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Two-state Model (two-state + model)
Selected AbstractsCharacterization of Zebrafish Cx43.4 Connexin and its ChannelsEXPERIMENTAL PHYSIOLOGY, Issue 6 2003T. Desplantez Connexins (Cx) form intercellular junctional channels which are responsible for metabolic and electrical coupling. We report here on the biochemical and immunohistochemical characterization of zebrafish connexin zfCx43.4, an orthologue of mammalian and avian Cx45, and the electrophysiological properties of junctional channels formed by this protein. The investigations were performed on transfected COS-7 cells or HeLa cells. Using site-directed antibodies, zfCx43.4 cDNA (GenBank accession no. X96712) was demonstrated to code for a protein with a Mr of 45 000. In transfected cells, zfCx43.4 was localized in cell-cell contact areas as expected for a gap junction protein. zfCx43.4 channels were shown to transfer Lucifer Yellow. The multichannel currents were sensitive to the transjunctional voltage (Vj). Their properties were consistent with a two-state model and yielded the following Boltzmann parameters for negative/positive Vj: Vj,0= -38.4/41.9 mV; gj,min= 0.19/0.18; z = 2.6/2.3. These parameters deviate somewhat from those of zfCx43.4 channels expressed in Xenopus oocytes and from those of Cx45, an orthologue of zfCx43.4, expressed in mammalian cells or Xenopus oocytes. Conceivably, the subtle differences may reflect differences in experimental methods and/or in the expression system. The single channel currents yielded two prominent levels attributable to a main conductance state (,j,main= 33.2 ± 1.5 pS) and a residual conductance state (,j,residual= 11.9 ± 0.6 pS). [source] The conformational stability of the Streptomyces coelicolor histidine-phosphocarrier proteinFEBS JOURNAL, Issue 11 2004Characterization of cold denaturation, protein interactions Thermodynamic parameters describing the conformational stability of the histidine-containing phosphocarrier protein from Streptomyces coelicolor, scHPr, have been determined by steady-state fluorescence measurements of isothermal urea-denaturations, differential scanning calorimetry at different guanidinium hydrochloride concentrations and, independently, by far-UV circular dichroism measurements of isothermal urea-denaturations, and thermal denaturations at fixed urea concentrations. The equilibrium unfolding transitions are described adequately by the two-state model and they validate the linear free-energy extrapolation model, over the large temperature range explored, and the urea concentrations used. At moderate urea concentrations (from 2 to 3 m), scHPr undergoes both high- and low-temperature unfolding. The free-energy stability curves have been obtained for the whole temperature range and values of the thermodynamic parameters governing the heat- and cold-denaturation processes have been obtained. Cold-denaturation of the protein is the result of the combination of an unusually high heat capacity change (1.4 ± 0.3 kcal·mol,1·K,1, at 0 m urea, being the average of the fluorescence, circular dichroism and differential scanning calorimetry measurements) and a fairly low enthalpy change upon unfolding at the midpoint temperature of heat-denaturation (59 ± 4 kcal·mol,1, the average of the fluorescence, circular dichroism and differential scanning calorimetry measurements). The changes in enthalpy (m,Hi), entropy (m,Si) and heat capacity (m,Cpi), which occur upon preferential urea binding to the unfolded state vs. the folded state of the protein, have also been determined. The m,Hi and the m,Si are negative at low temperatures, but as the temperature is increased, m,Hi makes a less favourable contribution than m,Si to the change in free energy upon urea binding. The m,Cpi is larger than those observed for other proteins; however, its contribution to the global heat capacity change upon unfolding is small. [source] The refolding of type II shikimate kinase from Erwinia chrysanthemi after denaturation in ureaFEBS JOURNAL, Issue 8 2002Eleonora Cerasoli Shikimate kinase was chosen as a convenient representative example of the subclass of ,/, proteins with which to examine the mechanism of protein folding. In this paper we report on the refolding of the enzyme after denaturation in urea. As shown by the changes in secondary and tertiary structure monitored by far UV circular dichroism (CD) and fluorescence, respectively, the enzyme was fully unfolded in 4 m urea. From an analysis of the unfolding curve in terms of the two-state model, the stability of the folded state could be estimated as 17 kJ·mol,1. Approximately 95% of the enzyme activity could be recovered on dilution of the urea from 4 to 0.36 m. The results of spectroscopic studies indicated that refolding occurred in at least four kinetic phases, the slowest of which (k = 0.009 s,1) corresponded with the regain of shikimate binding and of enzyme activity. The two most rapid phases were associated with a substantial increase in the binding of 8-anilino-1-naphthalenesulfonic acid with only modest changes in the far UV CD, indicating that a collapsed intermediate with only partial native secondary structure was formed rapidly. The relevance of the results to the folding of other ,/, domain proteins is discussed. [source] Length-dependence of electron transfer coupling matrix in polyene wires: Ab initio molecular orbital theory study,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2009Govind Mallick Abstract The electron transfer (ET) properties of ,-electron conjugated quasi-one-dimensional molecular wires, consisting of polyene, [>CC<]n (n = 1,11), including ,-carotene, is investigated using ab initio molecular orbital theory within Koopmans theorem (KT) approach. The ET coupling matrix element, VDA, for 1,3- trans -butadiene molecule calculated with the KT approach shows excellent agreement with the corresponding results obtained with two-state model. The calculated values of VDA for the polyene oligomers exhibit exponential decrease in magnitude with increasing length of the wire. However, the decay curve exhibits three different regimes. The magnitude of the decay constant, ,, decreases with the increase in length of the wire. A highly delocalized ,-electron cloud in the polyene chain appears to facilitate retention of the electronic coupling at large separations between the donor and acceptor centers. Published 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Bayesian analysis of single-molecule experimental dataJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 3 2005S. C. Kou Summary., Recent advances in experimental technologies allow scientists to follow biochemical processes on a single-molecule basis, which provides much richer information about chemical dynamics than traditional ensemble-averaged experiments but also raises many new statistical challenges. The paper provides the first likelihood-based statistical analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single deoxyribonucleic acid (DNA) hairpin molecule. The conformational change is initially treated as a continuous time two-state Markov chain, which is not observable and must be inferred from changes in photon emissions. This model is further complicated by unobserved molecular Brownian diffusions. Beyond the simple two-state model, a competing model that models the energy barrier between the two states of the DNA hairpin as an Ornstein,Uhlenbeck process has been suggested in the literature. We first derive the likelihood function of the simple two-state model and then generalize the method to handle complications such as unobserved molecular diffusions and the fluctuating energy barrier. The data augmentation technique and Markov chain Monte Carlo methods are developed to sample from the posterior distribution desired. The Bayes factor calculation and posterior estimates of relevant parameters indicate that the fluctuating barrier model fits the data better than the simple two-state model. [source] On the use of second-order descriptors to predict queueing behavior of MAPsNAVAL RESEARCH LOGISTICS: AN INTERNATIONAL JOURNAL, Issue 4 2002Allan T. Andersen Abstract The contributions of this paper are the following: We derive a formula for the IDI (Index of Dispersion for Intervals) for the Markovian Arrival Process (MAP). We show that two-state MAPs with identical fundamental rate, IDI and IDC (Index of Dispersion for Counts), define interval stationary point processes that are stochastically equivalent; this is true for the time stationary point processes they define too. Special cases of the two-state MAP are frequently used as source models in the literature. The result shows that, fitting to the rate, IDC and IDI of a source completely determine the interval stationary and time stationary behavior of the two-state model. We give various illustrative numerical examples on the merits in predicting queueing behavior on the basis of first- and second-order descriptors by considering queueing behavior of MAPs with constant fundamental rate and IDC, respectively, constant fundamental rate and IDI. Disturbing results are presented on how different the queueing behavior can be with these descriptors fixed. Even MAPs with NO correlations in the counting process, i.e., IDC(t) = 1 are shown to have very different queueing behavior. © 2002 Wiley Periodicals, Inc. Naval Research Logistics 49: 391,409, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/nav.10015 [source] Recursive Modeling of Nonlinear Dynamics in UK Stock ReturnsTHE MANCHESTER SCHOOL, Issue 4 2003Massimo Guidolin This paper presents results from recursive modeling of nonlinear dynamics in UK stock returns. A specification search suggests a two-state model and we demonstrate the ability of this model to capture time-varying volatility, skew and kurtosis in UK stock returns. An out-of-sample forecasting experiment confirms the strong statistical evidence of nonlinearity and shows that accounting for regimes leads to improved forecasting performance. [source] Physicochemical properties of thiol proteinase inhibitor isolated from goat pancreasBIOPOLYMERS, Issue 8 2010Medha Priyadarshini Abstract Thiol proteinase inhibitors are crucial to proper functioning of all living tissues consequent to their cathepsin regulatory and myriad important biologic properties. Equilibrium denaturation of dimeric goat pancreas thiol proteinase inhibitor (PTPI), a cystatin superfamily variant has been studied by monitoring changes in the protein's spectroscopic and functional characteristics. Denaturation of PTPI in guanidine hydrochloride and urea resulted in altered intrinsic fluorescence emission spectrum, diminished negative circular dichroism, and loss of its papain inhibitory potential. Native like spectroscopic properties and inhibitory activity are only partially restored when denaturant is diluted from guanidine hydrochloride unfolded samples demonstrating that process is partially reversible. Coincidence of transition curves and dependence of transition midpoint (3.2M) on protein concentration in guanidine hydrochloride-induced denaturation are consistent with a two-state model involving a native like dimer and denatured monomer. On the contrary, urea-induced unfolding of PTPI is a multiphasic process with indiscernible intermediates. The studies demonstrate that functional conformation and stability are governed by both ionic and hydrophobic interactions. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 708,717, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | |||||||||||||