Control of luminescence decay and flavin binding by the LuxA carboxyl-terminal regions in chimeric bacterial luciferases.

Bacterial luciferases (LuxAB) can be readily classed as slow or fast decay luciferases based on their rates of luminescence decay in a single turnover assay. Luciferases from Vibrio harveyi and Xenorhabdus (Photorhabdus) luminescens have slow decay rates, and those from the Photobacterium genus, such as P. (Vibrio) fischeri, P. phosphoreum, and P. leiognathi, have rapid decay rates. By generation of an X. luminescens-based chimeric luciferase with a 67 amino acid substitution from P. phosphoreum LuxA in the central region of the LuxA subunit, the "slow" X. luminescens luciferase was converted into a chimeric luciferase, LuxA(1)B, with a significantly more rapid decay rate. Two other chimeras with P. phosphoreum sequences substituted closer to the carboxyl terminal of LuxA, LuxA(2)B and LuxA(3)B, retained the characteristic slow decay rates of X. luminescens luciferase but had weaker interactions with both reduced and oxidized flavins, implicating the carboxyl-terminal regions in flavin binding. The dependence of the luminescence decay on concentration and type of fatty aldehyde indicated that the decay rate of "fast" luciferases arose due to a high dissociation constant (K(a)) for aldehyde (A) coupled with the rapid decay of the resultant aldehyde-free complex via a dark pathway. The decay rate of luminescence (k(T)) was related to the decanal concentration by the equation: k(T) = (k(L)A + k(D)K(a))/(K(a) + A), showing that the rate constant for luminescence decay is equal to the decay rate via the dark- (k(D)) and light-emitting (k(L)) pathways at low and high aldehyde concentrations, respectively. These results strongly implicate the central region in LuxA(1)B as critical in differentiating between "slow" and "fast" luciferases and show that this distinction is primarily due to differences in aldehyde affinity and in the decomposition of the luciferase-flavin-oxygen intermediate.     

M?ssbauer and EPR studies of the photoactivation of nitrile hydratase.

The alphabeta dimer of active nitrile hydratase from Rhodococcus sp. R312 contains one low-spin ferric ion that is coordinated by three Cys residues, two N-amide groups from the protein backbone, and one OH(-). The enzyme isolated from bacteria grown in the dark is inactive and contains the iron site as a six-coordinate diamagnetic Fe-nitrosyl complex, called NH(dark). The active state can be obtained from the dark state by photolysis of the Fe-NO bond at room temperature. Activation is accompanied by the conversion of NH(dark) to a low-spin ferric complex, NH(light), exhibiting an S = (1)/(2) EPR signal with g values of 2.27, 2.13, and 1.97. We have characterized both NH(dark) and NH(light) with M?ssbauer spectroscopy. The z-axis of the 57Fe magnetic hyperfine tensor, A, of NH(light) was found to be rotated by approximately 45 degrees relative to the z-axis of the g tensor (g(z) = 1.97). Comparison of the A tensor of NH(light) with the A tensors of low-spin ferric hemes indicates a substantially larger degree of covalency for nitrile hydratase. We have also performed photolysis experiments between 2 and 20 K and characterized the photolyzed products by EPR and M?ssbauer spectroscopy. Photolysis at 4.2 K in the M?ssbauer spectrometer yielded a five-coordinate low-spin ferric species, NH(A), which converted back into NH(dark) when the sample was briefly warmed to 77 K. We also describe preliminary EPR photolysis studies that have yielded new intermediates.     

Dimethylsulfoxide oxidizes glutathione in vitro and in human erythrocytes: kinetic analysis by 1H NMR

The interaction of dimethylsulfoxide (Me2SO) with glutathione was investigated under non-equilibrium conditions in solution using 1H NMR and in intact erythrocytes using 1H spin-echo NMR. In solution the reaction was observed to follow second-order kinetics (Rate = k1[glutathione][Me2SO]) at 300 K pH 7.4, k(sol) = 4.7 x 10(-5)mol(-1)L(1)s(-1). In intact erythrocytes the rate constant for the cellular environment, k(cell), was found to be slightly larger at 8.1 x 10(-5)mol(-1)L(1)s(-1). Furthermore, the reaction of Me2SO with erythrocyte glutathione showed a biphasic dependence on the Me2SO concentration, with little oxidation of glutathione occurring until the Me2SO concentration exceeded 0.5 molL(-1). The results suggest that at lower concentrations, Me2SO can be effectively removed, most probably by reaction with glutathione, which is regenerated by glutathione reductase, although preferential reaction with other cellular components (e.g., membrane or cellular thiols) cannot be ruled out. Thus the concentrations of Me2SO that are commonly used in cryopreservation of mammalian cells ( approximately 1.4 molL(-1)) can cause oxidation of intracellular glutathione.     

Effect of mass transfer in a recirculation batch reactor system for immobilized penicillin amidase

The effect of external mass transfer resistance on the overall reaction rate of the immobilized whole cell penicillin amidase of E. coli in a recirculation batch reactor was investigated. The internal diffusional resistance was found negligible as indicated by the value of effectiveness factor, 0.95. The local environmental change in a column due to the pH drop was successfully overcome by employing buffer solution. The reaction rate was measured by pH-stat method and was found to follow the simple Michaelis-Menten law at the initial stage of the reaction. The values of the net reaction rate experimentally determined were used to calculate the substrate concentration at the external surface of the catalyst pellet and then to calculate the mass transfer coefficient, k(L), at various flow rates and substrate concentrations. The correlation proposed by Chilton and Colburn represented adequately the experimental data. The linear change of log j(D) at low log N(Re) with negative slope was ascribed to the fact that the external mass transfer approached the state of pure diffusion in the limit of zero superficial velocity.     

Light-induced changes of extra- and intracellular potassium concentration in photoreceptors of the leech,Hirudo medicinalis

Summary The potassium concentration was measured in the cytoplasm, perimicrovillar extracellular space (=vacuole) and intercellular space of leech photoreceptors with double-barrelled potassium-sensitive microelectrodes in darkness and upon photostimulation. The mean intracellular potassium concentration in cells with membrane potentials >50 mV was 100±34 mmol/l. Photostimulation with 90 saturating 20 ms light flashes (1/s) evoked a potassium loss of 10.6±7.6 mmol/l. In the dark, there was no potassium concentration gradient between vacuole and intercellular space (K _VAC ⁺ =4.5±0.9 mmol/l, K _ECS ⁺ =4.5±0.5 mmol/l). In both compartments the potassium concentration increased upon repetitive photostimulation. Thus, the potassium loss from the cell is due to potassium movements across both the receptive and the non-receptive membrane domains.The time courses of K⁺ accumulation and clearance differed in the two extracellular compartments: In the vacuole, potassium increased by 2.8±2.5 mmol/l to a ceiling level which was maintained during the standard train of light flashes. Potassium clearing in the dark was exponential with a half time of 60±26 s. In the intercellular space, repetitive photostimulation produced an initial rapid increase (half time <1 s) of the K⁺ concentration (mean K _max ⁺ =1.5±0.6 mmol/l). K⁺ clearing showed two superimposed components. A rapid one clears intercellular K⁺ after each light flash. The resultant K⁺ pulses ride on a slowly decreasing intercellular K+ level, and, following the last flash, K⁺ transiently undershoots the dark concentration.Ouabain or a decrease in specimen temperature affect only the slow component and abolish the poststimulation K⁺ undershoot. Thus, the rapid component is interpreted as due to passive K⁺ dispersal by diffusion through the intercellular spaces, and the slow component and the poststimulation undershoot to K⁺ clearing by active reuptake of K⁺ into the photoreceptor cells.K⁺ disappearance from the vacuole was not affected by ouabain, but a decrease in specimen temperature decreased the rate constant of K⁺ clearing, which has a Q₁₀ of 1.48. It is concluded that K⁺ clearing from the vacuole is dominated by passive processes, and that the Na⁺/K⁺-pump is possibly localized only in the non-receptive membrane domain.     

Tracking single secretory granules in live chromaffin cells by evanescent-field fluorescence microscopy

We have observed secretory granules beneath the plasma membrane of chromaffin cells. Using evanescent-field excitation by epiillumination, we have illuminated a thin layer of cytosol where cells adhere to glass coverslips. Up to 600 frames could be recorded at diffraction-limited resolution without appreciable photodynamic damage. We localized single granules with an uncertainty of approximately 30 nm and tracked their motion in three dimensions. Granules in resting cells wander randomly as if imprisoned in a cage that leaves approximately 70 nm space around a granule. The "cage" itself moves only slowly (D = 2 x 10(-12) cm2/s). Rarely do granules arrive at or depart from the plasma membrane of resting cells. Stimulation increases lateral motion only slightly. After the plasma membrane has been depleted of granules by exocytosis, fresh granules can be seen to approach it at an angle. The method will be useful for exploring the molecular steps preceding exocytosis at the level of single granules.     

Photooxidation of mitochondrial cytochrome c by isolated bacterial reaction centers: Evidence for tight-binding and diffusional pathways

The binding of horse heart mitochondrial cytochrome c to isolated reaction centers from Rhodopseudomonas sphaeroides is described. The kinetics of photooxidation of cytochrome c following a short actinic flash is compared to the expected binding state of the cytochrome at various concentrations and at different ionic strengths. At low ionic strength a very tight binding site (K_D10^-8 M) is apparent which is nonfunctional with respect to electron donation to the bound reaction center. This tightly bound cytochrome can react with another reaction center in a diffusion limited, second order process. A weaker binding site (K_D0.3 · 10^-6 M) is also boserved which is associated with rapid, first order electron transfer from cytochrome to reaction center. Both binding processes are weakened in the presence of salt and there is no detectable binding in 100 mM NaCl. Under such conditions cytochrome oxidation is entirely a diffusional, second order process. However, analysis of the flash intensity dependence of the extent of cytochrome oxidation, by the method of van Grondelle (van Grondelle, R. (1978) Ph.D. Thesis, State University, Leiden) indicated that the cytochrome was not freely mobile even in 100 mM NaCl, at least in the sense that reduced cytochrome only slowly dissociates from unactivated reaction centers. An overall kinetic/equilibrium scheme for cytochrome c binding and photooxidation by reaction centers is presented. This is very similar to that described earlier for cytochrome c₂ (Overfield, R.E., Wraight, C.A. and DeVault, D. (1979) FEBS Lett. 105, 137–142), but the tight binding site and associated diffusion controlled oxidation is unique to cytochrome c.Dedicated to Prof. L.N.M. Duysens on the occasion of his retirement.     

Correlation between flash-induced oxygen evolution and fluorescence yield kinetics in the 0 to 16 mus range in Chlorella pyyrenoidosa during incubation with hydroxylamine.

Following flash excitation, oxygen pulses and fluorescence kinetics in the time range 0-16 mus were studied in the alga Chlorella pyrenoidosa during incubation with various concentrations of hydroxylamine. The obtained results could be explained considering four effects of hydroxylamine. 1. Hydroxylamine removes (reduces) oxidizing equivalents, generated in the water-splitting system by flash excitation. This process does not markedly affect the fluorescence yield kinetics between 0 and 16 mus following the ignition of a flash and reaches a constant rate within a few minutes, but possibly within a few seconds, after addition of hydroxylamine. In a sequence of flashes separated by dark time td, the steady-state oxygen yield in the flashes is exp(-ktd), the yield at td=0 being taken equal to 1, where k=(0.1 + beta[NH2OH])s-1, with [NH2OH] in mM and beta=0.6 mM-1, provided [NH2OH]greater than or equal to 0.5 mM. 2. An inhibition between Z, the physiological donor and the oxidized reaction center pigment P+ occurs, proceeding as exp (-kiti)where ti is the incubation time with hydroxylamine and ki=(alpha[NH2OH]) min-1, with [NH2OH] in mM and alpha=0.14 mM-1. This process not only inhibits oxygen evolution capability, but also decreases the amplitude of the fluorescence yield difference deltaphi=phi(16 mus)-phi(2 mus) induced by a flesh in the steady state. In a fraction of the reaction centers this inhibition occurs "immediately" after the addition of hydroxylamine. These observations, combined with the conslusion of Cheniae and Martin (1971, Plant Physiol. 47, 568-575) that the inhibition of the Hill reaction is related to the extraction of bound manganese indicate that the reaction between Z and P+ requires bound manganese. 3. In the inhibited centers a second donor for P+, D, connected to an entry site for the artificial electron donor hydroxylamine becomes apparent. 4. A flash-induced oxygen uptake signal was observed in the presence of hydroxylamine, which was shown to be caused by a system II reaction. The effects under (1) and (4) were reversed in the dark if hydroxylamine was removed by washing. The effects under (2) and (3) were reversed during illumination of a washed sample.     

Diffusional effects on the heterogeneous kinetics of two-substrate enzymic reactions.

When a two-substrate reaction is catalyzed by a surface bound enzyme, the diffusion of both substrates can considerably modify the kinetic properties of the reaction. According to this theoretical analysis, limitations in substrate diffusion yield very different effects depending whether the two substrates have similar or different affinities for the enzyme. With two substrates of comparable affinities the diffusion of the two substrates can be limiting, and similar activity dependences on the two substrate concentrations are obtained. Under these conditions, diffusional limitations may only slightly influence half-maximal-activity substrate concentrations. With two substrates of widely different affinities, on the contrary, the rate of the enzymic reaction can only be limited by the diffusion of the high-affinity substrate, used at the lower concentration. Under these conditions, in the presence of diffusional limitations the activity dependence on the two substrate concentrations are highly different, and the half-maximal-activity concentration is increased and decreased for the high- and low-affinity substrates, respectively. The theoretical results are verified by experimental data previously obtained with collagen-bound aspartate aminotransferase and sorbitol dehydrogenase.     

Generation of xylose solutions from Eucalyptus globulus wood by autohydrolysis-posthydrolysis processes: posthydrolysis kinetics

Eucalyptus wood samples were treated with water under selected operational conditions (autohydrolysis reaction) to obtain a liquid phase containing hemicellulose-decomposition products (mainly acetylated xylooligosaccharides, xylose and acetic acid). In a further acid-catalysed step (posthydrolysis reaction), xylooligosaccharides were converted into xylose, a carbon source for further fermentation. The kinetic pattern governing the posthydrolysis step was established by reacting xylooligosaccharide-containing liquors at 100.5 degrees C, 115 degrees C, 125 degrees C or 135 degrees C in media containing 0.5, 1.0, 1.5 or 2 wt% of catalyst (sulphuric acid). The time course of the concentrations of xylooligosaccharides, xylose, furfural and acetic acid were determined, and the results were interpreted by means of a kinetic model which allowed a close reproduction of the experimental data. Almost quantitative conversion of xylooligosaccharides into xylose was achieved under a variety of experimental conditions. The first-order, kinetic coefficient for xylooligosaccharide hydrolysis (k1, h(-1)) varied with both temperature (T, K) and molar sulphuric acid concentration (C) according to the equation In k1 = 36.66 + 1.00lnC - 108.0/(8.314T). The hydrolysis of acetyl groups followed a first-order kinetics. The corresponding kinetic coefficient (ka, h(-1) was correlated with the operational conditions by the equation Inka = 26.80+ 1.18 InC - 73.37/(8.314T).     

A new rapid and simple method to determine the kinetics of electrode reactions of biologically relevant compounds from the half-peak width of the square-wave voltammograms

A new method is introduced to determine the kinetic parameters of electron transfer reactions of biologically important compounds, based on the measurements of the half-peak width (DeltaE(p/2)) of the square-wave voltammograms. A simple surface (diffusionless) redox reaction, and a simple electrode reaction occurring from dissolved state are considered as model systems. In the region of quasireversible electron transfer, the half-peak widths of theoretical square-wave voltammograms are linear functions of the logarithm of the dimensionless kinetic parameter ln(K) that characterizes the rate of the electron transfer reaction. The dimensionless kinetic parameter K is defined as K=k(s)(fD)(-0.5) for the redox reaction taking place from dissolved state, whereas for the surface redox reaction K is defined as K=k(s)/f (k(s) is the standard rate constant of electron transfer, f is the SW frequency, and D is the diffusion coefficient). A set of linear regression equations for the dependences DeltaE(p/2)vs. ln(K) are derived, which can be used for rapid and precise determination of the charge-transfer kinetic parameters. The estimated values for the standard rate constants of various biologically relevant redox systems using this approach are in very good agreement with the experimental values determined by other square-wave voltammetric methods. The square-wave voltammetric half-peak width method can be used as a simple and reliable alternative to other voltammetric methods developed for the kinetic characterization of electron transfer rates.     

Diffusion of molecules on biological membranes of nonplanar form. A theoretical study.

Lateral mobility of molecules on cell membranes has been recently studied by fluorescence photobleaching recovery (FPR) techniques. The interpretation of these results in terms of diffusion along the membranes is based on the assumption that the surface is planar, although biological membranes may have blebs and microvilli. To study the effect of nonplanarity on the diffusion rate, the diffusion equation along curved surfaces was derived and was solved numerically for a "wavy" surface of the form A cos kx cos ky. Calculations show that for k = 10 pi micrometer-1 and a bleached spot of 1 micrometer in diameter, the time dependence of the intensity of fluorescence in the bleached spot depends on A at A less than 0.5 micrometer, while at higher values of A (a and 2 micrometer) the dependence is weak. If one calculates diffusion coefficients from FPR measurements and assumes that the membrane is planar, the resulting diffusion coefficient is not less than about half of the real one. Because of the tortuous shape of the spot boundary, increasing the microvilli length from 0.5 micrometer to 1 or 2 micrometer does not change the diffusion rates. These considerations are valid for times when the diffusion is dominated by molecules that were initially located close to the spot boundary.     

Highly nonproductive complexes with Anabaena ferredoxin at low ionic strength are induced by nonconservative amino acid substitutions at Glu139 in Anabaena ferredoxin:NADP+ reductase

Ferredoxin (Fd) and ferredoxin:NADP(+) reductase (FNR) from Anabaena function in photosynthetic electron transfer (et). The et interaction between the FNR charge-reversal mutant E139K and Fd at 12 mM ionic strength (mu) is extremely impaired relative to the reaction with wt FNR, and the dependency of k(obs) on E139K concentration shows strong upward curvature at protein concentrations > or = 10 microM. However, at values of mu > or = 200 mM, reaction rates approach those of wild-type FNR, and normal saturation kinetics are observed. For the E139Q mutant, which is also significantly impaired in its et interaction with Fd at low FNR concentrations and low mu values, the dependency of k(obs) on E139Q concentration shows a smaller degree of upward curvature at mu = 12 and 100 mM and shows saturation kinetics at higher values of mu. wt FNR and the E139D mutant both show a slight amount of upward curvature at FNR concentrations >30 microM at mu = 12 mM but show the expected saturation kinetics at higher values of mu. These results are explained by a mechanism in which the mutual orientation of the proteins in the complex formed at low ionic strength with the E139K mutant is so far from optimal that it is almost unreactive. At increased E139K concentrations, the added mutant FNR reacts via a collisional interaction with the reduced Fd present in the unreactive complex. The et reactivity of the low ionic strength complexes depends on the particular amino acid substitution, which via electrostatic interactions alters the specific geometry of the interface between the two proteins. The presence of a negative charge at position 139 of FNR allows the most optimal orientations for et at ionic strengths below 200 mM.     

The control of rat-heart phosphofructokinase by citrate and other regulators

1. The effects of ATP, inorganic phosphate and citrate on the relationship between fructose 6-phosphate concentration and initial velocity of reaction has been investigated with a partially purified preparation of rat-heart phosphofructokinase. 2. At low concentrations of ATP (<80mum) rate curves for fructose 6-phosphate approximated to Michaelis-Menten kinetics. At higher ATP concentrations rate curves were sigmoid, the K(m) for fructose 6-phosphate increased and the reaction appeared to be first-order with respect to fructose 6-phosphate at concentrations above its K(m) and of a higher order at concentrations below its K(m). Inorganic phosphate lowered the K(m) for fructose 6-phosphate and the concentration at which the apparent kinetic order decreased. 3. At 40mum-ATP, citrate was an activator at low concentration (<100mum) and an inhibitor at higher concentrations. At 0.5mm-ATP, citrate was inhibitory at all concentrations tested. 4. A new method for phosphofructokinase assay using [U-(14)C]fructose 6-phosphate is described which allows measurements to be made of the velocity of the forward reaction at known concentrations of the products of the reaction. With this method confirmatory evidence has been obtained that concentrations of ATP, AMP, phosphate and citrate may regulate phosphofructokinase in the perfused rat heart.     

Influence of substrate and product diffusion on the heterogeneous kinetics of enzymic reversible reactions

When a reversible reaction is catalyzed by a surface bound enzyme, the diffusion of both substrate and product can considerably modify the kinetic properties of the reaction. According to this theoretical analysis, the enzyme activity is decreased due to the presence of substrate and product concentration gradients in the enzyme microenvironment, and the relative kinetic importance of the two diffusion steps mainly depend on the value of a dimensionless criterion inversely proportional to the equilibrium constant. Moreover diffusional effects increase with increasing bound enzyme activity, but decrease with increasing substrate and product concentration. Analytical expressions are established for the limiting values of substrate and product concentrations in the enzyme microenvironment, as well as for the increase in half-maximal-activity substrate concentration in the presence of substrate and product diffusional limitations.     

Extracellular space diffusion in central nervous system: anisotropic diffusion measured by elliptical surface photobleaching

Diffusion in the extracellular space (ECS) is crucial for normal central nervous system physiology. The determinants of ECS diffusion include viscous interactions with extracellular matrix/plasma membranes ("viscosity") and ECS geometry ("tortuosity"). To resolve viscosity versus tortuosity effects, we measured direction-dependent (anisotropic) diffusion in ECS in mouse spinal cord by photobleaching using an elliptical spot produced by a cylindrical lens in the excitation path. Anisotropic diffusion slowed fluorescence recovery when the long axis of the ellipse was parallel versus perpendicular to the direction of faster diffusion. A mathematical model was constructed to deduce diffusion coefficients (D(x), D(y)) from fluorescence recovery measured for parallel and perpendicular orientations of the long axis of the ellipse. Elliptical spot photobleaching was validated by photobleaching aqueous-phase fluorophores on a diffraction grating, where diffusion is one-dimensional. Measurement of the diffusion of 70 kDa FITC-dextran in spinal cord in living mice indicated that viscosity slows diffusion by approximately 1.8-fold compared with its diffusion in solution. ECS geometry hinders diffusion across (but not along) axonal fibers in spinal cord further by approximately fivefold. In cerebral cortex, however, approximately 50% of the hindrance to ECS diffusion comes from viscosity and approximately 50% from tortuosity. We suggest that the extracellular matrix might have evolved to facilitate rather than hinder diffusion even for large molecules.     

Kinetics and thermodynamics of ouabain binding by intact turkey erythrocytes: effects of external sodium ion, potassium ion, and temperature

The kinetics of association and dissociation for the ouabain-Na+,K+- dependent ATPase complex have been studied in intact turkey erythrocytes as a function of external Na+ concentration, K+ concentration, and temperature. At free ligand concentrations substantially exceeding the concentration of available binding sites, the association reaction exhibits pseudo-first-order kinetics with an association rate constant (k1) that is conveniently determined over a wide range of temperatures (5-37 degrees C). The dissociation reaction exhibits strict first-order kinetics with a dissociation rate constant (k-1) that has the unusual property, in the turkey cell, of being sufficiently great to permit its direct determination even at temperatures as low as 5 degrees C. Values for the equilibrium binding constant for the ouabain-ATPase complex (KA) predicted from the ratio of the association and dissociation rate constants agree closely with independently measured values of KA determined directly under conditions of equilibrium binding. KA is a sensitive function of the composition of the external ionic environment, rising with increasing Na+ concentration and falling with increasing K+ concentration. These changes in KA are shown to be quantitatively attributable to changes in the rate constant k1, k-1 in contrast being unaffected at any given temperature by even very large changes in Na+ or K+ concentration. Arrhenius plots of k1 and k-1 both yield straight lines over the entire temperature range corresponding to activation energies for association and dissociation of 29.5 and 24.2 kcal/mol, respectively. These observations have made it possible to calculate the following standard values for the ouabain binding reaction in the presence of 150 mM Na+: delta G degree = -9.8 kcal/mol; delta H degree = +5.3 kcal/mol; delta S degree = +48.7 cal/degree/mol. The large positive value of delta S degree presumably reflects a highly ordered configuration of the ouabain-free ATPase molecule that is lost upon ouabain binding and that "drives" the reaction despite the positive value of delta H degree.     

Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents

We have investigated the potential of sedimentation velocity analytical ultracentrifugation for the measurement of the second virial coefficients of proteins, with the goal of developing a method that allows efficient screening of different solvent conditions. This may be useful for the study of protein crystallization. Macromolecular concentration distributions were modeled using the Lamm equation with the approximation of linear concentration dependencies of the diffusion constant, D = D(o) (1 + k(D)c), and the reciprocal sedimentation coefficient s = s(o)/(1 + k(s)c). We have studied model distributions for their information content with respect to the particle and its non-ideal behavior, developed a strategy for their analysis by direct boundary modeling, and applied it to data from sedimentation velocity experiments on halophilic malate dehydrogenase in complex aqueous solvents containing sodium chloride and 2-methyl-2,4-pentanediol, including conditions near phase separation. Using global modeling for three sets of data obtained at three different protein concentrations, very good estimates for k(s) and s degrees and also for D degrees and the buoyant molar mass were obtained. It was also possible to obtain good estimates for k(D) and the second virial coefficients. Modeling of sedimentation velocity profiles with the non-ideal Lamm equation appears as a good technique to investigate weak inter-particle interactions in complex solvents and also to extrapolate the ideal behavior of the particle.     

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.     

The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of Hhai methyltransferase

Kinetic and binding studies involving a model DNA cytosine-5-methyltransferase, M.HhaI, and a 37-mer DNA duplex containing a single hemimethylated target site were applied to characterize intermediates on the reaction pathway. Stopped-flow fluorescence studies reveal that cofactor S-adenosyl-l-methionine (AdoMet) and product S-adenosyl-l-homocysteine (AdoHcy) form similar rapidly reversible binary complexes with the enzyme in solution. The M.HhaI.AdoMet complex (k(off) = 22 s(-)1, K(D) = 6 microm) is partially converted into products during isotope-partitioning experiments, suggesting that it is catalytically competent. Chemical formation of the product M.HhaI.(Me)DNA.AdoHcy (k(chem) = 0.26 s(-)1) is followed by a slower decay step (k(off) = 0.045 s(-)1), which is the rate-limiting step in the catalytic cycle (k(cat) = 0.04 s(-)1). Analysis of reaction products shows that the hemimethylated substrate undergoes complete (>95%) conversion into fully methylated product during the initial burst phase, indicating that M.HhaI exerts high binding selectivity toward the target strand. The T250N, T250D, and T250H mutations, which introduce moderate perturbation in the catalytic site, lead to substantially increased K(D)(DNA(ternary)), k(off)(DNA(ternary)), K(M)(AdoMet(ternary)) values but small changes in K(D)(DNA(binary)), K(D)(AdoMet(binary)), k(chem), and k(cat). When the target cytosine is replaced with 5-fluorocytosine, the chemistry step leading to an irreversible covalent M.HhaI.DNA complex is inhibited 400-fold (k(chem)(5FC) = 0.7 x 10(-)3 s(-)1), and the Thr-250 mutations confer further dramatic decrease of the rate of the covalent methylation k(chem). We suggest that activation of the pyrimidine ring via covalent addition at C-6 is a major contributor to the rate of the chemistry step (k(chem)) in the case of cytosine but not 5-fluorocytosine. In contrast to previous reports, our results imply a random substrate binding order mechanism for M.HhaI.