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Schultz, J, Rupprecht, A, Song, Z, Piskur, J, Nordenskiöld, L, Lahajnar, G
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Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex.
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We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems.
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Chen, Y Z, Prohofsky, E W
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Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model.
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We discuss the requirement of type II DNA topoisomerase in the process of mitotic chromosome condensation. Using a known model describing the collapse of homopolymers, we propose that the compaction process necessitates a change in the topological state (i.e., a self-knotting) of the chromosomal chain. We argue that the enzymes are necessary to reach the compact metaphase state in a time interval that is much smaller than the time expected in the uncatalyzed process. The folding process is such that the potential entanglement points are localized at particular regions of the chromosome known as the scaffold-associated regions. The concentration of entanglements in the metaphase chromosome is related to the average size of the radial loops. A phantom chain model for the condensation process, in which each potential entanglement point is dealt with by a topoisomerase II molecule, is proposed.
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Sikorav, J L, Jannink, G
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Photoinduced volume changes associated with the early transformations of bacteriorhodopsin: a laser-induced optoacoustic spectroscopy study.
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Volume changes associated with the primary photochemistry of bacteriorhodopsin (BR) were measured by temperature-dependent laser-induced optoacoustic spectroscopy (LIOAS). Excitation was performed with 8-ns flashes establishing a photoequilibrium between the BR and the K states (BR<-->hvK). The concentration of K at the end of the laser pulse, which is an important parameter for the calculation of the volume change per molecule from the LIOAS data, was determined by flash photolysis with optical detection under the specific conditions (concentration, photon density) of the LIOAS experiment. Temperature-dependent measurements yielded a linear dependency of the ratio of the optoacoustic signals for BR and for a calorimetric reference (CoCl2) with the cubic thermal expansion coefficient beta of water. From the slope of this linear ratio a contraction of 11 cm3/mol was determined.
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Schulenberg, P J, Rohr, M, Gärtner, W, Braslavsky, S E
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Excited state dynamics in chlorophyll-based antennae: the role of transfer equilibrium.
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We present computer simulations of excited state dynamics in models of PS I and PS II which are based upon known structural and spectral properties of the antennae. In particular, these models constrain the pigment binding sites to three-dimensional volumes determined from molecular properties of the antenna complexes. The simulations demonstrate that within a 10-30 ps after light absorption, rapid energy transfer among coupled antenna chlorophylls leads to a quasiequilibrium state in which the fraction of the excited state on any antenna chlorophyll, normalized to the total excited state remaining on the model, remains constant with time. We describe this quasiequilibrium state as a "transfer equilibrium" (TE) state because of its dependence on the rates of processes that couple excited state motion and quenching in the antenna as well as on the individual antenna site energies and temperature. The TE state is not a true equilibrium in that loss of the excited state primarily due to photochemistry (but also due to fluorescence, thermal emission, and intersystem crossing) continues once TE is established. Depending on the dynamics of the system, the normalized distribution of excited state at TE may differ substantially from the Boltzmann distribution (the state of the model at infinite time in the absence of any avenues for decay of excited state). The models predict lifetimes, equilibration times, and photochemical yields that are in agreement with experimental data and affirm trap-limited dynamics in both photosystems. The rapid occurrence of TE states implies that any excited state dynamics that depends on antenna structure and excitation wavelength must occur before the TE state is established. We demonstrate that the excited state distribution of the TE state is central to determining the excited state lifetime and quantum efficiency of photochemistry.
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Laible, P D, Zipfel, W, Owens, T G
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Light scattering by bovine alpha-crystallin proteins in solution: hydrodynamic structure and interparticle interaction.
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We have studied diluted bovine eye lens alpha-crystallin solutions by using light scattering. The protein particles were modeled as hard spheres, showing electrostatic repulsion, due to surplus electric charges, and weak attractive interaction. The repulsive potential VR is defined by the radius of the particles, the Debye length kappa-1, and the number of charges at the Gouy layer; the attractive potential has been described by the London-van der Waals potential and is defined by the Hamaker constant A. We have used the diluted gas approximation and the one component macrofluid model to relate the experimental static factor Ki to the theoretical expression of the interaction potential V(x). This resulted in a Hamaker constant A of 0.06 +/- 0.01 KBT and an effective charge q ranging from 18 +/- 1 at low ionic strength (omega = 0.0022 M) to 50 +/- 5 at high ionic strength (omega = 0.1472 M).
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Xia, J Z, Aerts, T, Donceel, K, Clauwaert, J
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A novel method for rapid measurement of membrane resistance, capacitance, and access resistance.
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During patch clamp recordings, measurement of passive parameters such as access resistance (Ra), membrane resistance (Rm), and membrane capacitance (Cm) often provides useful information regarding physiological changes in the cell. In particular, an increase in capacitance may indicate vesicle fusion events as occurs during exocytosis. Rapid capacitance changes are usually measured with a phase-sensitive detector set to a phase angle that is independent of resistance changes. However, this angle changes over time and may be difficult to determine in cells with a low membrane resistance. The present paper describes a technique for rapidly measuring Ra, Rm, and Cm by simultaneously applying two harmonic frequencies and calculating the passive parameters from the resultant electrode current. Calibration and operation are independent of the compensation circuit settings that may be set to null most of the electrode current. The technique may be implemented on a standard patch clamp setup without other specialized equipment and should be particularly useful for the study of cells that have low Rm or undergo rapid changes in Ra or Rm.
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Donnelly, D F
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Stationary and nonstationary correlation-frequency analysis of heterodyne mode laser light scattering: magnitude and periodicity of canine tracheal ciliary beat frequency in vivo.
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Stationary and nonstationary correlation-frequency analysis of heterodyne laser light scattering were utilized to make automated, on-line, objective measurements of tracheal ciliary beat frequency (CBF) in intact, anesthetized canines. The stationary correlation-frequency analysis laser light-scattering technique was used to assess the magnitude of the CBF stimulatory responses induced by aerosolized 10(-5) M fenoterol (sympathomimetic), and 10(-8) M and 10(-6) M methacholine (parasympathomimetic) delivered to the whole lungs of eight barbiturate-anesthetized beagles. The nonstationary correlation-frequency analysis laser light-scattering technique was used to measure the effect on tracheal CBF of increasing the cytosolic calcium ion concentration with a calcium ionophore, A23187. Aerosolized A23187 was delivered to the isolated tracheal lumens of eight beagle dogs in cumulative doses ranging from 10(-9)M to 10(-6) M. Administration of the ionophore synchronized the CBF with a period of 5.3 min. Dose dependencies were observed in both the time to the peak CBF stimulation and the magnitude of the stimulatory response. The magnitude of CBF stimulation was inhibited by prior administration of aerosolized nifedipine (2 mg/ml), a voltage-operated calcium channel blocker. The A23187-induced modulation period of tracheal CBF, was unchanged by nifedipine. These are the first data to demonstrate that the magnitude and periodicity of CBF are two independent coupled processes. The cooperativity of these two processes could be determined in the effectiveness of mucociliary transport.
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Chandra, T, Yeates, D B, Miller, I F, Wong, L B
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Saturation effects in polarized fluorescence photobleaching recovery and steady state fluorescence polarization.
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The time-resolved anisotropy produced in polarized fluorescence photobleaching recovery experiments has been successfully used to measure rotational correlation times in a variety of biological systems, however the magnitudes of the reported initial anisotropies have been much lower than the theoretically predicted maximum values. This small time-zero anisotropy has been attributed to fluorophore motion, wobble and rotation, during the photobleaching pulse. We demonstrate that inclusion of the possibility of saturation of the fluorophore's transition from its ground state to its excited state during the photobleaching pulse leads to the prediction of reduced time-zero anisotropy. This eliminates the need to rely solely on the assumption of fluorophore motion during the photobleaching pulse as the cause of the reduced initial anisotropy. We present theoretical and experimental results which show that the initial anisotropy decreases as both the bleach pulse intensity is increased and bleach pulse duration is decreased so as to keep the total integrated bleach pulse constant. We also show theoretical and experimental results demonstrating that at high excitation intensity the effects of saturation cause the steady state fluorescence polarization to decrease. We estimate that saturation may occur using common photobleaching conditions.
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Hellen, E H, Burghardt, T P
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Pre-steady-state transient currents mediated by the Na/K pump in internally perfused Xenopus oocytes.
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Pre-steady-state transient currents have been investigated in the vegetal pole of Xenopus oocytes using the open-oocyte vaseline-gap technique of Taglialatela, Toro, and Stefani (Biophysical Journal. 61:78-82, 1992). Voltage pulses 40 ms in duration were made from a holding potential of -40 mV to command potentials over the range -160 to +60 mV in increments of 20 mV. Current records (averaged 20X; sampled every 200 microseconds) in the presence of dihydroouabain (DHO) or absence of external Na+ (Nao) were subtracted from current records obtained under Na/Na exchange conditions, i.e. internally perfused with 50 mM Na+, 5 mM ATP, and 5 mM ADP (K(+)-free) and externally superfused with 100 mM Na+,K(+)-free solution. Transient currents were dependent on intracellular Na+ and nucleotides, and diminished by activation of forward pumping; they were also reduced by 10 micrograms ml-1 of oligomycin B applied to the external solution. These properties of the pre-steady state currents are consistent with the Na/K pump operating in its electroneutral Na/Na exchange mode. The voltage dependence of the DHO- and Nao-sensitive transient currents was analyzed using a pseudo two-state model in which only the rate coefficient for Nao-binding/reocclusion is voltage-dependent (Rakowski, R. F. 1993. J. Gen. Physiol. 101:117-144). The apparent valence of the charge moved during the on (zq-on) and off (zq-off) of the pulse were 0.96 +/- 0.05 and 0.95 +/- 0.05 for Nao-sensitive, and 1.10 +/- 0.07 and 0.85 +/- 0.06 for DHO-sensitive transient currents, respectively. The total amount of charge moved (Qtot) and the mid-point voltage of the charge distribution (Vq) were 230 +/- 15 pC and -56.2 +/- 5.1 mV, and 268 +/- 34 pC and -67.0 +/- 7.6 mV for Nao- and DHO-sensitive transient currents, respectively. The apparent valence (zk) and the voltage at which the forward and backward rates are equal (Vk) obtained from the relaxation rates were 0.80 +/- 0.05 and -129.3 +/- 10.0 mV, and 0.86 +/- 0.10 and -135.1 +/- 9.0 mV for the Nao- and DHO-sensitive pre-steady state currents, respectively. The values of the parameters were not statistically significantly different between the Nao- and DHO-sensitive transient currents. Excluding the first 600 microseconds after the onset of a voltage step which was not temporally resolved, transient currents showed no indication of a rising phase. These results support the idea that charge translocation occurs within an external access channel at a rate that is governed by a voltage-dependent binding/reocclusion process and a voltage-independent deocclusion/unbinding process.
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Holmgren, M, Rakowski, R F
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Orientation of cholera toxin bound to model membranes.
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The orientation of cholera toxin bound to its cell-surface receptor, ganglioside GM1, in a supporting lipid membrane was determined by electron microscopy of negatively stained toxin-lipid samples. Image analysis of two dimensional crystalline arrays has shown previously that the B-subunits of cholera toxin orient at the membrane surface as a pentameric ring with a central channel (Reed, R. A., J. Mattai, and G.G. Shipley. 1987. Biochemistry. 26:824-832; Ribi, H. O., D. S. Ludwig, K. L. Mercer, G. K. Schoolnik, and R. D. Kornberg. 1988. Science (Wash, DC). 239:1272-1276). We recorded images of negatively stained cholera toxin and isolated B-pentamers oriented perpendicular to the lipid surface so that the pentamer ring is viewed from the side. The pentamer dimensions, estimated from the average of 100 molecules, are approximately 60 by 30 A. Images of side views of whole cholera toxin clearly show density above the pentamer ring away from the lipid layer. On the basis of difference maps between averages of side views of whole toxin and B-pentamers, this density above the pentamer has been identified as a portion of the A-subunit. The A-subunit may also extend into the pore of the pentamer. In addition, Fab fragments from a monoclonal antibody to the A-subunit were mixed with the toxin prior to binding to GM1. Density from the Fab was localized to the region of toxin above the pentamer ring confirming the location of the A-subunit. The structure determined for the homologous heat-labile enterotoxin from Escherichia coli shows that the A-subunit lies mostly on one face of this pentamer with a small region penetrating the pentamer pore (Sixma, T. K., S. E. Pronk, K. H. Kalk, E. S. Wartna, B. A. M. van Zanten, B. Witholt,and W. G. J. Hol. 1991. Nature (Lond.). 351:371-377). The putative GM1 binding sites are located on the opposite face of the B-pentamer. Cholera toxin, therefore appears to bind to a model membrane with its GM1 binding surface adjacent to the membrane. Low resolution density maps were constructed from the x-ray coordinates of the E. coli toxin and compared with the electron microscopy-derived maps.
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Cabral-Lilly, D, Sosinsky, G E, Reed, R A, McDermott, M R, Shipley, G G
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Distribution of electrical potential, pH, free Ca2+, and volume inside cultured adult rabbit cardiac myocytes during chemical hypoxia: a multiparameter digitized confocal microscopic study.
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Exploiting the optical sectioning capabilities of laser scanning confocal microscopy and using parameter-specific fluorescent probes, we determined the distribution of pH, free Ca2+, electrical potential, and volume inside cultured adult rabbit cardiac myocytes during ATP depletion and reductive stress with cyanide and 2-deoxyglucose ("chemical hypoxia"). During normoxic incubations, myocytes exhibited a cytosolic pH of 7.1 and a mitochondrial pH of 8.0 (delta pH = 0.9 units). Sarcolemmal membrane potential (delta psi) was -80 mV, and mitochondrial delta psi was as high as -100 mV, yielding a mitochondrial protonmotive force (delta p) of -155 mV (delta P = delta psi - 60 delta pH). After 30 min of chemical hypoxia, mitochondrial delta pH decreased to 0.5 pH units, but mitochondrial delta psi remained essentially unchanged. By 40 min, delta pH was collapsed, and mitochondrial and cytosolic free Ca2+ began to increase. Mitochondrial and sarcolemmal delta psi remained high. as Ca2+ rose, myocytes shortened, hypercontracted, and blebbed with a 30% decrease of cell volume. After hypercontraction, extensive mitochondrial Ca2+ loading occurred. After another few minutes, mitochondrial depolarized completely and released their load of Ca2+. After many more minutes, the sarcolemmal permeability barrier broke down, and viability was lost. These studies demonstrate a sequence of subcellular ionic and electrical changes that may underlie the progression to irreversible hypoxic injury.
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Chacon, E, Reece, J M, Nieminen, A L, Zahrebelski, G, Herman, B, Lemasters, J J
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Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations.
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Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.
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Podgornik, R, Rau, D C, Parsegian, V A
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Multiphasic desensitization of the GABAA receptor in outside-out patches.
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GABAA receptor function was studied in outside-out patches from guinea pig hippocampal neurons using a drug application system with an exchange time of under 1.5 ms. Application of GABA to these patches induced a Cl- conductance that desensitized with prolonged exposure. Increasing GABA concentrations induced larger conductance increases that were associated with more complex patterns of desensitization. Smaller GABA responses desensitized with monophasic kinetics, whereas large responses displayed bi- and triphasic kinetics. Desensitization of the response to 1 mM GABA was triphasic in about 70% of the patches (tau = 15.4, 207, and 1370 ms) and biphasic in about 30% of the patches (tau = 44 and 725 ms). All phases of desensitization reversed at the Cl- equilibrium potential. Over the concentration range from 3 microM to 3 mM, both the rate and the extent of desensitization increased; however, complete desensitization was rarely observed. The increase in desensitization rate was due to an increase in the relative contribution of the faster phases with increasing GABA. The time constants of the three phases were independent of concentration. The different phases are not mediated by separate receptor populations, because double pulse experiments demonstrated interconversion among the fastest phase and the two slower phases. We demonstrate the plausibility of a model in which multiphasic desensitization is a consequence of the faster association rate at higher GABA concentrations.
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Celentano, J J, Wong, R K
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Myelin basic protein interaction with zinc and phosphate: fluorescence studies on the water-soluble form of the protein.
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The interaction of myelin basic protein (MBP) with zinc and phosphate ions has been studied by using the emission properties of the single tryptophan residue of the protein (Trp-115). The studies have been carried out by means of both static and time-resolved fluorescence techniques. The addition of either zinc to MBP in the presence of phosphate or phosphate to MBP in the presence of zinc resulted in an increase of fluorescence intensity and a blue shift of the emission maximum wavelength. Furthermore, a concomitant increase in the scattering was also detected. Anisotropy decay experiments demonstrated that these effects are due to the formation of MBP molecules into large aggregates. A possible physiological role for such interaction is discussed.
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Cavatorta, P, Giovanelli, S, Bobba, A, Riccio, P, Szabo, A G, Quagliariello, E
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Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.
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The pH dependence of the two-dimensional 1H nuclear magnetic resonance spectra of hen and turkey egg-white lysozymes has been recorded over the pH range 1-7. By monitoring the chemical shifts of the resonances of the various protons of ionizable residues, individual pKa values for the acidic residues have been determined for both proteins. The pKa values are displaced, with the exception of those of the residues in the active site cleft, by an average of 1 unit to low pH compared to model compounds.
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Bartik, K, Redfield, C, Dobson, C M
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Conformational dynamics of bovine Cu, Zn superoxide dismutase revealed by time-resolved fluorescence spectroscopy of the single tyrosine residue.
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The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be described with a Lorentzian distribution of lifetimes. The lifetime distribution parameters (center and width) were markedly dependent on temperature. The distribution center (average lifetime) displayed Arrhenius behavior with an Ea of 4.2 kcal/mol, in contrast with an Ea of 7.4 kcal/mol for the single-exponential decay of L-tyrosine. This indicated that thermal quenching of tyrosine emission was not solely responsible for the effect of temperature on the lifetimes of BSOD. The distribution width was broad (1 ns at 8 degrees C) and decreased significantly at higher temperatures. Furthermore, the width of the lifetime distribution increased in parallel to increasing viscosity of the medium. The combined effects of temperature and viscosity on the fluorescence decay suggest the existence of multiple conformational substrates in BSOD that interconvert during the excited-state lifetime. Denaturation of BSOD by guanidine hydrochloride produced an increase in the lifetime distribution width, indicating a larger number of conformations probed by the tyrosine residue in the denatured state. The rotational mobility of the tyrosine in BSOD was also investigated. Analysis of fluorescence anisotropy decay data enabled resolution of two rotational correlation times. One correlation time corresponded to a fast (picosecond) rotation that contributed 62% of the anisotropy decay and likely reported local mobility of the tyrosine ring. The longer correlation time was 50% of the expected value for rotation of the whole (dimeric) BSOD molecule and appeared to reflect segmental motions in the protein in addition to overall tumbling. Comparison between rotational correlation times and fluorescence lifetimes of BSOD indicates that the heterogeneity in lifetimes does not arise from mobility of the tyrosine per se, but rather from dynamics of the protein matrix surrounding this residue which affect its fluorescence decay.
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Ferreira, S T, Stella, L, Gratton, E
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Effect of ATP concentration on CFTR Cl- channels: a kinetic analysis of channel regulation.
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Phosphorylated cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channels require nucleoside triphosphates, such as ATP, to open. As the concentration of intracellular ATP increases, the probability of the channel being open (Po) increases. To better understand how ATP regulates the channel, we studied excised inside-out membrane patches that contained single, phosphorylated CFTR Cl- channels and examined the kinetics of gating at different concentrations of ATP. As the ATP concentration increased from 0.1 to 3 mM the mean closed time decreased, but mean open time did not change. Analysis of the data using histograms of open- and closed-state durations, the maximum likelihood method, and the log-likelihood ratio test suggested that channel behavior could be described by a model containing one open and two closed states (C1<==>C2<==>O). ATP regulated phosphorylated channels at the transition between the closed states C1 and C2: as the concentration of ATP increased, the rate of transition from C1 to C2 (C1-->C2) increased. In contrast, transitions from C2 to C1 and between C2 and the open state (O) were not significantly altered by ATP. Addition of ADP in the presence of ATP decreased the transition rate from C1 to C2 without affecting other transition rates. These data suggest that ATP regulates CFTR Cl- channels through an interaction that increases the rate of transition from the closed state to a bursting state in which the channel flickers back and forth between an open and a closed state (C2). This transition may reflect ATP binding or perhaps a step subsequent to binding.
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Winter, M C, Sheppard, D N, Carson, M R, Welsh, M J
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Permeability and electrical properties of planar lipid membranes from thylakoid lipids.
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Electrical measurements were carried out on planar lipid membranes from thylakoid lipids. The specific capacitance of membranes formed from decane-containing monogalactosyldiacylglycerol (MGDG), which accounts for 57% of the total lipid content of thylakoids, showed that it adopted a bilayer structure. Solvent-free bilayers of MGDG were not formed, with very rare exceptions, indicating that decane is required to stabilize the planar conformation. However, this cone-shaped lipid produces bilayer structures in combination with other cylindrical thylakoid lipids even in the absence of organic solvent. We compared the properties of solvent-free and decane-containing bilayers from MGDG, soybean lecithin, and the quaternary mixture of lipids similar to that found in vivo. The conductance of decane-MGDG was 26 times higher than that of decane-lecithin. The flux through the decane-lecithin bilayer was found to be slightly dependent on pH, whereas the decane-MGDG membrane was not. The specific conductance of bilayers formed from the quaternary mixture of lipids was 5 to 10 times larger than lecithin (with alkane or not). Further experiments with bilayers made in the presence of a KCl gradient showed that decane-MGDG, decane-MGDG/DGDG/SQDG/PG, and solvent-free MGDG/DGDG/SQDG/PG were cation-selective. The permeability coefficient for potassium ranged from 4.9 to 8.3 x 10(-11) cm s-1. The permeability coefficient for protons in galactolipids, however, was determined to be about six orders of magnitude higher than the value for potassium ions. The HCl permeation mechanism through the lipid membranes was determined from diffusion potentials measured in HCl gradients. Our results suggest that HCl was not transported as neutral molecules. The data is discussed with regard to the function of galactolipids in the ion transport through thylakoid membranes.
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Fuks, B, Homblé, F
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The structure of an integral membrane peptide: a deuterium NMR study of gramicidin.
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Solid state deuterium NMR was employed on oriented multilamellar dispersions consisting of 1,2-dilauryl-sn-glycero-3-phosphatidylcholine and deuterium (2H) exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamic structure of the channel conformation of gramicidin in a liquid crystalline phase. The corresponding spectra were used to discriminate between several structural models for the channel structure of gramicidin (based on the left- and right-handed beta 6.3 LD helix) and other models based on a structure obtained from high resolution NMR. The oriented spectrum is complicated by the fact that many of the doublets, corresponding to the 20 exchangeable sites, partially overlap. Furthermore, the asymmetry parameter, eta, of the electric field gradient tensor of the amide deuterons is large (approximately 0.2) and many of the amide groups are involved in hydrogen bonding, which is known to affect the quadrupole coupling constant. In order to account for these complications in simulating the spectra in the fast motional regime, an ab initio program called Gaussian 90 was employed, which permitted us to calculate, by quantum mechanical means, the complete electric field gradient tensor for each residue in gramicidin (using two structural models). Our results indicated that the left-handed helical models were inconsistent with our observed spectra, whereas a model based on the high-resolution structure derived by Arseniev and coworkers, but relaxed by a simple energy minimization procedure, was consistent with our observed spectra. The molecular order parameter was then estimated from the motional narrowing assuming the relaxed (right-handed) Arseniev structure. Our resultant order parameter of SZZ = 0.91 translates into an rms angle of 14 degrees, formed by the helix axis and the local bilayer normal. The strong resemblance between our spectra (and also those reported for gramicidin in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) multilayers) and the spectra of the same peptide incorporated in a lyotropic nematic phase, suggests that the lyotropic nematic phase simulates the local environment of the lipid bilayer.
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Prosser, R S, Daleman, S I, Davis, J H
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Dynamics of an integral membrane peptide: a deuterium NMR relaxation study of gramicidin.
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Solid state deuterium (2H) NMR inversion-recovery and Jeener-Broekaert relaxation experiments were performed on oriented multilamellar dispersions consisting of 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine and 2H exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamics of the channel conformation of the peptide in a liquid crystalline phase. Our dynamic model for the whole body motions of the peptide includes diffusion of the peptide around its helix axis and a wobbling diffusion around a second axis perpendicular to the local bilayer normal in a simple Maier-Saupe mean field potential. This anisotropic diffusion is characterized by the correlation times, tau R parallel and tau R perpendicular. Aligning the bilayer normal perpendicular to the magnetic field and graphing the relaxation rate, 1/T1Z, as a function of (1-S2N-2H), where S2N-2H represents the orientational order parameter, wer were able to estimate the correlation time, tau R parallel, for rotational diffusion. Although in the quadrupolar splitting, which varies as (3 cos2 theta D-1), has in general two possible solutions to theta D in the range 0 < or = theta D < or = 90 degrees, the 1/T1Z vs. (1-S2N-2H) curve can be used to determine a single value of theta D in this range. Thus, the 1/T1Z vs. (1-S2N-2H) profile can be used both to define the axial diffusion rate and to remove potential structural ambiguities in the splittings. The T1Z anisotropy permits us to solve for the two correlation times (tau R parallel = 6.8 x 10(-9) s and tau R perpendicular = 6 x 10(-6) s). The simulated parameters were corroborated by a Jeener-Broekaert experiment where the bilayer normal was parallel to the principal magnetic field. At this orientation the ratio, J2(2 omega 0)/J1(omega 0) was obtained in order to estimate the strength of the restoring potential in a model-independent fashion. This measurement yields the rms angle, <theta 2>1/2 (= 16 +/- 2 degrees at 34 degrees C), formed by the peptide helix axis and the average bilayer normal.
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Prosser, R S, Davis, J H
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Studies on lipid membranes by two-dimensional Fourier transform ESR: Enhancement of resolution to ordering and dynamics.
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The first two-dimensional Fourier-transform electron spin resonance (2D-FT-ESR) studies of nitroxide-labeled lipids in membrane vesicles are reported. The considerable enhancement this experiment provides for extracting rotational and translational diffusion rates, as well as orientational ordering parameters by means of ESR spectroscopy, is demonstrated. The 2D spectral analysis is achieved using theoretical simulations that are fit to experiments by an efficient and automated nonlinear least squares approach. These methods are applied to dispersions of 1-palmitoyl-2oleoyl-sn-glycerophosphatidylcholine (POPC) model membranes utilizing spin labels 1-palmitoyl-2-(16-doxyl stearoyl) phosphatidylcholine and the 3-doxyl derivative of cholestan-3-one (CSL). Generally favorable agreement is obtained between the results obtained by 2D-FT-ESR on vesicles with the previous results on similar systems studied by continuous wave (cw) ESR on aligned samples. The precision in determining the dynamic and ordering parameters is significantly better for 2D-FT-ESR, even though the cw ESR spectra from membrane vesicles are resolved more poorly than those from well aligned samples. Some small differences in results by the two methods are discussed in terms of limitations of the methods and/or theoretical models, as well as possible differences between dynamic molecular structure in vesicles versus aligned membranes. An interesting observation with CSL/POPC, that the apparent homogeneous linewidths seem to increase in "real time," is tentatively attributed to the effects of slow director fluctuations in the membrane vesicles.
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Crepeau, R H, Saxena, S, Lee, S, Patyal, B, Freed, J H
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Pressure-induced correlation field splitting of vibrational modes: structural and dynamic properties in lipid bilayers and biomembranes.
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Correlation field splittings of the vibrational modes of methylene chains in lipid bilayers, isolated lipid molecules in perdeuterated lipid bilayers, crystalline lipid, and interdigitated lipid bilayers have been investigated by pressure-tuning Fourier-transform infrared spectroscopy. The correlation field splittings of these modes are originating from the vibrational coupling interactions between the fully extended methylene chains with different site symmetry along each bilayer leaflet. The interchain-interactions of the methylene chains with the same site symmetry only contribute to frequency shift of the vibrational modes. The magnitude of the correlation field splitting is a measure of the strength of the interchain-interactions, and the relative intensities of the correlation field component bands provide information concerning the relative orientation of the zig-zag planes of the interacting methylene chains. It has been demonstrated in the present work that the correlation field splitting of the CH2 bending and rocking modes commonly observed in the vibrational spectra of lipid bilayers is the result of the intermolecular interchain-interactions among the methylene chains of the neighboring molecules. The intramolecular interchain-interactions between the sn-1 and sn-2 methylene chains within each molecule are weak. The correlation field splitting resulting from the intramolecular interchain-interactions exhibits a much smaller magnitude than that from the intermolecular interchain-interactions and is observed only at very high pressure. Interdigitation of the opposing bilayer leaflets disturbs significantly the intermolecular interchain-interactions and results in dramatic changes in the pressure profiles of the correlation field component bands of both the CH2 bending and rocking modes. The relative intensities of the correlation field component bands of these modes and the magnitude of the splitting are also altered significantly. These results provide further evidence that the correlation field splitting of the CH2 bending and rocking modes in the vibrational spectra of lipid bilayers is due to the intermolecular interchain-interactions. The present work has also demonstrated that the correlation field splitting of the vibrational modes in lipid bilayers is mainly contributed by the intermolecular interchain-interactions among the nearest neighboring molecules and that the long-range correlation interactions beyond the second neighboring molecules are insignificant.
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Wong, P T
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An electron spin resonance study of interactions between phosphatidylcholine and phosphatidylserine in oriented membranes.
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A detailed electron spin resonance (ESR) study of mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and phosphatidylserine (POPS) in oriented multilayers in the liquid crystalline phase is reported with the purpose of characterizing the effects of headgroup mixing on the structural and dynamical properties of the acyl chains. These studies were performed over a range of blends of POPC and POPS and temperatures, utilizing the spin-labeled lipids 16-phosphatidylcholine and 5-phosphatidylcholine as well as cholestane (CSL). The ESR spectra were analyzed by nonlinear least-squares fitting using detailed spectral simulations. Whereas CSL shows almost no variation in ordering and rotational dynamics versus mole fraction POPS, (i.e. XPS), and 5-PC shows small effects, the weakly ordered end-chain labeled 16-PC shows large relative effects, such that the orientational order parameter, S is at a minimum for XPS = 0.5 where it is about one-third the value observed for XPS = 0 and 1. This is directly reflected in the ESR spectrum as a substantial variation in the hyperfine splitting with XPS. The least-squares analysis also shows a reduction in rotational diffusion coefficient, R perpendicular by a fractor of 2 for XPS = 0.5 and permits the estimation of S2, the ordering parameter representing deviations from cylindrically symmetric alignment. These results are contrasted with 2H NMR studies which were insensitive to effects of mixing headgroups on the acyl chains. The ESR results are consistent with a somewhat increased disorder in the end-chain region as well as a small amount of chain tilting upon mixing POPC and POPS. They demonstrate the high sensitivity of ESR to subtle effects in chain ordering and dynamics.
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Ge, M, Budil, D E, Freed, J H
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Low-temperature energy transfer in LHC-II trimers from the Chl a/b light-harvesting antenna of photosystem II.
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Temperature dependence in electronic energy transfer steps within light-harvesting antenna trimers from photosystem II was investigated by studying Chl a pump-probe anisotropy decays at several wavelengths from 675 to 682 nm. The anisotropy lifetime is markedly sensitive to temperature at the longest wavelengths (680-682 nm), increasing by factors of 5 to 6 as the trimers are cooled from room temperature to 13 K. The temperature dependence is muted at 677 and 675 nm. This behavior is modeled using simulations of temperature-broadened Chl a absorption and fluorescence spectra in spectral overlap calculations of Förster energy transfer rates. In this model, the 680 nm anisotropy decays are dominated by uphill energy transfers from 680 nm Chl a pigments at the red edge of the LHC-II spectrum; the 675 nm anisotropy decays reflect a statistical average of uphill and downhill energy transfers from 676-nm pigments. The measured temperature dependence is consistent with essentially uncorrelated inhomogeneous broadening of donor and acceptor Chl a pigments.
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Savikhin, S, van Amerongen, H, Kwa, S L, van Grondelle, R, Struve, W S
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Structures of wild-type and mutant signal sequences of Escherichia coli ribose binding protein.
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The structure of a chemically synthesized 25-residue-long functional signal peptide of Escherichia coli ribose binding protein was compared with that of a nonfunctional mutant-signal peptide using circular dichroism and two-dimensional 1H NMR in solvents mimicking the amphiphilic environments. The functional peptide forms an 18-residue-long alpha-helix starting from the NH2-terminal region and reaching to the hydrophobic stretch in a solvent consisting of 10% dimethylsulfoxide, 40% water, and 50% trifluoroethanol (v/v). The nonfunctional mutant peptide, which contains a Pro at position 9 instead of a Leu in the wild-type peptide, does not have any secondary structure in that solvent but forms a 12-residue-long alpha-helix within the hydrophobic stretch in water/trifluoroethanol (50:50, v/v) solvent. It seems that the Pro-9 residue in the nonfunctional peptide disturbs the helix propagation from the hydrophobic stretch to the NH2-terminal region. Because both of these peptides have stable helices within the hydrophobic stretch, it may be concluded that the additional 2 turns of the alpha-helix in the NH2-terminal region of the wild-type signal peptide is important for its function.
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Yi, G S, Choi, B S, Kim, H
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Structure and activation dynamics of RBL-2H3 cells observed with scanning force microscopy.
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Surface and subsurface dynamics of Rat Basophilic Leukemia cells, a model system of stimulated secretion, were imaged using Scanning Force Microscopy (SFM) at a rate of 50-60 s/image. Cytoskeletal elements and organelles were tracked within quiescent cells and those activated after IgE receptor crosslinking. In addition, surface waves were observed moving within the plasma membrane. The structures seen in quiescent and activated cells can be correlated with those seen in electron micrographs and topographic SFM images of fixed detergent-extracted cells. Furthermore, images of the detergent-extracted nuclei reveal the presence of numerous nuclear pore complexes. High-magnification images of the nuclear pore complexes show evidence of subunit structure and exhibit dimensions consistent with those reported previously using electron microscopy. The behavior and overall change in morphology of cells observed during activation was consistent with that observed under similar conditions with Differential Interference Contrast microscopy. This study demonstrates that SFM, unlike other techniques, can be used to provide high-resolution information in both fixed and living cells.
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Braunstein, D, Spudich, A
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Cooperative action between band 3 and glycophorin A in human erythrocytes: immobilization of band 3 induced by antibodies to glycophorin A.
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The ability of transmembrane receptor proteins to change their association with the cytoskeleton in response to ligand binding seems to be a key mechanism of signal transduction across membranes. To investigate the molecular features of this mechanism we have used the red cell membrane as a model system to study signal transduction through the integral protein, glycophorin A. In these studies the lateral mobility of integral proteins was measured in situ by fluorescence recovery after photobleaching, and membrane rigidity was characterized by micropipette aspiration technique. We found that binding either a monoclonal antibody or its monovalent Fab to the exoplasmic domain of glycophorin A in normal red cells immobilized the receptor and rigidified the membrane. Further, immobilization and rigidification did not occur when antibodies were bound to Miltenberger V cells containing a mutant form of glycophorin A lacking the cytoplasmic domain. These results imply that the site of the immobilization/rigidification lies within the membrane skeletal structure, not in exofacial receptor crosslinking, and requires the extended cytoplasmic domain of normal glycophorin A. In addition, we found that glycophorin A immobilization and membrane skeletal rigidification were accompanied by immobilization of band 3 receptors. This unexpected result indicates a cooperative coupling between liganded glycophorin A, band 3, and the membrane skeleton. We speculate that cooperation of this type may represent a general mechanism for cytoskeletal linkage and transformation initiated by receptors with short cytoplasmic sequences, such as integrins.
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Knowles, D W, Chasis, J A, Evans, E A, Mohandas, N
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Anisotropic propagation of Ca2+ waves in isolated cardiomyocytes.
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Digital imaging microscopy of fluor-3 fluorescence was used to study the propagation of intracellular Ca2+ waves in isolated adult rat cardiomyocytes from 17 to 37 degrees C. Ca2+ waves spread in both transverse and longitudinal direction of a myocyte. Transverse propagation was pronounced in waves starting from a focus at the edge of a myocyte and in waves following an irregular, curved path (spiral waves). For the former type of waves, propagation velocities were determined. Both transverse and longitudinal wave components propagated at constant velocity ranging from 30 to 125 micron/s. Myocytes were anisotropic with respect to wave propagation: waves propagated faster in the longitudinal than in the transverse direction. The ratio between longitudinal and transverse velocity increased from 1.30 at 17 degrees C to 1.55 at 37 degrees C. Apparent activation energies for transverse and longitudinal wave propagation were estimated to be -20 kJ/mol, suggesting that these processes are limited by diffusion of Ca2+. Direction-dependent propagation velocities are interpreted to result from the highly ordered structure of the myocytes, especially from the anisotropic arrangement of diffusion obstacles such as myofilaments and mitochondria.
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Engel, J, Fechner, M, Sowerby, A J, Finch, S A, Stier, A
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Pattern recognition and classification of images of biological macromolecules using artificial neural networks.
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The goal of this work was to analyze an image data set and to detect the structural variability within this set. Two algorithms for pattern recognition based on neural networks are presented, one that performs an unsupervised classification (the self-organizing map) and the other a supervised classification (the learning vector quantization). The approach has a direct impact in current strategies for structural determination from electron microscopic images of biological macromolecules. In this work we performed a classification of both aligned but heterogeneous image data sets as well as basically homogeneous but otherwise rotationally misaligned image populations, in the latter case completely avoiding the typical reference dependency of correlation-based alignment methods. A number of examples on chaperonins are presented. The approach is computationally fast and robust with respect to noise. Programs are available through ftp.
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Marabini, R, Carazo, J M
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Gating of the squid sodium channel at positive potentials. I. Macroscopic ionic and gating currents.
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Macroscopic ionic sodium currents and gating currents were studied in voltage-clamped, dialyzed giant axons of the squid Loligo pealei under conditions of regular and inverse sodium gradients. Sodium currents showed regular kinetics but inactivation was incomplete, showing a maintained current for depolarizations lasting 18 ms. The ratio of the maintained current to the peak current increased with depolarization and it did not depend on the direction of the current flow or the sodium gradient. The time constant of inactivation was not affected by the sodium gradient. Double-pulse experiments allowed the separation of a normal inactivating component and a noninactivating component of the sodium currents. In gating current experiments, the results from double-pulse protocols showed that the charge was decreased by the prepulse and that the slow component of the 'on' gating current was preferentially depressed. As expected, charge immobilization was established faster at higher depolarizations than at low depolarizations, however, the amount of immobilized charge was unaffected by the pulse amplitude. This indicates that the incomplete sodium inactivation observed at high depolarizations is not the result of decreased charge immobilization; the maintained current must be due to a conductance that appears after normal charge immobilization and fast inactivation.
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Correa, A M, Bezanilla, F
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Ca(2+)-dependent inactivation of a cloned cardiac Ca2+ channel alpha 1 subunit (alpha 1C) expressed in Xenopus oocytes.
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The alpha 1 subunit of cardiac Ca2+ channel, expressed alone or coexpressed with the corresponding beta subunit in Xenopus laevis oocytes, elicits rapidly inactivating Ca2+ currents. The inactivation has the following properties: 1) It is practically absent in external Ba2+; 2) it increases with Ca2+ current amplitudes; 3) it is faster at more negative potentials for comparable Ca2+ current amplitudes; 4) it is independent of channel density; and 5) it does not require the beta subunit. These findings indicate that the Ca2+ binding site responsible for inactivation is encoded in the alpha 1 subunit and suggest that it is located near the inner channel mouth but outside the membrane electric field.
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Neely, A, Olcese, R, Wei, X, Birnbaumer, L, Stefani, E
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Potassium secretion by vestibular dark cell epithelium demonstrated by vibrating probe.
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Detection of motion and position by the vestibular labyrinth depends on the accumulation of potassium within a central compartment of the inner ear as a source of energy to drive the transduction process. Much circumstantial evidence points to the vestibular dark cell (VDC) epithelium as being responsible for concentrating K+ within the lumen. We have used the vibrating probe technique to directly observe voltage and ion gradients produced by this tissue to put this assumption on a solid experimental footing. Relative current density (Isc,probe) over the apical membrane of VDC epithelium was measured with the vibrating voltage-sensitive probe, and this technique was validated by performing maneuvers known to either stimulate or inhibit the transepithelial equivalent short circuit current. Basolateral bumetanide (5 x 10(-5) M) and ouabain (1 x 10(-3) M) caused a decrease in Isc,probe by 55 +/- 6% and 39 +/- 3%, respectively while raising the basolateral K+ concentration from 4 to 25 mM caused an increase by 35 +/- 8%. A K+ gradient directed toward the apical membrane was detected with the vibrating K(+)-selective electrode, demonstrating that, indeed, the VDC epithelium secretes K+ under control conditions. This secretion was inhibited by bumetanide (by 94 +/- 7%) and ouabain (by 52 +/- 8%). The results substantiate the supposition that dark cells produce a K+ flux and qualitatively support the correlation between this flux and the transepithelial current.
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Marcus, D C, Shipley, A M
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Increased adhesion between neutral lipid bilayers: interbilayer bridges formed by tannic acid.
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Tannic acid (TA) is a naturally occurring polyphenolic compound that aggregates membranes and neutral phosolipid vesicles and precipitates many proteins. This study analyzes TA binding to lipid membranes and the ensuing aggregation. The optical density of dispersions of phosphatidylcholine (PC) vesicles increased upon the addition of TA and electron micrographs showed that TA caused the vesicles to aggregate and form stacks of tightly packed disks. Solution calorimetry showed that TA bound to PC bilayers with a molar binding enthalpy of -8.3 kcal/mol and zeta potential measurements revealed that TA imparted a small negative charge to PC vesicles. Monolayer studies showed that TA bound to PC with a dissociation constant of 1.5 microM and reduced the dipole potential by up to 250 mV. Both the increase in optical density and decrease in dipole potential produced by TA could be reversed by the addition of polyvinylpyrrolidone, a compound that chelates TA by providing H-bond acceptor groups. NMR, micropipette aspiration, and x-ray diffraction experiments showed that TA incorporated into liquid crystalline PC membranes, increasing the area per lipid molecule and decreasing the bilayer thickness by 2 to 4%. 2H-NMR quadrupole splitting measurements also showed that TA associated with a PC molecule for times much less than 10(-4) s. In gel phase bilayers, TA caused the hydrocarbon chains from apposing monolayers to fully interdigitate. X-ray diffraction measurements of both gel and liquid crystalline dispersions showed that TA, at a critical concentration of about 1 mM, reduced the fluid spacing between adjacent bilayers by 8-10 A. These data place severe constraints on how TA can pack between adjacent bilayers and cause vesicles to adhere. We conclude that TA promotes vesicle aggregation by reducing the fluid spacing between bilayers by the formation of transient interbilayer bridges by inserting its digallic acid residues into the interfacial regions of adjacent bilayers and spanning the interbilayer space.
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Simon, S A, Disalvo, E A, Gawrisch, K, Borovyagin, V, Toone, E, Schiffman, S S, Needham, D, McIntosh, T J
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