Cooperativity in the mechanism of malate dehydrogenase.

Cooperativity in the catalytic mechanism of porcine cytoplasmic malate dehydrogenase (sMDH) has been a point of ongoing discussion. Though previous investigations revealed little evidence of cooperativity, chemical modification studies reported by this laboratory demonstrate that binding of cofactor or cofactor plus substrate causes the enzyme's subunits to become chemically nonidentical. Therefore, we have reexamined the enzyme's steady-state kinetic and ligand-binding properties. To aide in characterizing sMDH kinetics, activities of the native enzyme and of sMDH, which was partially inactivated by an active-site-specific reagent, were examined. As expected for a negatively cooperative enzyme, steady-state kinetics (at pH 8.0, the pH optimum of the enzyme) are characterized by concave Eadie-Hofstee plots. Further, qualitative as well as quantitative results from partially inactivated sMDH strongly support negative cooperativity and eliminate many alternative mechanisms. Finally, results from equilibrium binding experiments are consistent with cytoplasmic malate dehydrogenase binding NADH in a negatively cooperative manner. Together, these results indicate that cytoplasmic malate dehydrogenase acts as a negatively cooperative enzyme.

Analysis of progress curves by simulations generated by numerical integration.

A highly flexible computer program written in FORTRAN is presented which fits computer-generated simulations to experimental progress-curve data by an iterative non-linear weighted least-squares procedure. This fitting procedure allows kinetic rate constants to be determined from the experimental progress curves. Although the numerical integration of the rate equations by a previously described method [Barshop, Wrenn & Frieden (1983) Anal. Biochem. 130, 134-145] is used here to generate predicted curves, any routine capable of the integration of a set of differential equations can be used. The fitting program described is designed to be widely applicable, easy to learn and convenient to use. The use, behaviour and power of the program is explored by using simulated test data.

pH-induced changes in G-actin conformation and metal affinity.

Metal-induced conformational changes in actin at 20 degrees C have been investigated as a function of pH using actin labeled at Cys-374 with N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine. At pH 8, the addition of a high Ca2+ concentration (2 mM) to G-actin gives an instantaneous fluorescence increase while the addition of a high Mg2+ concentration gives both an instantaneous and a slow fluorescence increase. The instantaneous increase is interpreted as divalent cation binding to low-affinity, relatively nonspecific sites, while the slow response is attributed to Mg2+ binding to specific sites of moderate affinity [Zimmerle, C.T., Patane, K., & Frieden, C. (1987) Biochemistry 26, 6545-6552]. The magnitudes of both the instantaneous and slow fluorescence increases associated with Mg2+ addition to G-actin are shown here to decrease as the pH is lowered while the fluorescence of labeled G-actin in the presence of low or moderate Ca2+ concentrations (less than 200 microM) increases. The pH-dependent data suggest that protonation of a single class of residues with an approximate pK of 6.8 alters the immediate environment of the label differently depending upon the cation bound at the moderate-affinity site. The pH-dependent changes in the magnitude of the slow fluorescence response upon Mg2+ addition to Ca2+-actin are not associated with changes in the Mg2+ affinity at the moderate-affinity site but result from protonation altering the fluorescence response to Mg2+ binding. Protonation of this same class of residues is proposed to induce an actin conformation similar to that induced by cation binding at the low-affinity sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of pH on the mechanism of actin polymerization.

The effect of pH on the Mg2+-induced polymerization of rabbit skeletal muscle G-actin at 20 degrees C was examined. Polymerization data were obtained at various initial concentrations of Mg2+, Ca2+, and G-actin between pH 6 and 7.5. The data were found to fit a kinetic mechanism for actin polymerization previously proposed at pH 8 in which Mg2+ binding at a moderate-affinity site on actin induces an isomerization of the protein enabling more favorable nucleation [Frieden, C. (1982) J. Biol. Chem. 257, 2882-2886]. The data also suggest the formation of actin dimers induced by Mg2+ binding is over 2 orders of magnitude more favorable at pH 6 than at pH 8. Little effect on trimer formation is found over this pH range. In addition, the conformation induced by nonspecific binding of metal to low-affinity sites becomes more favorable as the pH is lowered. The critical concentration for filament formation is also decreased at lower pH. The kinetic data do not support fragmentation occurring under any of the conditions examined. Furthermore, as Mg2+ exchange for Ca2+ at a high-affinity site (Kd less than 10(-9) M) fails to alter significantly the polymerization kinetics, Ca2+ release from this site appears unnecessary for either the nucleation or the elongation of actin filaments.

Ligand-induced asymmetry between active sites of cytoplasmic malate dehydrogenase: a chemical modification study.

The iodoacetate-dependent and iodoacetamide-dependent inhibition of cytoplasmic malate dehydrogenase (s-MDH) has been examined. We have confirmed previous reports that iodoacetate inhibits this dimeric enzyme by modifying a single active site methionine per s-MDH subunit. Time courses for the inactivation of the solution-state enzyme with both reagents indicate each s-MDH subunit is modified with equal rapidity in the absence of substrate or cofactor. However, the subunits react with distinctly different rates in the presence of cofactor or cofactor/substrate combinations, indicating some conformational asymmetry between subunits occurs when these ligands are bound. This is consistent with solution-state s-MDH behaving as a cooperative enzyme. Apo and holo crystalline s-MDH are also inhibited by iodoacetic acid. However, subunits of the crystalline enzyme are inhibited with different rates in the presence or absence of active site ligands. This suggests subunit conformations of the dimeric enzyme are not identical in crystalline s-MDH preparations regardless of ligand binding. Furthermore, by the criterion of inhibition rate constants, subunit conformations of the crystalline enzyme are not rigid but are perturbed by ligand binding. Comparisons of inactivation time courses for solution- and crystalline-state s-MDH suggest crystalline s-MDH exhibits at least some of the subunit asymmetry associated with the solution-state enzyme.

Divalent cation binding to the high- and low-affinity sites on G-actin.

Metal binding to skeletal muscle G-actin has been assessed by equilibrium dialysis using 45Ca2+ and by kinetic measurements of the increase in the fluorescence of N-acetyl-N'-(5-sulfo-1-naphthyl)-ethylenediamine-labeled actin. Two classes of cation binding sites were found on G-actin which could be separated on the basis of their Ca2+ affinity: a single high-affinity site with a Kd considerably less than 1 microM and three identical moderate-affinity binding sites with a Kd of 18 microM. The data for the Mg2+-induced fluorescence enhancement of actin labeled with N-acetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine support a previously suggested mechanism [Frieden, C. (1982) J. Biol. Chem. 257, 2882-2886] in which Ca2+ is replaced by Mg2+ at the moderate affinity site(s), followed by a slow actin isomerization. This isomerization occurs independently of Ca2+ release from the high-affinity site. The fluorescence data do not support a mechanism in which this isomerization is directly related to Ca2+ release from the high-affinity site. Fluorescence changes of labeled actin associated with adding metal chelators are complex and do not reflect the same change induced by Mg2+ addition. Fluorescence changes in the labeled actin have also been observed for the addition of Cd2+ or Mn2+ instead of Mg2+. It is proposed actin may undergo a host of subtle conformational changes dependent on the divalent cation bound. We have also developed a method by which progress curves of a given reaction can be analyzed by nonlinear regression fitting of kinetic simulations to experimental reaction time courses.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of temperature on the mechanism of actin polymerization.

The rate of the Mg2+-induced polymerization of rabbit skeletal muscle G-actin has been measured as as function of temperature at pH 8 by using various concentrations of Mg2+, Ca2+, and G-actin. A polymerization mechanism similar to that proposed at this pH [Frieden, C. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 6513-6517] was found to fit the data from 10 to 35 degrees C. From the kinetic data, no evidence for actin filament fragmentation was found at any temperature. Dimer formation is the most temperature-sensitive step, with the ratio of forward and reverse rate constants changing 4 orders of magnitude from 10 to 35 degrees C. Over this temperature change, all other ratios of forward and reverse rate constants change 7-fold or less, and the critical concentration remains nearly constant. The reversible Mg2+-induced isomerization of G-actin monomer occurs to a greater extent with increasing temperature, measured either by using N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine-labeled actin or by simulation of the full-time course of the polymerization reaction. This is partially due to Mg2+ binding becoming tighter, and Ca2+ binding becoming weaker, with increasing temperature. Elongation rates from the filament-pointed end, determined by using actin nucleated by plasma gelsolin, show a temperature dependence slightly larger than that expected for a diffusion-limited reaction.

Crystallization-induced modification of cytoplasmic malate dehydrogenase structure and function.

In an effort to assess the effects of phase-state changes on protein conformations, we have compared several properties of cytoplasmic malate dehydrogenase in the crystalline and solution states. Two crystalline forms of the enzyme have been examined: one crystallized in the presence of nicotinamide adenine dinucleotide and the other in its absence. Though both forms catalyze cytoplasmic malate dehydrogenase's normal substrate conversions, they have specific activities 150-3000-fold less than the solution-state enzyme. These dramatic activity decreases cannot be accounted for by diffusion constraints imposed by the crystal lattice nor do they result from the manipulations necessary to crystallize or cross-link the enzyme. Further, crystal- and solution-state enzymes have different pH dependences of their enzymatic activities, have different sensitivities toward inactivation by the covalent inhibitor iodoacetate, and respond differently to nicotinamide adenine dinucleotide protection against this inactivation. Finally, crystals of the enzyme grown in the presence and absence of cofactor are also distinguishable from one another by using the same criteria. Taken together, these results suggest that crystallization perturbs the dynamics and, perhaps, the average conformation of cytoplasmic malate dehydrogenase.