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J A Rupley

Publications and source records attributed to J A Rupley.

At least 19 recordsLinked to original sources
PubMed1992

In vitro analysis of mutant LexA proteins with an increased rate of specific cleavage.

Specific cleavage of LexA repressor plays a crucial role in the SOS response of Escherichia coli. In vivo, cleavage requires an activated form of RecA protein. However, previous work has shown that the mechanism of cleavage is unusual, in that the chemistry of cleavage is probably carried out by residues in the repressor, and not those in RecA; RecA appears to facilitate this reaction, acting as a coprotease. We recently described a new type of lexA mutation, a class termed lexA (IndS) and here called IndS, that confers an increased rate of in vivo cleavage. Here, we have characterized the in vitro cleavage of these IndS mutant proteins, and of several double mutant proteins containing an IndS mutation and one of several mutations, termed Ind-, that decrease the rate of cleavage. We found, first, that the autodigestion reaction for the IndS mutant proteins had a higher maximum rate and a lower apparent pKa than wild-type LexA. Second, the IndS mutations had little or no effect on the rate of RecA-mediated cleavage, measured at low protein concentrations, implying that the value of Kcat/Km was unaffected. Third, the rate of autodigestion for the double-mutant proteins, relative to wild-type, was about that rate predicted from the product of the effects of the two single mutations. Finally, by contrast, these proteins displayed the same rate of RecA-mediated cleavage as did the single Ind- mutant protein. We interpret these data to mean that the IndS mutations mimic to some extent the effect of RecA on cleavage, perhaps by favoring a conformational change in LexA. We present and analyze a model that embodies these conclusions.

Bacterial Proteins↗
PubMed1988

Two-dimensional protonic percolation on lightly hydrated purple membrane.

The capacitance and dielectric loss factor were measured for a sample of purple membrane of Halobacterium halobium as a function of hydration level (0.017 to >0.2 g of water/g of membrane) and frequency (10 kHz to 10 MHz). The capacitance and the derived conductivity show explosive growth above a threshold hydration level, h(c) approximately 0.0456. The conductivity shows a deuterium isotope effect, H/(2)H = 1.38, in close agreement with expectation for a protonic process. The level h(c) is frequency independent and shows no deuterium isotope effect. These properties are analogous to those found for lysozyme in a related study. Protonic conduction for the purple membrane can be considered, as for lysozyme, within the framework of a percolation model. The critical exponent, t, which describes the conductivity of a percolative system near the threshold, has the value 1.23. This number is in close agreement with expectation from theory for a two-dimensional percolative process. The dielectric properties of the purple membrane are more complex than those of lysozyme, seen in the value of h(c) and in the frequency and hydration dependence of the loss factor. There appear to be preferred regions of proton conduction. The percolation model is based upon stochastic behavior of a system partially populated with conducting elements. This model suggests that ion transport in membranes and its control can be based on pathways formed of randomly connected conducting elements and that a fixed geometry (a proton wire) is not the only possible basis for a mechanism of conduction.

Journal Article↗
PubMed1986

Intramolecular cleavage of LexA and phage lambda repressors: dependence of kinetics on repressor concentration, pH, temperature, and solvent.

LexA repressor of Escherichia coli and phage lambda repressor are inactivated in vivo and in vitro by specific cleavage of an Ala-Gly peptide bond in reactions requiring RecA protein. At mildly alkaline pH, the in vitro cleavage reaction also proceeds spontaneously, suggesting that peptide bond hydrolysis is an activity of the repressors rather than of RecA. The spontaneous cleavage reaction, termed "autodigestion", has been characterized for the LexA and lambda repressors. The results show that the reaction is intramolecular. The rate of LexA autodigestion was studied over the pH range 7.15-11.77 and over the temperature range 4-46 degrees C. The logarithm of the rate constant increased linearly with pH and reached a plateau value (2.5 X 10(-3) s-1 at 37 degrees C) at pH above 10. The data closely followed a model in which a single residue side chain (apparent pK = 9.8 at 37 degrees C) must be deprotonated for the protein to show activity. Analysis of the temperature dependence gave the heat of proton dissociation as 19.9 kcal/mol and the heat of activation for hydrolysis as 15.3 kcal/mol at 25 degrees C. Autodigestion of lambda repressor, studied over the pH range 8.65-10.70 at 37 degrees C, was similar to the LexA reaction in its pH dependence, yielding a pK of 9.8. The maximum rate at 37 degrees C for lambda repressor, 6.1 X 10(-5) s-1, was 40 times slower than for LexA, a difference similar to that previously observed in vivo and in vitro for RecA-dependent cleavage reactions. There was no significant solvent deuterium isotope effect on the autodigestion of LexA. Changes in buffer composition, including high concentrations of glycine for lambda repressor and of imidazole or hydroxylamine for LexA, indicated that solvent components other than water do not participate in the rate-determining step. Removal or addition of metal ions did not significantly affect LexA autodigestion. These and other observations suggest that the deprotonated form of an amino acid side chain plays a central role in the chemistry of the cleavage reaction. The above observations establish repressor autodigestion as a member of an emerging set of biologically important self-processing reactions.

Bacterial Proteins↗
PubMed1986

Proton percolation on hydrated lysozyme powders.

The framework of percolation theory is used to analyze the hydration dependence of the capacitance measured for protein samples of pH 3-10, at frequencies from 10 kHz to 4 MHz. For all samples there is a critical value of the hydration at which the capacitance sharply increases with increase in hydration level. The threshold h(c) = 0.15 g of water per g of protein is independent of pH below pH 9 and shows no solvent deuterium isotope effect. The fractional coverage of the surface at h(c) is in close agreement with the prediction of theory for surface percolation. We view the protonic conduction process described here for low hydration and previously for high hydration as percolative proton transfer along threads of hydrogen-bonded water molecules. A principal element of the percolation picture, which explains the invariance of h(c) to change in pH and solvent, is the sudden appearance of long-range connectivity and infinite clusters at the threshold h(c). The relationship of the protonic conduction threshold to other features of protein hydration is described. The importance of percolative processes for enzyme catalysis and membrane transport is discussed.

Journal Article↗
PubMed1985

Hydrogen exchange of lysozyme powders. Hydration dependence of internal motions.

The rate of exchange of the labile hydrogens of lysozyme was measured by out-exchange of tritium from the protein in solution and from powder samples of varied hydration level, for pH 2, 3, 5, 7, and 10 at 25 degrees C. The dependence of exchange of powder samples on the level of hydration was the same for all pHs. Exchange increased strongly with increased hydration until reaching a rate of exchange that is constant above 0.15 g of H2O/g of protein (120 mol of H2O/mol of protein). This hydration level corresponds to coverage of less than half the protein surface with a monolayer of water. No additional hydrogen exchange was observed for protein powders with higher water content. Considered in conjunction with other lysozyme hydration data [Rupley, J. A., Gratton, E., & Careri, G. (1983) Trends Biochem. Sci. (Pers. Ed.) 8, 18-22], this observation indicates that internal protein dynamics are not strongly coupled to surface properties. The use of powder samples offers control of water activity through regulation of water vapor pressure. The dependence of the exchange rate on water activity was about fourth order. The order was pH independent and was constant from 114 to 8 mol of hydrogen remaining unexchanged/mol of lysozyme. These results indicate that the rate-determining step for protein hydrogen exchange is similar for all backbone amides and involves few water molecules. Powder samples were hydrated either by isopiestic equilibration, with a half-time for hydration of about 1 h, or by addition of solvent to rapidly reach final hydration. Samples hydrated slowly by isopiestic equilibration exhibited more exchange than was observed for samples of the same water content that had been hydrated rapidly by solvent addition. This difference can be explained by salt and pH effects on the nearly dry protein. Such effects would be expected to contribute more strongly during the isopiestic equilibration process. Solution hydrogen exchange measurements made for comparison with the powder measurements are in good agreement with published data. Rank order was proven the same for all pHs by solution pH jump experiments. The effect of ionic strength on hydrogen exchange was examined at pH 2 and pH 5 for protein solutions containing up to 1.0 M added salt. The influence of ionic strength was similar for both pHs and was complex in that the rate increased, but not monotonically, with increased ionic strength.

Animals↗
PubMed1985

Protonic conductivity of hydrated lysozyme powders at megahertz frequencies.

Dielectric losses were measured for lysozyme powders of varied hydration level by a dielectric-gravimetric technique in the frequency range of 10 kHz to 10 MHz. The relaxation showed an isotope effect and pH dependence, indicating that the inferred conductivity is protonic. The transport process is likely restricted to the surface of individual macromolecules and involves shifting of protons between ionizable side chain groups of the protein. The time constant of the relaxation shows cooperativity in its seventh-order dependence on bound protons. The process develops in the hydration region critical for the onset of the catalytic properties of the enzyme. The binding of a substrate increases the relaxation time by a factor of 2. These observations suggest that the megahertz dispersion reflects behavior at the protein surface, specifically the cooperative channeling of proton flow through the active site, that may be of particular significance for the enzymatic and other functional properties of proteins.

Electric Conductivity↗
PubMed1984

Experimental identification of a theoretically predicted "left-sided" binding mode for (GlcNAc)6 in the active site of lysozyme.

Using conformational energy calculations, we previously predicted that there are two distinct binding modes for hexasaccharide substrates of hen egg white lysozyme (HEWL), a "left-sided" binding mode and a "right-sided" one. The former involves such residues as Arg-45, Asn-46, and Thr-47, while the latter involves such residues as Asn-113 and Arg-114. The left-sided binding mode was predicted to predominate for (GlcNAc)6. We now present two lines of experimental evidence that indicate that left-sided binding occurs for this substrate. First, we show that ring-necked pheasant lysozyme (RNPL), in which Lys and His replace Asn and Arg at positions 113 and 114, respectively, has the same affinity for (GlcNAc)6 as does HEWL, indicating that the "right" side is not involved in equilibrium binding to the substrate. Second, we show that a monoclonal antibody, HyHEL-5, which binds specifically to an epitope including residues Arg-45, Asn-46, Thr-47, Asp-48, and Arg-68 on the far "left" side of HEWL, is competitively displaced by (GlcNAc)5 and (GlcNAc)6 but not by GlcNAc, (GlcNAc)2, or (GlcNAc)4. Only the former two substrates can bind in site F in the lower active site. Since these two substrates are the only ones that competitively displace HyHEL-5, our results suggest that the terminal saccharide residues of these substrates bind to the left side of the active site cleft, as predicted from theory.

Animals↗
PubMed1984

Nucleotide-induced changes in the heat capacity of beef cardiac myosin.

The heat of reaction of ATP with beef cardiac myosin has been determined in a flow microcalorimeter at two different temperatures. The reaction heat obtained by extrapolation to infinite flow rate is interpreted to be the heat of formation of the steady-state set of myosin-nucleotide complexes. The large temperature dependence of this heat, an apparent change in heat capacity, could be caused by an isomerization between two myosin conformations. The enthalpies and heat capacities of binding of ADP, AMP, and pyrophosphate have also been measured and are discussed in terms of this model.

Adenosine Diphosphate↗
PubMed1981

Thermodynamics of dihexanoylphosphatidylcholine aggregation.

Heats of dilution of aqueous solutions of dihexanoylphosphatidylcholine were determined by use of a flow microcalorimeter to monitor an exponential dilution gradient. Three different models of micelle formation were tested: monomer in equilibrium with micelles of fixed size, with micelles of varied size, or with small aggregates and micelles. The heat of dilution data for low solute concentration could be fit only by assuming the existence of premicellar aggregates. The critical micelle concentration determined calorimetrically is 0.016 +/- 0.002 M and is independent of the model. The enthalpy change for transfer of monomer into the micelle is 1.6 +/- 0.2 kcal/mol; about one-third of this heat effect is produced in formation of the premicellar aggregation. Comparison of the calorimetric measurements with results obtained by using other methods indicates the complexity of the micellization process.

Chemical Phenomena↗
PubMed1981

Interaction of thyroxine with lysozyme.

L-thyroxine and hen's egg-white lysozyme form an insoluble complex at neutral pH. Previous reports have suggested that the enzyme and hormone alos associate in solution. No evidence for the soluble interaction between thyroxine and lysozyme was obtained by using spectral, enzymatic, and immunological techniques.

Animals↗
PubMed1980

Oxindolealanine-62 lysozyme: equilibrium, calorimetric, and kinetic studies of the reaction with N-acetylglucosamine oligosaccharides.

Oxindolealanine-62 lysozyme, formed by reaction with N-bromosuccinimide and purified by using affinity chromatography, was examined in its binding of homologous oligosaccharides of N-acetylglucosamine and in its catalysis of hydrolysis and of transglycosylation of the hexasaccharide of N-acetylglucosamine. Equilibrium binding constants were determined by changes in absorbance or fluorescence associated with ligand binding. Enthalpies of binding were measured calorimetrically. The pattern of variation of delta Go and delta Ho of binding with ligand chain length and pH was different for oxindolealanine-62 lysozyme compared with native lysozyme. These results indicate that the interactions of the ABC region of the active site with substrates are substantially altered by Trp-62 oxidation, more than expected for loss only of the Trp-62 interactions. The partitioning of the glycosyl enzyme intermediate between reaction with a saccharide acceptor (transglycosylation) and reaction with water is unaffected by oxidation of Trp-62. Similarly, the pattern of cleavage of the hexasaccharide, predominantly to tetra- and disaccharide, is unaffected by oxidation of Trp-62. The 2000-fold slower rate of catalytic reaction (relative to free enzyme and substrate) apparently reflects a sterically hindered fit of the substrate into the active site of the modified enzyme and not a special catalytic importance of Trp-62. The geometry of the transition state for oligosaccharide hydrolysis is inferred to be the same for native and oxidized enzymes.

Acetylglucosamine↗
PubMed1980

Correlation of IR spectroscopic, heat capacity, diamagnetic susceptibility and enzymatic measurements on lysozyme powder.

The interaction between protein and water is of fundamental importance for processes ranging from protein folding and enzymatic activity to anhydrobiosis. In this letter we bring together results from diverse types of measurements to give a unified picture of the hydration process for lysozyme. The data come principally from experiments with protein films and powders. The principal aim is to examine the relationship between the sites of water interaction, the extent of coverage, and the enzymatic activity, thus providing a better understanding of the relationship between water and enzyme dynamics.

Catalysis↗
PubMed1979

Binding of reduced and oxidized nicotinamide adenine dinucleotide to pig heart supernatant malate dehydrogenase.

The association reactions of NADH and NAD+ with dimeric pig heart supernatant malate dehydrogenase (s-MDH) have been measured at pH 6 and 8 by calorimetric and fluorescence methods, and the thermodynamic parameters describing these reactions have been evaluated. Coenzyme binding is associated with the uptake of 0.55 mol of H+/mol of NADH at pH 8 and 0.19 mol of H+ at pH 6. No significant effect of NAD+ binding on proton binding was observed. Increase in ionic strength strongly affects the free energies of binding of NAD+ and NADH. No cooperativity was observed in the enthalpy or free energy changes for binding of NAD+ or NADH. The differences in free energy of binding of NAD+ and NADH and the effect of pH on binding of NADH are entropy based. These effects are interpreted as reflecting a small number of interactions within the active site that are predominantly ionic.

Animals↗
PubMed1979

Protein--water interactions. Heat capacity of the lysozyme--water system.

Calorimetric measurements of the heat capacity of the lysozyme-water system have been carried out over the full range of system composition at 25 degrees C. The partial specific heat capacity of the protein in dilute solution is 1.483 +/- 0.009 J K-1 g-1. The heat capacity of the dry protein is 1.26 +/- 0.01 J K-1 g-1. The system heat capacity responds linearly to change in composition from dilute solution to 0.38 g of water per g of protein (h) and is an irregular function at lower water content. The break in the heat capacity function at 0.38 h defines the amount of water needed to develop the equilibrium solution properties of lysozyme as being 300 molecules of water/protein molecule, just sufficient for monolayer coverage. The heat capacity behavior at low water content describes three hydration regions. The most tightly bound water (0-0.07 h), probably principally bound to charged groups, is characterized by a partial specific heat capacity of 2.3 J K-1 g-1, a value close to that for ice. A heat of reaction associated with proton redistribution is reflected in the heat capacity function for the low-hydration region. Between 0.07 and 0.25 h the heat capacity increases strongly, which is understood to reflect the growth of patches of water covering polar and adjacent nonpolar portions of the protein surface. The hydration shell is completed by condensation of solvent over the weak-interacting portions of the surface, in a process displaying a transition heat.

Calorimetry↗
PubMed1979

Lifetimes and NADH quenching of tryptophan fluorescence in pig heart cytoplasmic malate dehydrogenase.

The time-resolved and steady state fluorescence properties were measured for pig heart cytoplasmic malate dehydrogenase at pH 6.0 and 8.0. The fluorescence decay can be described by two rate processes, according to the functions: I(t) = 0.7e(-t/1.0) + 0.3e(-t/4.4) for the free enzyme and I(t) = 0.7e(-t/0.8) + 0.3e(-t/2.0 for the enzyme . NADH complex. Quenching by NADH of the tryptophan fluorescence is linear. The only effect of pH is to change the association constant for NADH binding; the fluorescence of the free enzyme and the fluorescence quenching by NADH, I-, and acrylamide are unaffected by pH. Thus there are no changes in conformation of the free enzyme or of the NADH complex over the range of pH 6 to 8.

Animals↗
PubMed1979

Thermodynamics of glucagon aggregation.

Heats of dilution of concentrated glucagon solutions have been measured calorimetrically at 10 and 25 degrees C in 0.2 M potassium phosphate buffer of pH 10.6. Analysis of the data in terms of a monomer-trimer equilibrium gives the following thermodynamic parameters for the association reaction at 25 degrees C: delta G degrees = 7.34 kcal/mol of trimer, delta H degrees = -31.2 kcal/mol, deltaS degrees = -80 cal/(K mol), deltaCp = 430 cal/(K mol). The sensitivity of heat of dilution data to the association constant and stoichiometry of the reaction is discussed.

Calorimetry↗