balance for times t>t(p). In this region, the filament radius decreases exponentially with time R-min similar to exp[(t(p)-t)/lambda(1)], where lambda(1) is the characteristic time constant of the polymer molecules. Measurements of the relaxation times of polyethylene oxide solutions of varying concentrations and molecular weights obtained from high speed imaging of the rate of change of filament radius are significantly higher than the relaxation times estimated from Rouse-Zimm theory, even though the solutions are within the dilute concentration region as determined using intrinsic viscosity measurements. The effective relaxation times exhibit the expected scaling with molecular weight but with an additional dependence on the concentration of the polymer in solution. This is consistent with the expectation that the polymer molecules are in fact highly extended during the approach to the pinch region (i.e., prior to the elastocapillary filament thinning regime) and subsequently as the filament is formed they are further extended by filament stretching at a constant rate until full extension of the polymer coil is achieved. In this highly extended state, intermolecular interactions become significant, producing relaxation times far above theoretical predictions for dilute polymer solutions under equilibrium conditions. (C) 2006 American Institute of Physics

Molecular control of cell type diversity in the developing spinal cord

1, During embryonic development, a diverse array of neurons and glia are generated at specific positions along the dorsoventral and rostro-caudal axes of the spinal cord from a common pool of precursor cells. 2. This cell type diversity can be distinguished by the spatially and temporally coordinated expression of several transcription factors that are also linked to cell type specification at a very early stage of spinal cord development. 3, Recent studies have started to uncover that the generation of cell type diversity in the developing spinal cord. Moreover, distinct cell types in the spinal cord appear to be determined by the spatially and temporally coordinated expression of transcription factors. 4. The expression of these factors also appears to be controlled by gradients of factors expressed by ventral and dorsal midline cells, namely Sonic hedgehog and members of the transforming growth factor-beta family. 5, Changes in the competence of precursor cells and local cell interactions may also play important roles in cell type specification within the developing spinal cord.