353 research outputs found
A fluorescence anisotropy study of tetramer-dimer equilibrium of λ repressor and its implication for function
Tetramer-dimer equilibrium of λ repressor has been studied by fluorescence anisotropy techniques. We have chosen 1-dimethylamino naphthalene-5-sulfonyl chloride (dansyl chloride)-labeled repressor to study the dissociation-association equilibrium, because of relatively long life-time of the probe (> 10 ns). Polarization of the dansyl-labeled repressor decreases with decreasing protein concentrations in the range of 20 to 0.2 ÎŒM. The decrease of anisotropy was shown to be due to reversible dissociation of the protein. Size exclusion high-performance liquid chromatography studies and polyacrylamide gel electrophoresis under native conditions (Ferguson plot) confirmed that at around 20 ÎŒM concentrations the repressor exists in predominantly tetrameric form, whereas in lower concentrations it exists in predominantly dimer form. A dissociation constant of 2.3 ± 0.9 ÎŒM was estimated in 0.1 M potassium phosphate, pH 8.0, at 25° C. A stoichiometric amount of isolated single operator shifted the tetramer-dimer equilibrium toward the dimer. Increased ionic strength had only a modest effect on the dissociation constant. The thermodynamic constants for the dissociation reaction calculated from the Van't Hoff plot was +26.6 kcal/mol for ÎH and +64.7 e.u. for ÎS. The rotational correlation times derived from isothermal Perrin plot indicated elongated dimers and tetramers
An operator-induced conformational change in the C-terminal domain of the λ repressor
4,4'-bis(1-anilino-8-naphthalenesulfonic acid (Bis-ANS), an environment-sensitive fluorescent probe for hydrophobic region of proteins, binds specifically to the C-terminal domain of λ repressor. The binding is characterized by positive cooperativity, the magnitude of which is dependent on protein concentration in the concentration range where dimeric repressor aggregates to a tetramer. In this range, positive cooperativity becomes more pronounced at higher protein concentrations. This suggests a preferential binding of Bis-ANS to the dimeric form of the repressor. Binding of single operator OR1 to the N-terminal domain of the repressor causes enhancement of fluorescence of the C-terminal domain bound Bis-ANS. The binding of single operator OR1 also leads to quenching of fluorescence of tryptophan residues, all of which are located in the hinge or the C-terminal domain. Thus two different fluorescent probes indicate an operator-induced conformational change which affects the C-terminal domain. The significance of this conformational change with respect to the function of λ repressor has been discussed
Generalization of escape rate from a metastable state driven by external cross-correlated noise processes
We propose generalization of escape rate from a metastable state for
externally driven correlated noise processes in one dimension. In addition to
the internal non-Markovian thermal fluctuations, the external correlated noise
processes we consider are Gaussian, stationary in nature and are of
Ornstein-Uhlenbeck type. Based on a Fokker-Planck description of the effective
noise processes with finite memory we derive the generalized escape rate from a
metastable state in the moderate to large damping limit and investigate the
effect of degree of correlation on the resulting rate. Comparison of the
theoretical expression with numerical simulation gives a satisfactory agreement
and shows that by increasing the degree of external noise correlation one can
enhance the escape rate through the dressed effective noise strength.Comment: 9 pages, 1 figur
Analytical and numerical investigation of escape rate for a noise driven bath
We consider a system-reservoir model where the reservoir is modulated by an
external noise. Both the internal noise of the reservoir and the external noise
are stationary, Gaussian and are characterized by arbitrary decaying
correlation functions. Based on a relation between the dissipation of the
system and the response function of the reservoir driven by external noise we
numerically examine the model using a full bistable potential to show that one
can recover the turn-over features of the usual Kramers' dynamics when the
external noise modulates the reservoir rather than the system directly. We
derive the generalized Kramers' rate for this nonequilibrium open system. The
theoretical results are verified by numerical simulation.Comment: Revtex, 25 pages, 5 figures. To appear in Phys. Rev.
Quantum state-dependent diffusion and multiplicative noise: a microscopic approach
The state-dependent diffusion, which concerns the Brownian motion of a
particle in inhomogeneous media has been described phenomenologically in a
number of ways. Based on a system-reservoir nonlinear coupling model we present
a microscopic approach to quantum state-dependent diffusion and multiplicative
noise in terms of a quantum Markovian Langevin description and an associated
Fokker-Planck equation in position space in the overdamped limit. We examine
the thermodynamic consistency and explore the possibility of observing a
quantum current, a generic quantum effect, as a consequence of this
state-dependent diffusion similar to one proposed by B\"{u}ttiker [Z. Phys. B
{\bf 68}, 161 (1987)] in a classical context several years ago.Comment: To be published in Journal of Statistical Physics 28 pages, 3 figure
Generalized quantum Fokker-Planck, diffusion and Smoluchowski equations with true probability distribution functions
Traditionally, the quantum Brownian motion is described by Fokker-Planck or
diffusion equations in terms of quasi-probability distribution functions, e.g.,
Wigner functions. These often become singular or negative in the full quantum
regime. In this paper a simple approach to non-Markovian theory of quantum
Brownian motion using {\it true probability distribution functions} is
presented. Based on an initial coherent state representation of the bath
oscillators and an equilibrium canonical distribution of the quantum mechanical
mean values of their co-ordinates and momenta we derive a generalized quantum
Langevin equation in -numbers and show that the latter is amenable to a
theoretical analysis in terms of the classical theory of non-Markovian
dynamics. The corresponding Fokker-Planck, diffusion and the Smoluchowski
equations are the {\it exact} quantum analogues of their classical
counterparts. The present work is {\it independent} of path integral
techniques. The theory as developed here is a natural extension of its
classical version and is valid for arbitrary temperature and friction
(Smoluchowski equation being considered in the overdamped limit).Comment: RevTex, 16 pages, 7 figures, To appear in Physical Review E (minor
revision
Borrelia burgdorferi Requires the Alternative Sigma Factor RpoS for Dissemination within the Vector during Tick-to-Mammal Transmission
While the roles of rpoSBb and RpoS-dependent genes have been studied extensively within the mammal, the contribution of the RpoS regulon to the tick-phase of the Borrelia burgdorferi enzootic cycle has not been examined. Herein, we demonstrate that RpoS-dependent gene expression is prerequisite for the transmission of spirochetes by feeding nymphs. RpoS-deficient organisms are confined to the midgut lumen where they transform into an unusual morphotype (round bodies) during the later stages of the blood meal. We show that round body formation is rapidly reversible, and in vitro appears to be attributable, in part, to reduced levels of Coenzyme A disulfide reductase, which among other functions, provides NAD+ for glycolysis. Our data suggest that spirochetes default to an RpoS-independent program for round body formation upon sensing that the energetics for transmission are unfavorable
Data from an International Multi-Centre Study of Statistics and Mathematics Anxieties and Related Variables in University Students (the SMARVUS Dataset)
This large, international dataset contains survey responses from N = 12,570 students from 100 universities in 35 countries, collected in 21 languages. We measured anxieties (statistics, mathematics, test, trait, social interaction, performance, creativity, intolerance of uncertainty, and fear of negative evaluation), self-efficacy, persistence, and the cognitive reflection test, and collected demographics, previous mathematics grades, self-reported and official statistics grades, and statistics module details. Data reuse potential is broad, including testing links between anxieties and statistics/mathematics education factors, and examining instrumentsâ psychometric properties across different languages and contexts. Data and metadata are stored on the Open Science Framework website [https://osf.io/mhg94/]
Discrete element modeling of the machining processes of brittle materials: recent development and future prospective
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