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D S Auld

Publications and source records attributed to D S Auld.

At least 91 records · Page 5Linked to original sources
PubMed1984

Direct observation of enzyme substrate complexes by stopped-flow fluorescence: mathematical analyses.

The fluorescence changes which occur upon the interaction of enzyme and substrate under stopped-flow conditions can provide a sensitive means to directly observe ES complexes. The interconversion of the intermediates during catalysis causes changes in fluorescence, signaling directly their existence, and allowing their quantitation. We have studied extensively an approach which measures radiationless energy transfer (RET) between enzyme tryptophanyl residues and a fluorescent peptide or ester substrate. Our studies of a number of proteolytic enzymes have validated the approach, which is sensitive and applicable to a variety of enzymes under a wide range of experimental conditions, including subzero temperatures. Direct excitation of fluorescent substrates can also be used to observe ES complex formation and breakdown and is complementary to the RET approach. Here we review both the RET and direct excitation kinetic approaches, with particular emphasis on the mathematical foundations we have developed which are critical to the successful interpretation of these or any other spectroscopic approach which yields a signal that is unique to the ES complex.

Carboxypeptidases↗
PubMed1984

Cryospectrokinetic characterization of intermediates in biochemical reactions: carboxypeptidase A.

Cryospectrokinetic studies provide concurrent structural, kinetic, and chemical data on short-lived intermediates in the course of the interactions of enzymes with their substrates and of other, similar pairs of biomolecules. Subzero temperatures extend the lifetimes of these intermediates and, combined with rapid-mixing and rapid-scanning instrumentation, allow simultaneous measurement of both their physical-chemical and kinetic characteristics. For carboxypeptidase A, the spectra of a chromophoric, enzymatically functional cobalt atom at the active site signal the structure of the coordination complex during catalysis, while radiationless energy transfer between enzyme tryptophans and the fluorescent dansyl blocking group of rapidly hydrolyzed peptide and ester substrates provides the basis for measurement of the rates of formation and breakdown of intermediates. Subzero radiationless energy transfer kinetic studies of the zinc and cobalt enzymes disclose two intermediates in the hydrolysis of both peptides and esters and furnish all the rate and equilibrium constants for the reaction scheme E + S in equilibrium ES1 in equilibrium ES2----E + P. The chemical and kinetic data indicate that neither of these is an acylenzyme intermediate. Both absorption and EPR spectra of the ES2 reaction intermediates consistently demonstrate the formation of transient metal complexes, differences between the effects induced by peptides and esters, and strong similarities between those induced by all peptides on the one hand and all esters on the other. The marked alterations of the cobalt spectra likely reflect the coordination of a substrate carboxyl and/or carbonyl group to the metal at a critical step in the course of catalysis. The cryospectrokinetic approach developed here in the mechanistic study of this metalloenzyme is applicable to the examination of transients of biochemical reactions in general. It will allow molecular characterization of previously elusive intermediates and greatly magnify the range of mechanistic questions that can be answered.

Animals↗
PubMed1983

ES complexes of Aeromonas aminopeptidase: direct observation by stopped-flow fluorescence.

Intermediates of Aeromonas aminopeptidase are monitored through fluorescence generated by radiationless energy transfer (RET) between enzyme tryptophans and the dansyl group of the bound substrate. Upon binding of the substrate enzyme tryptophan fluorescence is quenched and substrate dansyl fluorescence enhanced. These processes are reversed upon hydrolysis of the Leu-Ala bond and release of Ala-DED from the enzyme. Stopped-flow RET kinetic analysis yields values of kcat = 36 sec-1 and Km = 3.7 microM at pH 7.5 and 20 degrees C. These values represent the highest kcat/Km ratio, 1 X 10(7) M-1 sec-1, of any substrate for Aeromonas aminopeptidase. The excellent binding properties of the peptide permit direct visualization of ES complexes even at enzyme concentrations of 10(-7) M.

Aeromonas↗
PubMed1980

Stopped-flow radiationless energy transfer kinetics: direct observation of enzyme-substrate complexes at steady state.

Measurement of radiationless energy transfer (RET) between enzyme tryptophan residues and a fluorescent dansyl (5-dimethylaminonaphthalene-1-sulfonyl) substrate under stopped-flow conditions forms the basis of a rapid and sensitive kinetic approach to delineation of enzyme mechanisms. Both the pre steady state and steady state can be studied on one experiment. The ES complexes of even rapidly turned over dansyl substrates are observed directly at enzyme concentrations of 10(-8)-10(-6) M. If [ET] < Km, a steady state of ES complex formation and breakdown can be achieved and maintained even though the reaction is completed in a few seconds. RET kinetic analysis under stopped-flow steady-state conditions both simplifies and supplements conventional initial rate kinetic studies as illustrated here with bovine and yeast carboxypeptidases and alpha-chymotrypsin acting on Dns-(Gly)3-L-OPhe and Dns-(Gly)2-L-PheOMe, respectively. Since both the concentration and rate of breakdown of intermediates are observed, the kinetic parameters Kcat and Km can be determined precisely by multiple means. The capability of observing both steady-state and pre-steady-state RET kinetics in the same experiment greatly reduces errors in quantitative analysis, allowing a more rigorous definition of enzyme mechanisms.

Energy Transfer↗
PubMed1979

Methionyl-tRNA synthetase of Escherichia coli. A zinc metalloprotein.

The native dimeric form of methionyl-tRNA synthetase of Escherichia coli contains two zinc atoms per dimer, one per subunit. The bound zinc is retained upon trypsin modification which yields a monomer with one zinc atom. The enzymatic activity of both the dimeric forms is reversibly inhibited by 1,10-phenanthroline but not by its non-chelating analogues. In addition, the native enzyme binds two Mn2+ per dimer with a binding constant of approx. 70 micron but no binding is observed with the trypsin-modified monomer.

Amino Acyl-tRNA Synthetases↗
PubMed1979

Determination of enzyme mechanisms by radiationless energy transfer kinetics.

Rigorous definition of the elementary steps of an enzymatic reaction requires visualization of transient enzyme-substrate (ES) complexes. Measurement of radiationless energy transfer (RET) between enzyme tryptophan residues and a fluorescent dansyl (5-dimethylaminonaphthalene-1-sulfonyl) substrate provides a sensitive means to observe ES complexes directly. Analysis of the rate of formation and breakdown of ES complexes by RET can serve as the basis of a rapid kinetic approach to enzyme mechanisms. Both pre-steady-state and steady-state kinetics can be performed in the same RET experiment. Analysis at steady state precisely determines k(cat) and K(m) values by multiple means. Analysis at pre-steady state determines the number of intermediates, the type of reaction mechanism, and all the individual binding and rate constants. Chymotrypsin was chosen as a standard of reference for RET kinetics because extensive investigations have established both the existence of transient intermediates in the course of its catalytic process and the range of values to be expected for pertinent kinetic constants. As predicted, RET kinetics readily detects the two known intermediates in the alpha-chymotrypsincatalyzed hydrolysis of specific ester substrates. The results are both qualitatively and quantitatively in accord with data derived for this enzyme from classical kinetics. Hence, this experimental study both validates and demonstrates the theoretical advantages and potential of RET kinetics. The generality of the approach has been investigated by synthesizing a family of dansyl-labeled substrates designed to meet the specificity requirements of a number of metallo- and nonmetallo- exo- and endopeptidases. In all cases, the ES complex is observed readily at micromolar or lower concentrations of enzyme under stopped-flow conditions. The success of the RET kinetic approach on proteolytic enzymes shows its broad utility.

Carboxypeptidases↗
PubMed1975

Intramolecular arsanilazotyrosine-248-Zn complex of carboxypeptidase A: a monitor of catalytic events.

The intensely chromophoric intramolecular coordination complex formed between arsanilazotyrosine-248 and the active site zinc atom of azocarboxypeptidase A (Johansen, J. T. & Vallee, B. L. (1971) Proc. Nat. Acad. Sci. USA 68, 2532-2535) is a spectrokinetic probe of catalytic events. The interconversion of the azoTyr-248-Zn complex and its constituents is measured by stopped-flow pH and temperature-jump methods. The rate of interconversion, 64,000 sec-1, is orders of magnitude faster than that of the catalytic step itself (about 0.01-100 sec-1). Rapidly turned over peptide and ester substrates disrupt the azoTyr-248-Zn complex before hydrolysis occurs. As a consequence, formation of azoTyr-248, substrate binding, and catalysis can all be monitored while catalysis is actually in progress. The results of these dynamic studies specify a course of catalytic events, different from those postulated based on x-ray structure analysis. If azoTyr-248 is displaced, the direction is opposite to the inward movement postulated on the basis of x-ray studies and is not unique to induction by substrates, since rapid changes in pH also result in analogous spectral changes. AzoTyr-248 carboxypeptidase has all the features which are essential for mechanistic studies: (1) It is enzymatically active; (2) the spectra of the metal complex differ characteristically from those of its constituents; (3) it responds dynamically to environmental factors; and (4) the response time of the probe itself is much more rapid than is required for the measurement of the catalytic step. These combined kinetic and spectral properties of the metal complex render it a powerful spectrokinetic probe to visualize and discern microscopic details of the catalytic process.

Arsenicals↗
PubMed1975

Intramolecular arsanilazotyrosine-248-Zn complex of carboxypeptidase A: a monitor of multiple conformational states in solution.

The red azoTyr-248-Zn complex of arnilazocarboxypeptidase, previously used to demonstrate differences in conformation of the enzyme in crystals and in solution, has now provided means to detect multiple conformations of the enzyme in solution by stopped-flow pH and temperature jump experiments. These studies identify two distinct processes. Er + H+ in equilibrium Ey (I), is the extremely rapid, Kfast about 10(5) sec-1, pH dependent dissociation of the metal complex. Ey in equilibrium Ey' (II), is much slower, Kslow about 5 sec-1, pH independent interconversion of two distinct populations of protein molecules, Ey and Ey', in which the yellow azo-Tyr-248 is different conformations. These two conformations can be differentiated readily by stopped-flow pH-jump experiments, since I is three to four orders of magnitude faster than II. Mathematical expressions derived from this mechanism accurately predict all observations over the pH range from 6.0 to 8.5. In a previous stopped-flow pH-jump experiment, Lipcomb and coworkers [Quiocho, F. A., McMurray, C. H. & Lipcomb, W. H. (1972), Proc. Nat. Acad. Sci. USA 69, 2850-2854] recognized only a single process with a rate constant of about 6 sec-1, but not the major, very rapid rate observed here. The failure to detect this fast process led to the postulation of a number of explanations intended to account for the detection of only a single, slow rate. The present observations show that the premise for those conjectures is not valid. The azoprobe reveals the existence of rapidly interconvertible substructures of carboxypeptidase A, and the results support the view that in solution, enzymes can adopt multiple, readily interconvertible and related conformations which could then either facilitate or impede catalysis. In crystals, rearrangement of molecular structure could be severely impaired or restricted, and crystallization might single out either active or inactive conformations. In the latter case, such crystals would have greatly reduced activities and markedly altered catalytic behavior, as is observed for carboxypeptidase A. In combination with detailed kinetic analysis of crystals, conformational analysis in solution should be a valuable guide to discern enzyme mechanisms and select crystals for x-ray structure analysis.

Azo Compounds↗
PubMed1975

Microanalytical system for determination of picogram quantities of metals in metalloenzymes, as illustrated with zinc-containing enzymes.

Microwave-induced emission spectrometry combined with gel-exclusion chromatography provides a microanalytical system capable of precisely measuring 10 minus 10 to 10 minus 13 g of metal in microgram amounts of enzyme. Such sensitivity greatly exceeds that of other, more conventional methods. Metal quenching agents and low-molecular-weight protein contaminants were removed from the enzyme by Sephadex G-100 chromatography in microbore columns (0.03 times 25 cm). Droplet fractions were analyzed for zinc by the present method, for enzyme activity, and for protein content. With this analytical system we could demonstrate that stoichiometric amounts of zinc are present in the RNA-dependent DNA polymerase, the reverse transcriptase, from wooly monkey type C RNA tumor virus. The precision of the method for zinc was demonstrated by the coefficient of variation of 4.4 percent for 10 mug of zinc per liter. Validity and accuracy of the method were established by determining zinc in a series of zinc metalloenzymes of known metal content and stoichiometry.

Animals↗