Intermediates in the reaction of substrate-free cytochrome P450cam with peroxy acetic acid

Freeze-quenched intermediates of substrate-free cytochrome 57Fe-P450(cam) in reaction with peroxy acetic acid as oxidizing agent have been characterized by EPR and Mossbauer spectroscopy. After 8 ms of reaction time the reaction mixture consists of approximately 90% of ferric low-spin iron with g-factors and hyperfine parameters of the starting material; the remaining approximately 10% are identified as a free radical (S' = 1/2) by its EPR and as an iron(IV) (S= 1) species by its Mossbauer signature. After 5 min of reaction time the intermediates have disappeared and the Mossbauer and EPR-spectra exhibit 100% of the starting material. We note that the spin-Hamiltonian analysis of the spectra of the 8 ms reactant clearly reveals that the two paramagnetic species, e.g. the ferryl (iron(IV)) species and the radical, are not exchanged coupled. This led to the conclusion that under the conditions used, peroxy acetic acid oxidized a tyrosine residue (probably Tyr-96) into a tyrosine radical (Tyr*-96), and the iron(III) center of substrate-free P450(cam) to iron(IV).     

Fast stopped-flow microcalorimeter

A fast stopped-flow microcalorimeter using a thermistor and an a.c. bridge is described. Time resolution, limited by the response of the thermistor, is 3 ms for t 1/2 while sensitivity is 100 mu degree C in this bandpass. A reaction requires 0.3 ml of each reactant. The microcalorimeter is adiabatic to within 2% for 2 s and mixing may be repeated every 5 min. Computer finite element simulation techniques (FEST) are used to correct for the thermistor response time and heat losses. Results of tests with reactions of NaOH and HCl, NaHCO3, and HCl, and glyclyglycine and CO2 agree with published kinetic and thermodynamic values to within an experimental error of less than 2%.     

A quenched-flow apparatus which allows the measurement of the kinetics of a reaction in one stroke

A chemical quenched-flow apparatus is described which measures, in a unique stroke, enough data points (8–11) for establishing the kinetics curve of a reaction. Only very small volumes of reaction solutions (2 × 500 μl) are required. The time intervals between which the kinetic data may be measured range from 5 to 37 ms and from 120 to 450 ms with the corresponding mixing times of 0.6 and 5 ms, respectively. This apparatus was used to investigate the pre-steady-state domain of the aminoacylation reaction of tRNA^Val by valyl-tRNA synthetase from yeast.     

A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray

We describe here a second generation apparatus for studying transient reaction conformations in macromolecules and their complexes by electron cryo-microscopy. Reactions are trapped by rapid freezing in times ranging from a few milliseconds to tens of seconds after initiation. Blotting of the electron microscope grid and freezing it in liquid ethane uses computer controlled microstepping motors. For the fastest time resolution, a blotted grid containing a thin film of one reactant is sprayed with small droplets containing a second reactant just before freezing. The spray is produced electrically (electrospray), which gives a dense cloud of droplets <1 microm in diameter from the 1-2 microl of solution required per grid. A second method in which two solutions are first mixed by turbulent flow and then blotted prior to freezing is used for reactions with time courses >1s.     

On the implications of a sex difference in the reaction times of sprinters at the Beijing Olympics

Elite sprinters offer insights into the fastest whole body auditory reaction times. When, however, is a reaction so fast that it represents a false start? Currently, a false start is awarded if an athlete increases the force on their starting block above a given threshold before 100 ms has elapsed after the starting gun. To test the hypothesis that the fastest valid reaction times of sprinters really is 100 ms and that no sex difference exists in that time, we analyzed the fastest reaction times achieved by each of the 425 male and female sprinters who competed at the 2008 Beijing Olympics. After power transformation of the skewed data, a fixed effects ANOVA was used to analyze the effects of sex, race, round and lane position. The lower bounds of the 95, 99 and 99.9% confidence intervals were then calculated and back transformed. The mean fastest reaction time recorded by men was significantly faster than women (p<0.001). At the 99.9% confidence level, neither men nor women can react in 100 ms, but they can react in as little as 109 ms and 121 ms, respectively. However, that sex difference in reaction time is likely an artifact caused by using the same force threshold in women as men, and it permits a woman to false start by up to 21 ms without penalty. We estimate that female sprinters would have similar reaction times to male sprinters if the force threshold used at Beijing was lowered by 22% in order to account for their lesser muscle strength.     

Control of enzymatic velocity under near-equilibrium conditions

Algebraic derivations demonstrate that if a multireactant enzyme system is poised at equilibrium and the concentration of one of the reactants is then changed by a small fraction, the resulting net reaction velocity is hyperbolically related to the fractional perturbation rather than the initial or final absolute concentration of that reactant. For small fractional perturbations the velocity is almost identical regardless which reactant is perturbed. Similar results are obtained even if the reaction system is already displaced by up to 30% from equilibrium at the time of the perturbation. These conclusions are independent of the relationships between the reactant concentrations and the kinetic constants for the enzyme. Thus under any near-equilibrium condition each of the reactants for a multireactant enzyme system shares almost equally in control of the net reaction velocity.     

A double-beam rapid-scanning stopped-flow spectrophotometer.

A double-beam rapid-wavelength-scanning stopped-flow spectrophotometer system based on the Norcon model 501 spectrometer was construced, which enables u.v.-or visible absorbance spectra to be recorded at the rate of 800/s after the rapid mixing (within 3ms) of two reactant solutions. Each spectrum spans about 200nm in 1ms. It is possible to record difference spectra during reactions with half-lives less than 10ms involving absorbance changes of less than 0.1 absorbance unit. Analogue circuitry is used to produce spectra of absorbance against wavelength. Up to 32 such spectra can be recorded at pre-selected times during a reaction and stored in an 8Kx8-bit-word hard-wired data-capture system to be subsequently displaned individually or simultaneously. Time-courses at different wavelengths can also be displayed. By averaging up to 216 spectra it is possible to record spectra under conditions of low signal-to-noise ratios...     

Time-resolved analysis of macromolecular structures during reactions by stopped-flow electrooptics.

A stopped-flow field-jump instrument and its use for the analysis of macromolecular structure changes during reactions is described. The operation of the new instrument is simple and reliable, owing to a new type of cell construction with electrodes directly integrated in a quartz cuvette: major advantages are the relatively low demand on sample quantities and a high time resolution. The stopped flow is characterized by a dead time of approximately 0.5 ms. Electric field pulses with field strengths up to 20 kV/cm and rise times in the nanosecond range are applied at adjustable times after stop of the flow. The time resolution of the optical detection is up to the nanosecond time range. The instrument may be used for the combination of stopped flow with temperature-jump and field-jump experiments. A particularly useful new application is the analysis of macromolecular reactions by electrooptical measurements, because electrooptical data provide information about structures. This is demonstrated for the intercalation of ethidium into double-helical DNA. The transients, measured at 313 nm, where the signal is exclusively due to ethidium bound to the DNA, demonstrate a relatively high negative dichroism at 0.5 ms after mixing. The absolute value of this negative dichroism increases in the millisecond time range and approaches the equilibrium value within about a second. The dichroism decay time constants demonstrate a clear increase of the effective DNA length due to ethidium binding, already 0.5 ms after mixing; a further increase to the equilibrium value is found in the millisecond time range. The analysis of these data demonstrate the existence of up to three relaxation processes, depending on the conditions of the experiments. The dichroism amplitudes, together with the decay time constants, indicate that all the reaction states found in the present investigation are complexes with insertion of ethidium residues between basepairs. Moreover, the data clearly show the degree of intercalation in the intermediate states, which is very useful information for the quantitative assignment of the mechanism.     

Distributed Fading Memory for Stimulus Properties in the Primary Visual Cortex

It is currently not known how distributed neuronal responses in early visual areas carry stimulus-related information. We made multielectrode recordings from cat primary visual cortex and applied methods from machine learning in order to analyze the temporal evolution of stimulus-related information in the spiking activity of large ensembles of around 100 neurons. We used sequences of up to three different visual stimuli (letters of the alphabet) presented for 100 ms and with intervals of 100 ms or larger. Most of the information about visual stimuli extractable by sophisticated methods of machine learning, i.e., support vector machines with nonlinear kernel functions, was also extractable by simple linear classification such as can be achieved by individual neurons. New stimuli did not erase information about previous stimuli. The responses to the most recent stimulus contained about equal amounts of information about both this and the preceding stimulus. This information was encoded both in the discharge rates (response amplitudes) of the ensemble of neurons and, when using short time constants for integration (e.g., 20 ms), in the precise timing of individual spikes (≤∼20 ms), and persisted for several 100 ms beyond the offset of stimuli. The results indicate that the network from which we recorded is endowed with fading memory and is capable of performing online computations utilizing information about temporally sequential stimuli. This result challenges models assuming frame-by-frame analyses of sequential inputs.     

Chemical evolution as a concrete scheme for naturalizing the relative-state of quantum mechanics

The evolutionary onset of a reaction cycle such as an autocatalytic cycle requires a reliable framework for protecting the harbinger cycle, once it appears by any chance, against the hostile environments in the neighborhood. One natural candidate for protecting the fragile nascent cycle could be available from the operation of internal measurement envisioned in the relative-state formulation of quantum mechanics. Once every chemical reactant is taken to be relative to every other reactant in the act of measuring each other internally, the relative-state formulation provides the condition for favoring and protecting those events such that the reactions mediating between the reactants and the products may eventually form a reaction cycle.     

Dynamics of DNA condensation

The condensation of DNA induced by spermine and spermidine is investigated by equilibrium titrations and stopped-flow and field-jump experiments using scattered light detection. The spermine concentration required for the cooperative condensation process is measured at different DNA concentrations; these data are used to evaluate both the condensation threshold degree of spermine binding and the binding constant of spermine according to an excluded-site model. Stopped-flow measurements of the spermine-induced condensation demonstrate the existence of two processes: (1) A "fast" reaction is observed in the millisecond time range, when the reactant concentrations are around 1 microM; it is associated with a characteristic induction period and is assigned to the intramolecular condensation reaction. (2) A slow reaction with time constants of, e.g., 100 s strongly dependent upon both spermine and DNA concentrations is assigned to an intermolecular DNA association. The unusual time course of the intramolecular condensation reaction with the induction period provides evidence for a "threshold kinetics". During the induction period, spermine molecules are bound to DNA, but the degree of binding remains below the threshold value. As soon as the degree of ligand binding arrives at the threshold, the DNA is condensed in a relatively fast reaction. Model calculations of the spermine binding kinetics according to an excluded-site model demonstrate that the spermine molecules bound to DNA are mobile along the double helix. A comparison of the experimental data with the results of Monte Carlo simulations suggests a rate constant of approximately 200 s-1 for spermine movement by one nucleotide residue.(ABSTRACT TRUNCATED AT 250 WORDS)     

Optimization of a reactor assembly for the production of 6-APA from penicillin-V

The design and operation of an industrial penicillin-V deacylation reactor is simulated, using a kinetic expression and mass transport parameters for the immobilized enzyme particles which were determined experimentally in a previous study. It is desirable to use a series of equalsized plug flow reactors with pH control at the entrance to each reactor, and with a possibility of recycling reactant in each reactor. These measures are necessary to avoid a steep pH profile through the reactor; the deacylation reaction is accompanied by an increase of acidity of the reaction medium, and H(+) is a strong inhibitor and may deactivate the enzyme. The optimization study which is carried out at a fixed penicillin conversion of x = 0.99 shows that it is uneconomical to use penicillin feed concentrations above 150mM-175mM, and that the buffer concentration in the reaction medium should not be less than 50mM-75mM. Increasing the number of reactors from 4 to 8 or 10 leads to higher productivity of 6-APA, and a moderate recycle in the first couple of reactors diminishes the sharp decrease in pH which will be found in a straight plug flow reactor operation of the equipment. Higher pumping costs and lower productivity are unavoidable drawbacks of an operation mode where the separation costs for the product mixture are desired to be low.     

Effect of maintaining neck flexion on anti-saccade reaction time: an investigation using transcranial magnetic stimulation to the frontal oculomotor field

Background

Reaction time for anti-saccade, in which the gaze is directed to the position opposite to an illuminated target, shortens during maintenance of neck flexion. The present study applied transcranial magnetic stimulation (TMS) to the frontal oculomotor field, and investigated the effect of maintaining neck flexion on information processing time in the anti-saccade neural pathway before the frontal oculomotor field.

Methods

The reaction time was measured with the chin resting on a stand (‘chin-on’ condition) and with voluntary maintenance of neck flexion (‘chin-off’ condition) at 80% maximal neck flexion angle, with and without TMS. The TMS timing producing the longest prolongation of the reaction time was first roughly identified for 10 ms intervals from 0 to 180 ms after the target presentation. Thereafter, TMS timing was set finely at 2 ms intervals from −20 to +20 ms of the 10 ms step that produced the longest prolongation.

Results

The reaction time without TMS was significantly shorter (21.9 ms) for the chin-off (235.9 ± 14.9 ms) than for the chin-on (257.5 ± 17.1 ms) condition. Furthermore, TMS timing producing maximal prolongation of the reaction time was significantly earlier (18.6 ms) for the chin-off than the chin-on condition. The ratio of the forward shift in TMS timing relative to the reduction in reaction time was 87.8%.

Conclusions

We confirmed that information processing time in the anti-saccade neural pathway before the frontal oculomotor field shortened while neck flexion was maintained, and that this reduction time accounted for approximately 88% of the shortening of reaction time.     

Analysis of coupled bimolecular reaction kinetics and diffusion by two-color fluorescence correlation spectroscopy: enhanced resolution of kinetics by resonance energy transfer

In two-color fluorescence correlation spectroscopy (TCFCS), the fluorescence intensities of two fluorescently-labeled species are cross-correlated over time and can be used to identify static and dynamic interactions. Generally, fluorophore labels are chosen that do not undergo F?rster resonance energy transfer (FRET). Here, a general TCFCS theory is presented that accounts for the possibility of FRET between reactants in the reversible bimolecular reaction, [reaction: see text] where k(f) and k(b) are forward and reverse rate constants, respectively (dissociation constant K(d) = k(b)/k(f)). Using this theory, we systematically investigated the influence on the correlation function of FRET, reaction rates, reactant concentrations, diffusion, and component visibility. For reactants of comparable size and an energy-transfer efficiency of approximately 90%, experimentally measurable cross-correlation functions should be sensitive to reaction kinetics for K(d) > 10(-8) M and k(f) >or= approximately 10(7) M(-1)s(-1). Measured auto-correlation functions corresponding to donor and acceptor labels are generally less sensitive to reaction kinetics, although for the acceptor, this sensitivity increases as the visibility of the donor increases relative to the acceptor. In the absence of FRET or a significant hydrodynamic difference between reactant species, there is little effect of reaction kinetics on the shape of auto- and cross-correlation functions. Our results suggest that a subset of biologically relevant association-dissociation kinetics can be measured by TCFCS and that FRET can be advantageous in enhancing these effects.     

Fluorescence correlation spectroscopy. II. An experimental realization

This paper describes the first experimental application of fluorescence correlation spectroscopy, a new method for determining chemical kinetic constants and diffusion coefficients. These quantities are measured by observing the time behaviour of the tiny concentration fluctuations which occur spontaneously in the reaction system even when it is in equilibrium. The equilibrium of the system is not disturbed during the experiment. The diffusion coefficients and chemical rate constants which determine the average time behaviour of these spontaneous fluctuations are the same as those sought by more conventional methods including temperature-jump or other perturbation techniques. The experiment consists essentially in measuring the variation with time of the number of molecules of specified reactants in a defined open volume of solution. The concentration of a reactant is measured by its fluorescence; the sample volume is defined by a focused laser beam which excites the fluorescence. The fluorescent emission fluctuates in proportion with the changes in the number of fluorescent molecules as they diffuse into and out of the sample volume and as they are created or eliminated by the chemical reactions. The number of these reactant molecules must be small to permit detection of the concentration fluctuations. Hence the sample volume is small (10^?8 ml) and the concentration of the solutes is low (～ 10^?9 M). We have applied this technique to the study of two prototype systems: the simple example of pure diffusion of a single fluorescent species, rhodamine 6G, and the more interesting but more challenging example of the reaction of macromolecular DNA with the drug ethidium bromide to form a fluorescent complex. The increase of the fluorescence of the ethidium bromide upon formation of the complex permits the observation of the decay of concentration fluctuations via the chemical reaction and consequently the determination of chemical rate constants.     

A Computer-Controlled Spraying-Freezing Apparatus for Millisecond Time-Resolution Electron Cryomicroscopy

Apparatus is described for the kinetic investigation of biological reactions by electron cryomicroscopy with time resolution on the order of milliseconds. This involves layering a grid with one reactant and then spraying on a second reactant immediately before freezing. Two-stage mixing can be achieved by mixing two solutions, holding them in a delay line for a preset interval, and then spraying the aged solution onto a grid carrying a third reactant. The individual steps of these procedures are under software control and can be adjusted independently. Spray-freezing is widely applicable since solutions of small molecules, proteins, and protein assemblies can be delivered as aerosols. Thus the method can be used to study both the effects of small molecules on macromolecules and for monitoring protein–protein interactions. It may also be useful in other situations, for instance in light microscopy.     

Acetylation of wheat straw hemicelluloses in ionic liquid using iodine as a catalyst

Wheat straw hemicelluloses were acetylated with acetic anhydride using iodine as a novel catalyst in 1-butyl-3-methylimidzolium chloride ([C₄mim]Cl) ionic liquid (IL). Acetylated hemicelluloses with yield and degree of substitution (DS) from 70.5% to 90.8% and between 0.49 and 1.53, respectively, are accessible in a complete homogeneous procedure by changing the reaction temperature, reaction duration, the dosage of catalyst, and the dosage of acetic anhydride. The preferred reaction parameters that resulted in the highest DS were follows: 20:1 reactant molar ratio, 100 °C, 30 min, 15% iodine, in which about 83% hydroxyl groups in native hemicelluloses were esterified. The structural features of the acetylated hemicelluloses were characterized by ¹³C NMR and FT-IR spectroscopy. The thermal stability of the acetylated hemicelluloses increased upon chemical modification. It is the first time that we have demonstrated that ILs could be used as an environmentally friendly solvent for the chemical modification of hemicelluloses.     

Lipase-Catalyzed Synthesis and Hydrolysis of Cholesterol Oleate in Aot/Isooctane Microemulsions

We have examined a lipase-catalyzed bidirectional ester synthesis/hydrolysis reaction in a water-in-oil microemulsion system. The reactants were cholesterol (alcohol), oleic acid (acid) and cholesterol oleate (ester), and the solvent system consisted of sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/isooctane/water. The reactions were assayed by using [³H]oleic acid, [³H]cholesterol, or [³H]cholesterol oleate for the synthesis and hydrolysis reactions, respectively (separate incubations). The lipase that we used derived from Candida cylindracea, and was used at a concentration of 0.1mg/ml microemulsion. The reactions were performed at 22°C as the reactions proceeded more slowly at higher temperatures. With the initial reactant concentrations set to 10 mM cholesterol, 1 min oleic acid, and 1 mM cholesterol oleate, it was observed that the optimal [H₂O]/[AOT] ratio was at about 9 both for the esterification reaction and for the hydrolysis reaction (after 24 h). The hydrolysis reaction was slower than the synthesis reaction at all [H₂O]/[AOT] ratios studied (0-20), but the difference in reaction yield for the synthesis and the hydrolysis reactions became smaller as the reaction time increased (up to 11 days). When the reaction yield was followed as a time function, it was observed that about 80% of the oleic acid was esterified within 3 days of reaction ([H₂O]/[AOT] ratio of 6), whereas the corresponding value of 80% hydrolysis of cholesterol oleate was reached within 11 days. The results of the present study indicate that by choosing optimal reactant concentrations and reaction conditions, it is at least in part possible to determine the direction of the lipase-catalyzed synthesis/hydrolysis reaction.     

Consistent Estimation of Gibbs Energy Using Component Contributions

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.