Evidence for a heparin-induced conformational change on antithrombin III

The effect of heparin on the conformation of antithrombin III (AT-III) was investigated. Solvent perturbation difference spectroscopy shows that the binding of heparin to AT-III results in exposure of two tyrosine residues and a partial burial of a tryptophan residue. The occurrence of a conformational change suggested by this study is also substantiated by circular dichroism (CD) findings in the aromatic and peptide regions. The data in the peptide region show that heparin produces a decrease in the β-structure of AT-III, with a compensatory increase in random coil.     

Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.

A new crystal form of the hexameric NAD(+)-linked glutamate dehydrogenase (GDH) from Clostridium symbiosum has been grown using the hanging drop method of vapour diffusion. The crystals are obtained either by using high concentrations of the amino acid substrate of the enzyme, glutamate, as the precipitant or by co-crystallization from ammonium sulphate in the presence of either p-chloromercuribenzene sulphonate or potassium tetracyanoplatinate. The crystals diffract well and X-ray photographs have established that they are in the space group R32. Considerations of the values of Vm indicate that the asymmetric unit of the R32 crystals contains a single subunit. Packing considerations based on the structure of the native enzyme determined from a different crystal form suggest that the molecule must undergo a significant conformational change in order to be accommodated in the new cell. Such a conformational rearrangement may represent an important step in the catalytic cycle.     

Ionic strength and pH dependence of the reaction between plastocyanin and Photosystem 1. Evidence of a rate-limiting conformational change

The electron-transfer reaction between spinach wild-type plastocyanin (Pc(WT)) two site-directed mutants, Pc(Thr79His) and Pc(Lys81His), and spinach Photosystem 1 particles, has been studied as a function of protein concentration, ionic strength and pH by using laser-flash absorption spectroscopy. The kinetic data are interpreted using the simplest possible three-step model, involving a rate-limiting conformational change preceding intracomplex electron transfer. The three proteins show similar concentration, pH and ionic strength dependencies. The effects of ionic strength and pH on the reaction indicate a strong influence of complementary charges on complex formation and stabilization. Studies with apoprotein support the opinion that the hydrophobic patch is critical for an productive interaction with the reaction center of Photosystem 1. Together with earlier site-directed mutagenesis studies, the absence of a detectable Photosystem 1 reaction in the presence of reduced azurin, stellacyanin, cytochrome c and cytochrome c₅₅₁, demonstrates the existence of a high level of specificity in the protein-protein interface in the formation of an efficient electron-transfer complex.     

Cryoenzymologic studies on arginine kinase: solvent, temperature and pH effects on the overall reaction.

The overall reaction catalyzed by the phosphotransferase arginine kinase was studied at normal and subzero temperatures. Ethylene glycol was used as the antifreeze and its effects on the Km values of substances, kcat and pH profiles were investigated in detail. a) The Km values for the substrate (2 mM for ATP and 0.6 mM for arginine) were little affected by the solvent composition or temperature of the reaction mixture. b) At concentration of ethylene glycol higher than 40% there was a sharp drop of enzyme activity. c) Ethylene glycol induces a large shift in the enzymic pK D) At -5 degrees C in 40% of solvent there was a break in the Arrhenius plot suggesting a change of the rate-limiting step. The relevance of these results to the reaction pathway of arginine kinase is discussed. In addition, controlled perturbations induced by cosolvent and temperature appear as useful tools for further kinetic investigations.     

Hsp85 conformational change within the heat shock temperature range.

One of the major mammalian heat shock proteins, hsp85, aggregates extensively when heated in the presence of non-ionic detergents (J Cell. Physiol. 140: 601-607, 1989). The present study used intrinsic fluorescence and susceptibility to tryptic proteolysis to probe hsp85 conformation within the physiological and heat shock temperature ranges. Fluorescence intensity decreased and the emission spectrum was red-shifted (2.5 nm) as hsp85 was heated from 15 degrees to 50 degrees C. Upon heating in the absence of detergent, the red shift, monitored by the ratio of fluorescence emission at 330 nm to that at 350 nm, began at 38 degrees-45 degrees C with a transition midpoint at 45 degrees-50 degrees C, depending on the rate of temperature increase. This transition was masked by 1% n-octyl-O-glucoside - a detergent previously shown to promote aggregation. The spectral changes were not reversible upon cooling to 15 degrees C. Susceptibility to proteolysis in the absence of detergent, measured by the degradation of characteristic large fragments, increased sharply between 40 degrees C and 45 degrees C. These findings suggest that hsp85 undergoes a major conformational change within the range of temperatures known to induce hsp synthesis. This change is consistent with partial unfolding which exposes additional sites to the aqueous environment and influences detergent binding.     

Mutagenesis of hydroxylamine oxidoreductase in Nitrosomonas europaea by transformation and recombination.

Mutagenesis of Nitrosomonas europaea was achieved by electroporation and recombination. To demonstrate this, an aminoglycoside 3'-phosphotransferase (kan) gene was specifically inserted into each of the three gene copies of hao individually. Southern hybridizations and PCR analysis showed the incorporation of the kan gene at the chosen genetic loci. The isolation of mutant strains was achieved in 7 to 14 days when the strains were grown on solid medium. The induced mutations were stable even in the absence of kanamycin-selective pressure for periods of up to 45 days in culture. The mutant strains did not show an observable phenotype different from that of the wild type when grown under the same conditions.     

Stability of proteins: temperature, pressure and the role of the solvent

We focus on the various aspects of the physics related to the stability of proteins. We review the pure thermodynamic aspects of the response of a protein to pressure and temperature variations and discuss the respective stability phase diagram. We relate the experimentally observed shape of this diagram to the low degree of correlation between the fluctuations of enthalpy and volume changes associated with the folding-denaturing transition and draw attention to the fact that one order parameter is not enough to characterize the transition. We discuss in detail microscopic aspects of the various contributions to the free energy gap of proteins and put emphasis on how a cosolvent may either enlarge or diminish this gap. We review briefly the various experimental approaches to measure changes in protein stability induced by cosolvents, denaturants, but also by pressure and temperature. Finally, we discuss in detail our own molecular dynamics simulations on cytochrome c and show what happens under high pressure, how glycerol influences structure and volume fluctuations, and how all this compares with experiments.     

Crystallization and preliminary X-ray studies of hydroxylamine oxidoreductase from Nitrosomonas europaea.

Hydroxylamine oxidoreductase [EC 1.7.3.4] from Nitrosomonas europaea was crystallized by the microdialysis method using ammonium sulfate. Its space group is P63 with cell dimensions of a = b = 96.4 A and c = 266.2 A. Its molecular weight was determined to be 190,000-195,000 by the X-ray small angle scattering and ultracentrifugal methods.     

A rapid reaction study of anthranilate hydroxylase. Evidence for a catalytically important conformational change during slow initial turnover with anthranilate

Rapid reaction kinetics of the flavoprotein anthranilate hydroxylase from Trichosporon cutaneum were examined for reactions involving anthranilate, the native substrate. As was reported earlier for the nonhydroxylated substrate analogue, salicylate, some reactions in the first turnover with anthranilate occur slower than those in subsequent turnovers (Powlowski, J., Massey, V., and Ballou, D. P. (1989) J. Biol. Chem. 264, 5606-5612). Evidence is presented for slow conformational changes that occur both on binding of the aromatic ligand and on reduction of the enzyme. These changes are apparently important for rapid anthranilate binding to occur in turnovers subsequent to the first. Moreover, bound anthranilate is required for rapid reduction of enzyme-bound FAD by NADPH. Studies to probe the accessibility of reagents to modified flavins that had been incorporated into the apoenzyme indicate that anthranilate binding causes a conformational change in the protein, allowing increased access to the benzene ring moiety of the flavin. An unusual isotope effect with (R)-NADPD (4(R)-2H] NADPH) is observed on Kd rather than on kred, which is consistent with a model involving slow interconversion of enzyme-substrate complexes before productive binding of NADPH and reduction of the enzyme flavin.     

Evidence for a conformational change in the DNA gyrase-DNA complex from hydroxyl radical footprinting.

We have used the technique of hydroxyl radical footprinting to probe the complex between DNA gyrase and a 198 bp DNA fragment containing the preferred gyrase cleavage site from plasmid pBR322. We find that gyrase protects 128 bp from the hydroxyl radical with the central 13 bp (adjacent to the gyrase cleavage site) being most strongly protected. Flanking the central region are arms showing periodic protection from the reagent suggesting a helical repeat of 10.6 bp, consistent with the DNA being wrapped upon the enzyme surface. The presence of 5'-adenylyl-beta,gamma-imidodiphosphate or a quinolone drug causes alteration of the protection pattern consistent with a conformational change in the complex involving one arm of the wrapped DNA. The significance of these results for the mechanism of DNA supercoiling by gyrase is discussed.     

Stereochemistry of the dTDP-glucose oxidoreductase reaction.

The stereochemical course of the dTDP-glucose oxidoreductase (EC 4.2.1.46) reaction was studied using enzyme partially purified from Escherichia coli and dTDP-(6R)- and (6S)-[4-2H, 6-3H]glucose as substrate. The latter was prepared enzymatically by reduction of (3R)- and (3S)-3-P-[3-3H]glycerate to the 1-deuterated 3-P-glyceraldehyde with (4S)-[4-2H]NADH, followed first by conversion to glucose-1-P with the glycolytic enzymes, and then by transformation into the dTDP derivative. The stereospecifically labeled dTDP-glucose samples were mixed with nonlabeled carrier material and converted to dTDP-4-keto-6-deoxyglucose, which contained a chiral methyl group as shown by chirality analysis of the acetic acid resulting from Kuhn-Roth oxidation of the sugar nucleotide. These results confirm that the hydrogen transfer from C4 to C6 is intramolecular and show that the migrating hydrogen replaces the 6-hydroxyl group with inversion of configuration. Assuming that the hydrogen transfer, since it is intramolecular, must be suprafacial, it follows that the elimination of water from C5 and C6 is formally syn, whereas the reduction of the resulting delta5,6-double bond formally involves an anti addition of H+ and H-.     

10-Formyltetrahydrofolate synthetase. Evidence for a conformational change in the enzyme upon binding of tetrahydropteroylpolyglutamates

The 10-formyltetrahydrofolate synthetase domain of the trifunctional enzyme C1-tetrahydrofolate synthase appears to undergo a conformational change in the presence of tetrahydropteroylpolyglutamates, MgATP, and ammonium ion. The binding of these ligands increases the denaturation temperature of the enzyme by 12 degrees C, abolishes the cold lability of the enzyme, and alters its susceptibility to digestion by chymotrypsin. The results suggest that a conformational change is dependent upon binding of the third glutamate residue of tetrahydropteroylpolyglutamates and the beta-phosphoryl group of MgATP. The Km values for MgATP and formate are lowered 3.6- and 520-fold, respectively, when tetrahydropteroyltriglutamate is used as the substrate in place of tetrahydropteroylmonoglutamate. A sensitive coupled assay involving C1-tetrahydrofolate synthase and serine hydroxymethyltransferase was developed to determine the activity of 10-formyltetrahydrofolate synthetase. The assay gives linear rates with the tetrahydropteroylpolyglutamates as substrates but not with the monoglutamate form.     

Evidence that the activation of aconitase involves a conformational change

Reduction of the iron–sulphur cluster of aconitase initiates a slow increase in catalytic activity. It has been proposed that activation involves a conformational change in the protein. Direct evidence for this is presented here in the demonstration that, after reduction of the cluster, the progressive increase in activity is parallelled by an increase in the fluorescence of the protein.     

The interaction between mitochondrial NADH-ubiquinone oxidoreductase and ubiquinol-cytochrome c oxidoreductase. Evidence for stoicheiometric association.

1. The NADH-ubiquinone oxidoreductase complex (Complex I) and the ubiquinol-cytochrome c oxidoreductase complex (Complex III) combine in a 1:1 molar ratio to give NADH-cytochrome c oxidoreductase (Complex I-Complex III). 2. Experiments on the inhibition of the NADH-cytochrome c oxidoreductase activity of mixtures of Complexes I and III by rotenone and antimycin indicate that electron transfer between a unit of Complex I-Complex III and extra molecules of Complexes I or III does not contribute to the overall rate of cytochrome c reduction. 3. The reduction by NADH of the cytochrome b of mixtures of Complexes I and III is biphasic. The extents of the fast and slow phases of reduction are determined by the proportion of the total Complex III specifically associated with Complex I. 4. Activation-energy measurements suggest that the structural features of the Complex I-Complex III unit promote oxidoreduction of endogenous ubiquinone-10.     

Evidence for a phosphorylation-induced conformational change in phospholamban cytoplasmic domain by CD analysis.

Phospholamban (PLB), an integral membrane protein of cardiac sarcoplasmic reticulum (SR), is described as the regulator of the Ca(2+)-ATPase pump, via its phosphorylation-dephosphorylation of Ser-16. Recently it has been shown that a direct interaction between the N-terminal hydrophilic domain of PLB and Ca(2+)-ATPase may be one of the mechanisms of regulation. In order to show that this interaction could be modulated by a phosphorylation-induced conformational change in PLB, we ran CD studies on the synthetic peptide PLB(2-33) in its phosphorylated and non-phosphorylated forms, at various pHs, concentrations and in the absence or presence of trifluoroethanol. The results show a clear difference in structure of the phosphorylated and non-phosphorylated peptide.