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At least 991 records · Page 55Linked to original sources
PubMed1978

Purification and properties of an NAD(P)+-linked formaldehyde dehydrogenase from Methylococcus capsulatus (Bath).

Crude soluble extracts of Methylococcus capsulatus strain Bath, grown on methane, were found to contain NAD(P)+-linked formaldehyde dehydrogenase activity. Activity in the extract was lost on dialysis against phosphate buffer, but could be restored by supplementing with inactive, heat-treated extract (70 degrees C for 12 min). The non-dialysable, heat-sensitive component was isolated and purified, and has a molecular weight of about 115000. Sodium dodecyl sulphate gel electrophoresis of the protein suggested there were two equal subunits with molecular weights of 57000. The heat-stable fraction, which was necessary for activity of the heat-sensitive protein, was trypsin-sensitive and presumed to be a low molecular weight protein or peptide. A number of thiol compounds and other common cofactors could not replace the component present in the heat-treated soluble extract. The purified formaldehyde dehydrogenase oxidized three other aldehydes with the following Km values: 0.68 mM (formaldehyde); 0.075 mM (glyoxal); 7.0 mM (glycolaldehyde); and 2.0 mM (DL-glyceraldehyde). NAD+ or NADP+ was required for activity, with Km values of 0.063 and 0.155 mM respectively, and could not be replaced by any of the artificial electron acceptors tested. The enzyme was heat-stable at 45 degrees C for at least 10 min and had temperature and pH optima of 45 degrees C and pH 7.2 respectively. A number of metal-binding agents and substrate analogues were not inhibitory. Thiol reagents gave varying degrees of inhibition, the most potent being p-hydroxymercuribenzoate which at 1 mM gave 100% inhibition. The importance of possessing an NAD(P)+-linked formaldehyde dehydrogenase, with respect to M. capsulatus, is discussed.

Aldehyde Oxidoreductases↗
PubMed1992

Functional expression in Escherichia coli of proteins B and C from soluble methane monooxygenase of Methylococcus capsulatus (Bath).

Methylococcus capsulatus (Bath) uses a soluble methane monooxygenase (sMMO) to catalyse the oxidation of methane to methanol. sMMO is comprised of three components; A, B and C. Protein C (the reductase) transfers electrons from NADH to protein A (the hydroxylase) which contains the active site, and protein B regulates this electron flow. The five genes encoding the sMMO proteins and their subunits are clustered and have been cloned in Escherichia coli. A DNA fragment containing mmoB, the gene encoding protein B, was subcloned into pT7-5, a plasmid of the T7 RNA polymerase promoter expression system. Upon induction, E. coli expressed protein B which was fully functional after purification. The gene encoding protein C, mmoC, was amplified with unique restriction sites at each end using the polymerase chain reaction and then subcloned into pT7-7 (a plasmid similar to pT7-5 but containing its own ribosome-binding site and ATG start codon). Protein C expressed in E. coli was also found to be functional. This is the first report of the functional expression of methanotroph methane monooxygenase genes in a heterologous host and represents a significant step forward in our analysis of the assembly and catalysis of sMMO.

Base Sequence↗
PubMed1992

Presence of methyl sterol and bacteriohopanepolyol in an outer-membrane preparation from Methylococcus capsulatus (Bath).

Cytoplasmic/intracytoplasmic and outer membrane preparations of Methylococcus capsulatus (Bath) were isolated by sucrose density gradient centrifugation of a total membrane fraction prepared by disruption using a French pressure cell. The cytoplasmic and/or intracytoplasmic membrane fraction consisted of two distinct bands, Ia and Ib (buoyant densities 1.16 and 1.8 g ml-1, respectively) that together contained 57% of the protein, 68% of the phospholipid, 73% of the ubiquinone and 89% of the CN-sensitive NADH oxidase activity. The only apparent difference between these two cytoplasmic bands was a much higher phospholipid content for Ia. The outer membrane fraction (buoyant density 1.23 - 1.24 g ml-1) contained 60% of the lipopolysaccharide-associated, beta-hydroxypalmitic acid, 74% of the methylsterol, and 66% of the bacteriohopanepolyol (BHP); phospholipid to methyl sterol or BHP ratios were 6:1. Methanol dehydrogenase activity and a c-type cytochrome were also present in this outer membrane fraction. Phospholipase A activity was present in both the cytoplasmic membrane and outer membrane fractions. The unique distribution of cyclic triterpenes may reflect a specific role in conferring outer membrane stability in this methanotrophic bacterium.

Biological Evolution↗
PubMed1996

Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions.

Methane is oxidized to methanol by the enzyme methane mono-oxygenase (MMO) in methanotrophic bacteria. In previous work, this multicomponent enzyme system has been extensively characterized at the biochemical and molecular level. Copper ions have been shown to irreversibly inhibit MMO activity in vivo and in vitro, but the effect of copper ions on transcription of the genes encoding the soluble (cytoplasmic) MMO (sMMO) has not previously been investigated. To examine more closely the regulation of bacterial methane oxidation and to determine the role of copper in this process, we have investigated transcriptional regulation of the sMMO gene cluster in the methanotrophic bacterium Methylococcus capsulatus (Bath). Using Northern blot analysis and primer extension experiments, it was shown that the six ORFs of the sMMO gene cluster are organized as an operon and the transcripts produced upon expression of this operon have been identified. The synthesis of these transcripts was under control of a single copper-regulated promoter, which is as yet not precisely defined.

Bacterial Proteins↗
PubMed1999

A low-molecular-mass protein from Methylococcus capsulatus (Bath) is responsible for the regulation of formaldehyde dehydrogenase activity in vitro.

An 8.6 kDa protein, which the authors call a modifin, has been purified from Methylococcus capsulatus (Bath) and has been shown to alter the substrate specificity and kinetics of NAD+-linked formaldehyde dehydrogenase (FDH) isolated from the same organism. Purification methods for both the modifin and FDH are presented which reliably produced pure protein for further analysis. Analysis of the molecular mass and N-terminal sequence of both FDH and the modifin indicate that they are unique proteins and show no similarity to alcohol or aldehyde dehydrogenase enzymes isolated from methylotrophic bacteria. Substrate specificity studies demonstrated that FDH oxidized formaldehyde exclusively in the presence of the modifin; a diverse range of aldehydes and alcohols were oxidized by FDH in the absence of the modifin. No formaldehyde oxidation was detected in the absence of the modifin. Attempts to replace the modifin with glutathione or high concentrations of methanol to stimulate formaldehyde oxidation failed. With acetaldehyde as substrate, FDH showed standard Michaelis-Menten kinetics; interaction of FDH with the modifin using formaldehyde as substrate altered the kinetics of the reaction to sigmoidal. Kinetic analysis during turnover experiments indicated that the FDH may be associated with bound formaldehyde following enzyme isolation and that NAD may also be associated with the enzyme but in a form that is less tightly bound than found with the methanol dehydrogenase from Bacillus methanolicus. Data are presented which indicate that the modifin may play an important role in regulating formaldehyde concentration in vivo.

Alcohols↗
PubMed2004

Formaldehyde dehydrogenase preparations from Methylococcus capsulatus (Bath) comprise methanol dehydrogenase and methylene tetrahydromethanopterin dehydrogenase.

In methylotrophic bacteria, formaldehyde is an important but potentially toxic metabolic intermediate that can be assimilated into biomass or oxidized to yield energy. Previously reported was the purification of an NAD(P)(+)-dependent formaldehyde dehydrogenase (FDH) from the obligate methane-oxidizing methylotroph Methylococcus capsulatus (Bath), presumably important in formaldehyde oxidation, which required a heat-stable factor (known as the modifin) for FDH activity. Here, the major protein component of this FDH preparation was shown by biophysical techniques to comprise subunits of 64 and 8 kDa in an alpha(2)beta(2) arrangement. N-terminal sequencing of the subunits of FDH, together with enzymological characterization, showed that the alpha(2)beta(2) tetramer was a quinoprotein methanol dehydrogenase of the type found in other methylotrophs. The FDH preparations were shown to contain a highly active NAD(P)(+)-dependent methylene tetrahydromethanopterin dehydrogenase that was the probable source of the NAD(P)(+)-dependent formaldehyde oxidation activity. These results support previous findings that methylotrophs possess multiple pathways for formaldehyde dissimilation.

Alcohol Oxidoreductases↗
PubMed1999

Emergence of on-off intermittency in systems nonlinearly coupled to a nonequilibrium bath.

Approximate analytic solutions are presented for the dynamics of a classical oscillator nonlinearly coupled to a nonequilibrium bath. It is shown that as a result of the combined effect of the nonlinear coupling, which leads to nonlinear friction and multiplicative noise in the description of the reduced system, and the nonthermal properties of the reservoir, which give a specific self-sustained character to the coarse-grained oscillator, on-off intermittency can occur. Properties of this phenomenon, such as the universality in the length distribution of the laminar phase and the qualitative changes caused by the presence of additive noise, can be traced back to characteristics of the starting microscopic model.

Journal Article↗
PubMed2001

Active and passive particles: modeling beads in a bacterial bath.

A simple model for the motion of passive particles in a bath of active, self-propelled ones is introduced. It is argued that this approach provides the correct framework within which to cast the recent experimental results obtained by Wu and Libchaber [Phys Rev. Lett. 84, 3017 (2000)] for the diffusive properties of polystyrene beads displaced by bacteria suspended in a two-dimensional fluid film. Our results suggest that superdiffusive behavior should indeed be generically observed in the transition region marking the onset of collective motion.

Bacterial Physiological Phenomena↗
PubMed2001

Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model.

Permeation of ions from one electrolytic solution to another, through a protein channel, is a biological process of considerable importance. Permeation occurs on a time scale of micro- to milliseconds, far longer than the femtosecond time scales of atomic motion. Direct simulations of atomic dynamics are not yet possible for such long-time scales; thus, averaging is unavoidable. The question is what and how to average. In this paper, we average a Langevin model of ionic motion in a bulk solution and protein channel. The main result is a coupled system of averaged Poisson and Nernst-Planck equations (CPNP) involving conditional and unconditional charge densities and conditional potentials. The resulting NP equations contain the averaged force on a single ion, which is the sum of two components. The first component is the gradient of a conditional electric potential that is the solution of Poisson's equation with conditional and permanent charge densities and boundary conditions of the applied voltage. The second component is the self-induced force on an ion due to surface charges induced only by that ion at dielectric interfaces. The ion induces surface polarization charge that exerts a significant force on the ion itself, not present in earlier PNP equations. The proposed CPNP system is not complete, however, because the electric potential satisfies Poisson's equation with conditional charge densities, conditioned on the location of an ion, while the NP equations contain unconditional densities. The conditional densities are closely related to the well-studied pair-correlation functions of equilibrium statistical mechanics. We examine a specific closure relation, which on the one hand replaces the conditional charge densities by the unconditional ones in the Poisson equation, and on the other hand replaces the self-induced force in the NP equation by an effective self-induced force. This effective self-induced force is nearly zero in the baths but is approximately equal to the self-induced force in and near the channel. The charge densities in the NP equations are interpreted as time averages over long times of the motion of a quasiparticle that diffuses with the same diffusion coefficient as that of a real ion, but is driven by the averaged force. In this way, continuum equations with averaged charge densities and mean-fields can be used to describe permeation through a protein channel.

Electrophysiology↗
PubMed2002

Density matrix negativity for two oscillators in an Agarwal bath.

A system of two harmonic oscillators is placed in an Agarwal bath. The resulting quantum master equations are studied with the help of quantum characteristic functions. The density matrix positivity is investigated in view of the recent interest in searching for a sound quantum dissipation theory. An analytical criterion is derived for density matrix negativity for two uncoupled oscillators. It is found that, for an initial two-oscillator squeezed state with a real squeezing parameter s, density matrix negativity occurs for two uncoupled oscillators at temperatures lower than Planck's over 2 pi omega/(k(B) ln coth/s/) with omega the oscillator frequency and k(B) the Boltzmann factor. As a by-product an analytical expression is also obtained for determining the quantum separability of two uncoupled oscillators. The effects of interoscillator coupling on density matrix negativity are discussed.

Journal Article↗
PubMed2004

Resonant activation in the presence of nonequilibrated baths.

We study the generic problem of the escape of a classical particle over a fluctuating barrier under the influence of non-Gaussian noise mimicking the effects of nonequilibrated bath. The model system is described by a Langevin equation with two independent noise sources, one of which stands for the dichotomous process and the other describes external driving by alpha-stable noise. Our attention focuses on the effect of the structure of stable noises on the mean escape time and on the phenomenon of resonant activation. Possible physical interpretation of the occurrence of Lévy noises and the relevance of the model for chemical kinetics is briefly discussed.

Journal Article↗
PubMed2004

Langevin equation for the extended Rayleigh model with an asymmetric bath.

In this paper a one-dimensional model of two infinite gases separated by a movable heavy piston is considered. The nonlinear Langevin equation for the motion of the piston is derived from first principles for the case when the thermodynamic parameters and/or the molecular masses of gas particles on the left and right sides of the piston are different. Microscopic expressions involving time correlation functions of the force between bath particles and the piston are obtained for all parameters appearing in the nonlinear Langevin equation. It is demonstrated that the equation has stationary solutions corresponding to directional fluctuation-induced drift in the absence of systematic forces. In the case of ideal gases interacting with the piston via a quadratic repulsive potential, the model is exactly solvable and explicit expressions for the kinetic coefficients in the nonlinear Langevin equation are derived. The transient solution of the nonlinear Langevin equation is analyzed perturbatively and it is demonstrated that previously obtained results for systems with the hard-wall interaction are recovered.

Journal Article↗
PubMed2006

Classical limit of master equation for a harmonic oscillator coupled to an oscillator bath with separable initial conditions.

The Wigner transform of the master equation describing the reduced dynamics of the system, of a harmonic oscillator coupled to an oscillator bath, was obtained by Karrlein and Grabert [Phys. Rev. E 55, 153 (1997)]. It was shown that for some special correlated initial conditions the master equation reduces, in the classical limit, to the corresponding classical Fokker-Planck equation obtained by Adelman [J. Chem Phys. 64, 124 (1976)]. However, for separable initial conditions the Adelman equations were not recovered. We resolve this problem by showing that, for separable initial conditions, the classical Langevin equations are somewhat different from the one considered by Adelman. We obtain the corresponding Fokker-Planck equation and show that they exactly match the classical limit of the evolution of the Wigner function obtained from the master equation for separable initial conditions. We also discuss why thermal initial conditions correspond to Adelman's solution.

Journal Article↗
PubMed2001

Extracting work from a single thermal bath via quantum negentropy.

Classical heat engines produce work by operating between a high temperature energy source and a low temperature entropy sink. The present quantum heat engine has no cooler reservoir acting as a sink of entropy but has instead an internal reservoir of negentropy which allows extraction of work from one thermal bath. The process is attended by constantly increasing entropy and does not violate the second law of thermodynamics.

Journal Article↗
PubMed2005

Physical limits of heat-bath algorithmic cooling.

Simultaneous near-certain preparation of qubits (quantum bits) in their ground states is a key hurdle in quantum computing proposals as varied as liquid-state NMR and ion traps. "Closed-system" cooling mechanisms are of limited applicability due to the need for a continual supply of ancillas for fault tolerance, and to the high initial temperatures of some systems. "Open-system" mechanisms are therefore required. We describe a new, efficient initialization procedure for such open systems. With this procedure, an n-qubit device that is originally maximally mixed, but is in contact with a heat bath of bias epsilon>>2(-n), can be almost perfectly initialized. This performance is optimal due to a newly discovered threshold effect: for bias epsilon<<2(-n) no cooling procedure can, even in principle (running indefinitely without any decoherence), significantly initialize even a single qubit.

Journal Article↗
PubMed2005

From bouncing to floating: noncoalescence of drops on a fluid bath.

When a drop of a viscous fluid is deposited on a bath of the same fluid, it is shown that its coalescence with this substrate is inhibited if the system oscillates vertically. Small drops lift off when the peak acceleration of the surface is larger than g. This leads to a steady regime where a drop can be kept bouncing for any length of time. It is possible to inject more fluid into the drop to increase its diameter up to several centimeters. Such a drop remains at the surface, forming a large sunk hemisphere. When the oscillation is stopped, the two fluids remain separated by a very thin air film, which drains very slowly (approximately 30 min). An analysis using lubrication theory accounts for most of the observations.

Journal Article↗
PubMed1987

Floating on a water bath and mounting glycol methacrylate and hydroxypropyl methacrylate sections influence final dimensions.

This paper reports the dimensional changes occurring in the different steps of the histoprocessing of tissues for light microscopy. Two water-miscible methacrylates used for embedding, namely 2-hydroxyethyl methacrylate and 2-hydroxypropyl methacrylate, were investigated. It was found that during stretching on the water bath and in the mounting step considerable size changes occur, which are of the same magnitude as during the dehydration step of histoprocessing. The final dimensions of the sections and of microscopic images are dependent on the response to surface tension at the water surface and mounting of the glycol and hydroxypropyl methacrylate sections, respectively. Between the two resins under study, significant differences in the size of the resin sections, with and without embedded liver tissue, were found. It is shown that the temperature at which the sections are mounted is of great importance. These observations indicate the importance of standardizing histotechniques if morphometry is to be applied.

Acrylates↗
PubMed1994

Bathing suit delivery of 8-methoxypsoralen for psoriasis: a double-blind, placebo-controlled study.

Twenty-four patients, 15 men and 9 women, aged 18-70 years with stable plaque-type psoriasis involving more than 20% of the body surface were subjected to a randomized, double-blind, age- and sex-matched, placebo-controlled study. Containers containing 25 mL of either 1% 8-MOP or a color-matched placebo were randomly numbered and stored. To 2 L of water was added 0.8 mL of 1% 8-MOP to obtain a concentration of 3.75 mg/L3, into which a bathing suit was soaked for 5 min. The suits were then gently squeezed to remove excess water and the patients were advised to put on the suit covered by a raincoat for 15 min. Immediately after removal of the raincoat and the suit, patients were irradiated with an initial dose of 4 J/cm2 UVA with increments of 0.5 J/cm2 on alternate days in a whole-body phototherapy unit obtained from the National Biological Corporation, Ohio. Erythema, scaling, and thickness (EST) of the index lesions were assessed on a 3-point scale (Table 1) and photographs were taken before and after completion of the study.

Adolescent↗