Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II.

Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O)3Y (X = O, OH; Y = H2O, OH) cluster in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the (1) analytical method and the (2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S1 and S3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to (a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S1 and S3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.

Estimation of parameters in Shot-Noise-Driven Doubly Stochastic Poisson processes using the EM algorithm--modeling of pre- and postsynaptic spike trains.

OBJECTIVES: To estimate the parameters, the impulse response (IR) functions of some linear time-invariant systems generating intensity processes, in Shot-Noise-Driven Doubly Stochastic Poisson Process (SND-DSPP) in which multivariate presynaptic spike trains and postsynaptic spike trains can be assumed to be modeled by the SND-DSPPs. METHODS: An explicit formula for estimating the IR functions from observations of multivariate input processes of the linear systems and the corresponding counting process (output process) is derived utilizing the expectation maximization (EM) algorithm. RESULTS: The validity of the estimation formula was verified through Monte Carlo simulations in which two presynaptic spike trains and one postsynaptic spike train were assumed to be observable. The IR functions estimated on the basis of the proposed identification method were close to the true IR functions. CONCLUSIONS: The proposed method will play an important role in identifying the input-output relationship of pre- and postsynaptic neural spike trains in practical situations.

EPR studies of the water oxidizing complex in the S1 and the higher S states: the manganese cluster and Y(Z) radical.

The parallel polarization electron paramagnetic resonance (EPR) method has been applied to investigate manganese EPR signals of native S1 and S3 states of the water oxidizing complex (WOC) in photosystem (PS) II. The EPR signals in both states were assigned to thermally excited states with S=1, from which zero-field interaction parameters D and E were derived. Three kinds of signals, the doublet signal, the singlet-like signal and g=11-15 signal, were detected in Ca2+-depleted PS II. The g=11-15 signal was observed by parallel and perpendicular modes and assigned to a higher oxidation state beyond S2 in Ca2+-depleted PS II. The singlet-like signal was associated with the g=11-15 signal but not with the Y(Z) (the tyrosine residue 161 of the D1 polypeptide in PS II) radical. The doublet signal was associated with the Y(Z) radical as proved by pulsed electron nuclear double resonance (ENDOR) and ENDOR-induced EPR. The electron transfer mechanism relevant to the role of Y(Z) radical was discussed.

pH-dependent characteristics of Y(Z) radical in Ca(2+)-depleted photosystem II studied by CW-EPR and pulsed ENDOR.

The Y(Z)-tyrosine radical was trapped by freezing immediately after illumination in Ca(2+)-depleted Photosystem II (PS II) membranes and the pH-dependent characteristics of the radical were investigated using CW-EPR and pulsed ENDOR. The spectrum of the Y*(Z) radical trapped in the Y*(Z)S(1) state at pH 5.5 was cation-like as reported in Mn-depleted PS II (H. Mino et al., Spectrochim. Acta A 53 (1997) 1465-1483). By illuminating the PS II-retaining S(2) state, the Y*(Z) radical and a broad doublet signal formed in the g approximately 2 region were trapped concomitantly. The spectrum of the trapped Y*(Z) radical in the Y*(Z)S(2) state was cation-like at pH 5.5 but the pulsed ENDOR measurements reveals the involvement of the neutral Y*(Z) radical in the doublet signal. At pH 7.0, the resulting Y*(Z) signal was the mixture of the cation-like and neutral radical spectra, and considerably different from the neutral radical found in Mn-depleted PS II. pH-Dependent changes in the properties of the Y*(Z) radical are discussed in relation to the redox events occurring in Ca(2+)-depleted PS II.

An FTIR study on the structure of the oxygen-evolving Mn-cluster of Photosystem II in different spin forms of the S(2) state.

The S(2) state of the oxygen-evolving Mn-cluster of Photosystem II (PS II) is known to have different forms that exhibit the g =2 multiline and g = 4.1 EPR signals. These two spin forms are interconvertible at > 200 K and the relative amplitudes of the two signals are dependent on the species of cryoprotectant and alcohol contained in the medium. Also, it was recently found that the mutiline form can be converted to the g = 4.1 form by absorption of near-infrared light by the Mn-cluster itself at around 150 K [Boussac et al. (1996) Biochemistry 35: 6984-6989]. We have used light-induced Fourier transform infrared (FTIR) difference spectroscopy to study the structural difference in these two S(2) forms. FTIR difference spectra for S(2)/S(1) as well as for S(2)Q(A) (-)/S(1)Q(A) measured at cryogenic temperatures using PS II membranes in the presence of various cryoprotectants, and monohydric alcohols did not show any specific differences except for intensities of amide I bands, which were larger when ethylene glycol or glycerol was present in addition to sucrose. This result was interpreted due to more flexible movement of the protein backbones upon S(2) formation with a higher cryoprotectant content. Light-induced difference spectra measured at 150 K using either blue light without near-infrared light or red plus near-infrared light also did not show any detectable difference. In addition, a different spectrum upon near-infrared illumination at 150 K of the PS II sample in which the S(2) state had been photogenerated at 200 K exhibited no meaningful signals. These results indicate that the two S(2) forms that give rise to the multiline and g = 4.1 signals have only minor differences, if any, in the structures of amino-acid ligands and polypeptide backbones. This conclusion suggests that conversion between the two spin states is caused by a spin-state transition in the Mn(III) ion rather than valence swapping within the Mn-cluster that would considerably affect the vibrations of ligands.

A method of estimating the rate of miniature end-plate potential occurrences based on parametric time series modeling.

This paper presents a parametric method of estimating the rate of miniature end-plate potential (MEPP) occurrences. We consider the case where the rate of MEPP occurrences is raised by the constant deporalization of presynaptic terminals by using high-concentration potassium solutions. Under such conditions, since MEPP occurrences cannot be identified by eye due to waveform superposition, it is necessary to estimate the rate with the aid of statistical techniques instead of counting the occurrences by eye. In this paper it is assumed according to the literatures that the MEPP data are modeled as a stationary Poisson impulse process filtered by the linear system the impulse response function of which is the sum of two exponentials. Then, the discretized MEPP data are shown to be a second-order autoregressive (AR(2)) process, driven by the sum of 2 first-order moving average (MA(1)) processes (the residual time series). An explicit formula for estimating the rate can be derived by combining the second- and third-order moments of the residual time series. The validity of the proposed estimation method is verified through Monte Carlo simulations in which the rate is varied ranging from 100 to 10,000 s-1. Likewise, the proposed method is applied to estimation of the rate of actual MEPP data, which were observed at the frog's neuromuscular junction under high-concentration potassium solutions.

A repeat-batch membrane bioreactor with a phase inversion for the desaturation of isopropyl palmitate by a mutant Rhodococcus strain.

A repeat-batch membrane bioreactor was constructed for the novel bioconversion of isopropyl hexadecanoate to isopropyl cis-6-hexadecenoate by a Rhodococcus mutant. The addition of glutamate, thiamine, and MgSO(4) was very effective in improving not only the rate and yield of the bioconversion but also the maintenance of desaturation activity during cell recycling. An oil-in-water (O/W) type emulsion of the reaction medium was inverted to a water-in-oil (W/O) type by discharging the water phase from the reaction mixture. The continuous oil phase containing the product could effectively be recovered through a hydrophobic hollow-fiber module. By decreasing the oil-to-water ratio upon addition of fresh medium, the medium was spontaneously inverted again to an O/W type emulsion to proceed with the next conversion. The batch reaction coupled with the phase inversion could be repeated more than 13 times for over about 300 h operation. Finally, a highly purified product was obtained with high yield by the urea adduct procedure.

A method of analyzing nonstationary ionic channel current fluctuations in the presence of an additive measurement noise.

A method of estimating the parameters of nonstationary ionic channel current fluctuations (NST-ICF's) in the presence of an additive measurement noise is proposed. The case is considered in which the sample records of NST-ICT's corrupted by the measurement noise are available for estimation, where the experiment can be repeated many times to calculate the statistics of noisy NST-ICF's. The conventional second-order regression model expressed in terms of the mean and variance of noisy NST-ICF's is derived theoretically, assuming that NST-ICF's are binomially distributed. Since the coefficients of the regression model are explicitly related to not only the parameters of NST-ICF's but also the measurement noise component, the parameters of NST-ICF's that are of interest can be estimated without interference from the additive measurement noise by identifying the regression coefficients. Furthermore, the accuracy of the parameter estimates is theoretically evaluated using the error-covariance matrix of the regression coefficients. The validity and effectiveness of the proposed method are demonstrated in a Monte Carlo simulation in which a fundamental kinetic scheme of Na+ channels is treated as a specific example.

A parametric modeling of ionic channel current fluctuations using third-order statistics and its application to estimation of the kinetic parameters of single ionic channels.

A parametric modeling of stationary ionic-channel current fluctuations (SICF's) using third-order cumulants is presented and its application to estimation of the kinetic parameters of single ionic channels is discussed. We consider the case where third-order cumulants of SICF's are nonzero, and where SICF's are corrupted by an unobservable additive colored Gaussian noise that is independent of SICF's. First, we construct a virtual synthesizer that yields an output whose third-order cumulants are equivalent to those of SICF's on a specific slice. The synthesizer output is expressed by the sum of N5 - 1 first-order differential equation systems, where N8 denotes the number of states of single ionic channels. Next, discretizing the synthesizer output, we derive a discrete autoregressive (AR(N8 - 1)) process driven by the sum of N8 - 1 moving average (MA(N9 - 2)) processes. Then the AR coefficients are explicitly related to the kinetic parameters of single ionic channels, implying that the kinetic parameters can be estimated by identifying the ARMA coefficients using the third-order cumulants. In order to assess the validity of the proposed modeling and the accuracy of parameter estimates, Monte Carlo simulation is carried out in which the closed-open and closed-open-blocked schemes are treated as specific examples.

A parametric modeling of membrane current fluctuations with its application to the estimation of the kinetic properties of single ionic channels.

A parametric autoregressive moving average (ARMA) signal modeling of membrane current fluctuations observed in biomembranes is described. Kinetic properties of single ionic channels contributing to membrane current fluctuations and the parameters of the corresponding ARMA process are explicitly related. The model was shown to be effectively applied to the estimation of the kinetic parameters of single ionic channels. Estimation of the parameters via ARMA signal identification was examined in detail for the basic closed-open scheme and the three-state sequential blocking scheme. The estimation accuracy of this method was theoretically evaluated. Computer simulation revealed the validity of the proposed modeling and the effectiveness of the parametric method for the estimation of kinetic parameters when the model was applied to the estimation. The proposed modeling may form a theoretical base for the parametric analysis of membrane current fluctuations in a variety of kinetic schemes.

Analysis of monophasic and biphasic electrical stimulation of nerve.

In an earlier study, biphasic and monphasic electrical stimulation of the auditory nerve was performed in cats with a cochlear implant. Single-unit recordings demonstrated that spikes resulting from monophasic and biphasic stimuli have different thresholds and latencies. Monophasic thresholds are lower and latencies are shorter under cathodic stimulation. Results from stochastic simulations of a biophysical model of electrical stimulation are similar. A simple analysis of a linear, "integrate to threshold" membrane model accounts for the threshold and latency differences observed experimentally and computationally. Since biphasic stimuli are used extensively in functional electrical stimulation, this analysis greatly simplifies the biophysical interpretation of responses to clinically relevant stimuli by relating them to the responses obtained with monophasic stimuli.

Effects of organic Ca antagonist, diltiazem, on neuromuscular transmission.

The effects of the organic "Ca antagonist" diltiazem on the frog neuromuscular junction was investigated. The addition of diltiazem to the bath solution increased the frequency of spontaneous miniature endplate potentials (MEPPs) and quantal content. The amplitude of the endplate current (EPC) recorded from a d-tubocurarine-blocked endplate was significantly decreased by diltiazem (20-200 microM). However, the amplitude of miniature endplate current (MEPC) was relatively unchanged by diltiazem. The same degree of decrease in the decay time constant was observed in both EPC and MEPC. ACh potentials induced by repetitive iontophoresis were depressed gradually by low concentrations of diltiazem (2, 5 microM), suggesting enhanced desensitization. Using a patch-clamp method, the effects of diltiazem on ACh-activated single current in chick cultured myotubes were examined. The addition of diltiazem to the bath solution shortened the mean open time in a dose-dependent manner between 10 and 50 microM. The voltage-dependence of mean open time disappeared in the presence of diltiazem, with little change in the channel conductance. The present experiments suggest that diltiazem acts on the ACh-activated channel as an open channel blocker.

Pulsed EPR studies of doublet signal and singlet-like signal in oriented Ca2+-depleted PS II membranes: location of the doublet signal center in PS II.

Doublet signal and singlet-like signal induced in Ca(2+)-depleted PS II were investigated by pulsed EPR in one-dimensionally oriented photosystem (PS) II membranes. The doublet signal showed marked angular dependent change in its spectrum in term of the applied magnetic field, indicating that the magnetic dipole-dipole interaction is mainly responsible for the doublet signal. The singlet-like signal also showed angular dependence, which was less pronounced than that of the doublet signal. The parameters of dipole and exchange interactions used to simulate the doublet signal indicate that the signal arises from a magnetically coupled organic radical pair. Angular dependence of the doublet signal indicates that the radius vector of the radical pair (r) and the normal of the thylakoid membrane is at an angle of 65 degrees. Pulsed ELDOR studies in the oriented membranes indicate that the vector (R) connecting the doublet-signal center with the Y(D)(*) radical and the plane of the thylakoid membrane are at an angle of 8 degrees. Furthermore, the angle between the projections of the R and r vectors on the plane of the thylakoid membrane was determined to be 64 degrees. The location of the doublet-signal species in PS II is discussed.