Structures of the mono- and divalent metal nucleotide complexes in the myosin ATPase

Off to a slow start: Analyzing lag phases and accelerating rates in steady-state enzyme kinetics

Steady-state enzyme kinetics typically relies on the measurement of 'initial rates', obtained when the substrate is not significantly consumed and the amount of product formed is negligible. Although initial rates are usually faster than those measured later in the reaction time-course, sometimes the speed of the reaction appears instead to increase with time, reaching a steady level only after an initial delay or 'lag phase'. This behavior needs to be interpreted by the experimentalists. To assist interpretation, this article analyzes the many reasons why, during an enzyme assay, the observed rate can be slow in the beginning and then progressively accelerate. The possible causes range from trivial artifacts to instances in which deeper mechanistic or biophysical factors are at play. We provide practical examples for most of these causes, based firstly on experiments conducted with ornithine δ-aminotransferase and with other pyridoxal-phosphate dependent enzymes that have been studied in our laboratory. On the side to this survey, we provide evidence that the product of the ornithine δ-aminotransferase reaction, glutamate 5-semialdehyde, cyclizes spontaneously to pyrroline 5-carboxylate with a rate constant greater than 3 s^-1.

Thiacalix[4]arenes Remove the Inhibitory Effects of Zn Cations on the Myosin ATPase Activity

Numerous female reproductive abnormalities are caused by uterine smooth muscle (myometrium) disorders. Heavy metals have an adverse effect on the contractility of the uterine smooth muscle. Although zinc is an essential biogenic element for most of the organisms, high doses of this element are toxic. The study of 0.5-5 mM Zn2+ effect on myosin S1 ATPase activity from the uterus found that 5 mM Zn2+ cations have the most pronounced inhibitory effect. The calculation of the kinetic parameters (Km and Vmax, ATP) revealed that the apparent maximum velocity of the hydrolysis ATP catalyzed by myosin in the presence of 5 mM Zn2+ decreased by 1.6 times. The value of Кm for ATP hydrolysis by myosin S1 in the presence of Zn2+ does not change statistically, although it tends to decrease. It was determined that uterine myosin S1 ATPase activity does not depend on the concentration of Mg2+ in the presence of 5 mM Zn2+. Also, it was demonstrated that tetrahydroxythiacalix[4]arene-tetrasulfosphonate (C-798) and tetrahydroxythiacalix[4]arene-tetraphosphonate (C-800) restored myosin S1 ATPase activity to the control level in the presence of 5 mM Zn2+. One of the most probable mechanisms of restoring the action of these thiacalix[4]arenes protective effect is based on its ability to chelate heavy metal cations from the incubation medium. The molecular docking of C-798 and C-800 into the myosin S1 region showed that these thiacalix[4]arenes could interact with Zn cation bond by myosin amino acid residues near the ATPase active site. Therefore, thiacalix[4]arenes may weaken the interaction between this cation and myosin S1. It was speculated that the obtained results could be used for further research with the aim of using this thiacalix[4]arenes as pharmacological compounds in the case of poisoning with high concentrations of zinc.

Phosphorothioate analogs of ATP as the substrates of dynein and ciliary or flagellar movement

The phosphorothioate analog of ATP has a sulfur atom replacing a non-bridging oxygen atom of the triphosphate moiety of ATP. Due to the tetrahedral nature of the phosphorus atom, stereoisomers are known to exist, designated as the Sp and Rp isomers. We have reported [Shimizu & Furusawa (1986) Biochemistry 25, 5787] on the hydrolytic activity of the 22S dynein from Tetrahymena cilia towards the phosphorothioate analogs of ATP. In this paper, we extend our study and report on the microtubule-dynein dissociation by these analogs and on their ability to support sea urchin flagellar dynein enzymatic activity as well as ciliary or flagellar motility. It has been shown that the microtubule--22S-dynein complex is dissociated by the binding of ATP to the dynein enzymatic sites [Porter & Johnson (1983) J. Biol. Chem. 258, 6575]. We studied the dissociation by adenosine 5'-[alpha-thio]triphosphate (ATP[alpha S]), Sp or Rp, by light-scattering stopped-flow methods. The dissociation by (Sp)ATP[alpha S] was rapid and the rate of the light-scattering change by (Sp)ATP[alpha S] was a hyperbolic function of the nucleotide concentration, indicating that dissociation was a two-step process. On the other hand, (Rp)ATP[alpha S] up to 2 mM induced only slow and partial dissociation of the complex, while, in the presence of vanadate, it induced complete dissociation with a slightly higher rate (0.5 s-1). The adenosine 5'-[beta-thio]triphosphate (ATP[beta S]) isomers did not induce dissociation. The hydrolytic activity of the outer arm dynein from sea urchin sperm flagella towards these analogs was similar to that of 22S dynein. The ratios of Vmax (nmol.mg protein-1.min-1)/apparent Km (microM) of this dynein were 400-720, 53, 9.7, 0.62 and 0.028 for ATP, ATP[alpha S] (Sp or Rp), ATP[beta S] (Sp or Rp), respectively, in the presence of Mg2+ as the supporting cation. This dynein exhibited the same stereospecificity at beta phosphate as the 22S dynein or myosin. The detergent models of Tetrahymena or sea urchin spermatozoa were reactivated only by ATP or (Sp)ATP[alpha S] while other analogs were ineffective. The maximal beat frequency of the cilia or flagella reactivated by (Sp)ATP[alpha S] was one-quarter to one-half of that produced by ATP reactivation.

Chromium(III) beta, gamma-bidentate guanine nucleotide complexes as probes of the GTP-activated cGMP cascade of retinal rod outer segments

The exchange-inert Cr(III) beta, gamma-bidentate guanine nucleotide complexes Cr(III)GTP and Cr(III)Gpp(NH)p were used to probe the role of transducin in activating the retinal cGMP cascade. The Cr(III) nucleotide complexes were found to have lower binding affinity for transducin as compared to the Mg2+ complexes. However, the rate of hydrolysis of the transducin-bound Cr(III)GTP was similar to that of Mg(II)GTP. Cr(III)Gpp(NH)p activated the cGMP phosphodiesterase of photolyzed rod outer segment membranes up to 75% of the Mg(II)Gpp(NH)p level but lacked the ability to dissociated the transducin subunits from the rod outer segment membrane. This result implies that the activation of the phosphodiesterase by transducin-GTP complex is a membrane-associated event and the formation of a soluble complex of transducin-GTP with the inhibitory peptide of the phosphodiesterase may not be an obligatory step. Both the delta and lambda screw sense stereoisomers of Cr(III)Gpp(NH)p were capable of activating the cGMP cascade with no apparent stereoselectivity. The nature of the interaction of the metal ion and GTP at the nucleotide-binding site of transducin is discussed together with the results from previous studies using the phosphorothioate GTP analogues [Yamanaka, G., Eckstein, F., & Stryer, L. (1985) Biochemistry 24, 8094-8101] and is compared to the site found in homologous GTP-binding proteins such as elongation factor Tu [Jurnak, F. (1985) Science (Washington, D.C.) 230, 32-36; la Cour, T.F.M., Nyborg, J., Thirup, S., & Clark, B.F.C. (1985) EMBO J. 4, 2385-2388]. The implications of the observed results on the molecular mechanism of visual signal transduction are discussed.

Stereochemical probes of the argininosuccinate synthetase reaction

The stereochemical course of the argininosuccinate synthetase reaction has been determined. The SP isomer of [alpha-17O,alpha-18O,alpha beta-18O]ATP is cleaved to (SP)-[16O,17O,18O]AMP by the action of argininosuccinate synthetase in the presence of citrulline and aspartate. The overall stereochemical transformation is therefore net inversion, and thus the enzyme does not catalyze the formation of an adenylylated enzyme intermediate prior to the synthesis of citrulline adenylate. The RP isomer of adenosine 5'-O-(2-thiotriphosphate) (ATP beta S) is a substrate in the presence of Mg2+, but the SP isomer is a substrate when Cd2+ is used as the activating divalent cation. Therefore, the lambda screw sense configuration of the beta,gamma-bidentate metal--ATP complex is preferred by the enzyme as the actual substrate. No significant discrimination could be detected between the RP and SP isomers of adenosine 5'-O-(1-thiotriphosphate) (ATP alpha S) when Mg2+ or Mn2+ are used as the divalent cation. Argininosuccinate synthetase has been shown to require a free divalent cation for full activity in addition to the metal ion needed to complex the ATP used in the reaction.

Guanosine thiophosphate derivatives as substrate analogues for phosphoenolpyruvate carboxykinase

The interactions of nucleotides with phosphoenolpyruvate carboxykinase were studied by using the stereospecific thiophosphate analogues of GDP and GTP. The metal ion dependent stereoselectivity of these analogues was determined by using steady-state kinetics. The RP and SP isomers of guanosine 5'-O-(1-thiodiphosphate) (GDP alpha S) were substrates with low turnover, and a small preference for the RP isomer was observed. Neither the enzyme-metal nor the nucleotide-metal complex elicited any substantial change in the selectivity. Guanosine 5'-O-(2-thiodiphosphate) (GDP beta S) exhibited no substrate activity for the enzyme, regardless of the cations. This nucleotide was a competitive inhibitor against GDP, however. Both RP and SP diastereomers of guanosine 5'-O-(1-thiotriphosphate) (GTP alpha S) were good substrates for phosphoenolpyruvate carboxykinase; in several cases, depending upon the cation, kcat and/or Vm/Km for the RP isomer is greater than for the substrate GTP. The enzyme-metal complex but not the nucleotide-metal complex affects the relative Km and the Vmax values. In contrast, guanosine 5'-O-(2-thiotriphosphate) (GTP beta S) (SP) is a much better substrate (greater than 50 times) than is GTP beta S (RP). The metal ions have little effect on the selectivity. These results suggest a specific interaction of the beta-phosphate of the nucleotide with the protein. The analogue guanosine 5'-O-(3-thiotriphosphate) (GPT gamma S) serves as a substrate to yield GDP and thiophosphoenolpyruvate. The latter was detected by 31P NMR and was shown to slowly hydrolyze to form phosphoenolpyruvate.(ABSTRACT TRUNCATED AT 250 WORDS)

Phospholipids chiral at phosphorus. Use of chiral thiophosphatidylcholine to study the metal-binding properties of bee venom phospholipase A2

It has been shown recently by 31P nuclear magnetic resonance (NMR) that phospholipase A2 (PL A2) from bee venom shows a high degree of stereoselectivity toward the "isomer B" of 1,2-dipalmitoyl-sn-glycero-3-thiophosphocholine (DPPsC) [Bruzik, K., Jiang, R.-T., & Tsai, M.-D. (1983) Biochemistry 22, 2478-2486]. We now report a quantitative kinetic study of PL A2 using 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and (RP)-, (SP)-, and (RP + SP)-DPPsC by a spectrophotometric assay. The substrates were mixed with Triton X-100 to form mixed micelles, and steady-state kinetic theories were applied. The enzyme was activated by Ca2+, which induced a conformational change of the enzyme, as shown by UV difference spectra. The apparent dissociation constant of Ca2+/PL A2 is 2.5 mM. In the presence of Ca2+, large substrate specificity and stereospecificity in Vmax (in mumol min-1 mg-1) were observed: DPPC, 1850; (RP)-DPPsC, 7.6; (RP + SP)-DPPsC, 64; (SP)-DPPsC, 0.044. On the other hand, relatively small variation in Km was observed, which suggests that the interfacial interaction is relatively nonspecific among the substrates studied. (SP)-DPPsC and Cd2+ were shown as competitive inhibitors for the hydrolysis of DPPC by Ca2+/PL A2. Binding of Cd2+ with apo-PL A2 was also demonstrated by UV difference spectra, with a dissociation constant of 0.59 mM. Activation of apo-PL A2 by Cd2+ was unequivocally demonstrated for (SP)-DPPsC by use of 31P NMR. The Vmax values of Cd2+/PL A2 were DPPC/(RP)-DPPsC/(SP)-DPPsC = 17.6/0.069/0.0044 mumol min-1 mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Stereochemistry of the elongation factor Tu X GTP complex

The geometry of the Me2+. GTP complex at the active site of EF-Tu from Bacillus stearothermophilus has been investigated using thiophosphate analogs of GTP to inhibit the kirromycin-induced GTPase reaction at 60 mM NH4Cl. There is no reversed selectivity for the diastereomers (Rp and Sp) of guanosine 5'-O-(1-thiotriphosphate) (GTP[alpha S]) on replacing Mg2+ by Cd2+, so that the observed specifity for the Sp isomer must be due to an interaction of the pro-R oxygen of the alpha-phosphate group with the protein. With the diastereomers of GTP[beta S] low specifity for the Rp isomers is seen in the presence of Mg2+. Moreover, both isomers are very weakly bound. In contrast, substitution of Mg2+ by Cd2+ results in a high specifity for the Sp isomer, and this is then recognized as well as Cd X GTP. These results indicate that in the EF-Tu X Me2+ X GTP complex, the pro-S oxygen of the beta-phosphate group is bound to the metal ion and the pro-R oxygen to the protein. GTP[gamma S] is a good analog of GTP regardless of the nature of the metal ion, suggesting that not all of the oxygens of the gamma-phosphate are involved in interactions to metal ion and protein. The thiophosphate analogs of GTP were also tested for their efficiency in ternary complex formation with EF-Tu and aminoacyl-tRNA and in the physiological GTPase of EF-Tu. The stereochemistry of the GTP binding site on EF-Tu in all three systems is found to be very similar.

The role of magnesium in binding of the nucleotide polyphosphate chain to the active site of myosin subfragment-1

The binding of adenosine 5'-[beta, gamma-imido]triphosphate, pyrophosphate and triphosphate to the active site of myosin subfragment-1 was assessed in the presence and absence of Mg2+ by direct and indirect methods. In addition, the affinity and stoichiometry of Mg2+ in the ternary complexes formed by protein, Mg2+ and each of these phosphate compounds have been determined. As direct methods, equilibrium dialysis, sedimentation and quantitative affinity chromatography were used in conjunction with the indirect method of monitoring reactivity changes of the critical thiol-1 and thiol-2 groups, which occur upon binding of the ligands at the active site. There was good agreement between the results yielded by the different methods. All three phosphate compounds alone bind just one molecule per isolated myosin head portion with similar affinities lying in the range 1-4 X 10(3) M-1. Again only one molecule/head portion binds when they exist in the form complexed with Mg2+, but now show much higher affinities of between 10(6)-10(7) M-1. In all cases Mg2+ was found to be associated in the ternary complexes with the very high affinity of 10(8)-10(9) M-1. It is postulated that this ion plays a prominent role in fixing the phosphate chain in the myosin active site. In contrast, Mg2+ scarcely affects the affinity of ADP and shows only a low affinity around 4 X 10(4) M-1 in the ternary complex [Watterson, J.G., Foletta, D., Kunz, P.A., and Schaub, M. C. (1983) Eur. J. Biochem. 131, 89-96]. As pyrophosphate displays binding parameters similar to the triphosphate compounds and widely different from ADP, it is argued that it may bind in the beta, gamma-phosphate positions at the active site.

Metal-ion-promoted dephosphorylation of the 5'-triphosphates of uridine and thymidine, and a comparison with the reactivity in the corresponding cytidine and adenosine nucleotide systems

First-order rate constants (50 degrees C; I = 0.1 M, NaClO4) for the dephosphorylation of UTP and TTP (1 mM) in the pH range 2-10 are compared with those of ATP and CTP; they all show the same properties indicating that the nucleic base has no influence on the rate. In the presence of Cu2+ or Zn2+ (NTP:M2+ = 1:1) this changes drastically: ATP-M2+ much greater than UTP-M2+ approximately equal to TTP-M2+ approximately equal to CTP-M2+ greater than NTP, the Cu2+ systems being always more reactive than the Zn2+ systems, and these more than the Ni2+ systems. An interaction between the nucleic base and metal ion is important for the Cu2+-ATP and Zn2+-ATP systems, but not for the pyrimidine-nucleotide systems (these behave like methyltriphosphate). Accordingly, prevention of the Cu2+-purine interaction by the addition of one equivalent of 2,2'-bipyridyl, leading to Cu(Bpy) (NTP)2-, strongly reduces the activity and all four ternary Cu2+ systems now show the same dephosphorylation rate. Addition of a second equivalent of Cu2+ to the Cu2+-UTP 1:1 system enhances the dephosphorylation rate significantly and Job's method provides evidence that a 2:1 complex is the most reactive intermediate. The relation between the initial rate, vo = d[PO3-4]/dt, and the concentration of Cu2+-UTP in 1:1 and 2:1 systems was determined. The results suggest that the reactive complex with pyrimidine nucleotides is a monomeric, dinuclear species of the type M2(NTP) (OH)- (its formation is inhibited by ligands like tryptophanate), while with M2+-ATP the reactive complex is a dimer. The connection between the indicated dephosphorylations in vitro, i.e. trans-phosphorylations to H2O, and related reactions in vivo are discussed.

Metal-nucleotide structure at the active sites of the mammalian hexokinases

The diastereomers of adenosine 5'-O-(2-thiotriphosphate) (ATP beta S) in the presence of Mg2+, Co2+ and Cd2+ have been used to determine the stereospecificity of the metal-nucleotide binding site of rat muscle hexokinase type II and rat liver glucokinase by the method developed by Jaffe and Cohn [J. Biol. Chem. 254, 10839-10845 (1979)]. The kinetic parameters, Km and V, for the mammalian hexokinase reaction have been determined for ATP beta S in the presence of the three divalent metal ions. In the presence of Mg2+, both enzymes exhibit a preference for the B diastereomer of ATP beta S (V ratio, B/A approximately equal to 20). With Cd+, the stereospecificity is reversed and the A diastereomer is the preferred substrate, suggesting direct coordination of S on the beta-P to this metal ion. Co2+ exhibits a decreased specificity for the B diastereomer over Mg2+. This decreasing order of stereo-specificity for the B isomer reflects primarily the decreasing ratios of nucleotide complexes coordinated to O rather than S on the beta-P as the metal ion is changed from Mg2+ to Co2+ to Cd2+. The kinetic parameters for the hexokinases have also been determined for adenosine 5'-O-(1-thiotriphosphate) (ATP alpha S) using the same three metal ions as activators. The A diastereomer is the preferred substrate regardless of the metal ion. This absence of reversal of stereospecificity for metal-ATP alpha S suggests that the alpha-P is not involved in coordinating the metal on the enzyme, unlike the beta-P. That is, the structural constraints of the ATP-binding site on the enzyme overcome the preferred coordination of Cd2+ to S. Given the greater stability of bidentate metal-ATP complexes over monodentate, these data are interpreted as indicating that MgATP binds to the mammalian hexokinases as the beta gamma-bidentate complex in the A screw sense geometry, as has been found for the yeast hexokinase (Jaffe and Cohn, reference cited above).