Nucleotide Complexes Research Articles

Energetic aspects of intramolecular coupling between the nucleotide binding site and the distal switch II region of the yeast RAS2 protein

We have studied the interaction of the yeast RAS2 protein with guanine nucleotides using energetic parameters for the dissociation of RAS.nucleotide complexes. The results indicated that a Gly-->Ser substitution at position 82 led to an altered interaction with GppNHp and, to a lesser extent, also with GDP. It was also possible to conclude that structural perturbation of Gly82 can stimulate nucleotide release by decreasing the energetic barrier for nucleotide dissociation. This, together with the observation that residues 80 and 81 are involved in the response of RAS to nucleotide exchange factors without affecting GDP binding per se, suggests a potential mechanism for exchange factor-stimulated GDP release.

Botulinum A and the light chain of tetanus toxins inhibit distinct stages of Mg · ATP‐dependent catecholamine exocytosis from permeabilised chromaffin cells

Susceptibilities of Mg.ATP-independent and Mg.ATP-requiring components of catecholamine secretion from digitonin-permeabilised chromaffin cells to inhibition by Clostridial botulinum type A and tetanus toxins were investigated. These toxins are Zn(2+)-dependent proteases which specifically cleave the 25-kDa synaptosomal-associated protein (SNAP-25) and vesicle-associated membrane protein (VAMP) II, respectively. When applied to permeabilised chromaffin cells they rapidly inhibited secretion in the presence of Mg.ATP but the catecholamine released in the absence of Mg.ATP, thought to represent fusion of primed granules, was not perturbed. The toxins can exert their effects per se in the absence of the nucleotide complex; therefore, Mg.ATP-requiring steps of secretion are implicated as roles for their targets. Primed release was lost rapidly after permeabilisation of the cells but could be maintained by including Mg.ATP during the incubation before stimulating release with Ca2+. This ability of Mg.ATP to maintain primed release was only partially inhibited by botulinum neurotoxin A whereas it was abolished by tetanus toxin, consistent with the distinct substrates for these toxins. This study reveals a component of release within which these proteins are either resistant to cleavage by these toxins or in such a position that degradation can no longer prevent granule fusion. Differences in the steps of release at which these toxins can affect inhibition are also revealed.

Characterization of platinum(II)-phosphato complexes of uridine nucleotides

Reactions of uridine 5'-di- and -triphosphates with cis-diamminedichloroplatinum(II) at or near neutral pH yielded substantial phosphato chelates. Each nucleotide afforded a pair of diastereomers due to the creation of an asymmetric center at the α- and β-phosphorus atoms of the UDP and UTP upon complexation to platinum(II). In addition to the phosphato complexes, nitrogen (N(3)) bound complexes are also formed.

Electronic Structure Determination of Co(II)-Nucleotide Complexes by Using Magnetic and Mößbauer Emission Measurements

Mößbauer emission spectroscopic and susceptibility measurements of several Co(II)-nucleotide complexes have been carried out. The electronic structure derived from these data for the Co(II) central cation has been related to the distortion and the symmetry of its environment. The susceptibility data are indicative of short antiferromagnetic ordering in the majority of the samples. For the hydrated Co-5′UMP (5′-uridine monophosphate) and Co-5′CMP (5′-cytidine-monophosphate) complexes, magnetic models involving Co(II) dimers and linear chains, respectively, are proposed to explain the susceptibility data observed below 50 K.

Chromium complexes of uric acid—synthesis, structure, and properties

Two different complexes of Cr3+ with uric acid, one containing one mole of ligand per atom of metal and the other with three moles, have been synthesized and purified. These have been characterized by elemental analysis, by analysis for their Cr3+ and ligand content and by IR and UV spectra and their properties are described. N and > C = O of uric acid have been demonstrated to be involved in chelation with Cr3+. All monomethyl uric acids, except N-7 methyl urate have been shown to yield Cr3+ complexes but with three moles of ligand per Cr3+ in each case. The inability of N-7 methyl urate to complex with Cr3+ constitutes additional evidence for the mandatory requirement of a free > NH grouping at position 7 of uric acid for complexation with Cr3+. The two complexes of uric acid with Cr3+ are formed directly on suitable reaction with the required relative proportions of the metal ion to ligand. Preliminary studies have indicated that the chromium—uric acid complexes, unlike chromium—nucleotide complexes, are not inhibitory analogs.

Molecular geometry of vanadyl-adenine nucleotide complexes determined by EPR, ENDOR, and molecular modeling

The interactions of the vanadyl ion (VO 2+ ) with the adenine nucleotides AMP, ADP, and ATP and the α,β-methylene analogue of ADP (AMP-CP) have been investigated by electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopy. By spectrometric titration of VO 2+ in solutions of different VO 2+ :nucleotide molar ratios near neutral pH, it was shown on the basis of the peak-to-peak amplitude of the-3/2 perpendicular EPR absorption feature that the stoichiometry of metal:ligand binding for ADP, AMP-CP, and ATP was 1:2

Stability and photochemical properties of vanadate-trapped nucleotide complexes of gizzard myosin in the 6S and 10S conformations: identification of an active-site serine

The properties of divalent metal.ADP.vanadate (V(i)) complexes of the 6S extended and 10S folded conformations of gizzard myosin before and after UV irradiation have been studied. The half-lives of both 6S and 10S myosin.MgADP.V(i) complexes in the dark at 0 degrees C are on the order of 2 weeks. Brief irradiation with UV light, however, photomodified the enzyme as suggested by changes in the NH(4+)-, K(+)-, and Ca(2+)-ATPase activities, and destabilized the complexes. The 6S complex, when irradiated, released ADP and V(i) rapidly (t1/2 less than or equal to 1 min) as has been observed in comparable experiments with skeletal myosin subfragment 1 (S1) [Grammer et al. (1988) Biochemistry 27, 8408-8415]. The irradiated 10S complex released approximately 20% of the ADP and V(i) rapidly (t1/2 less than or equal to 1 min), but the remainder stayed trapped, possibly as the vanadyl (VO2+).ADP complex, for much longer times (t1/2 approximately 8 h). The site of photomodification was sought by reducing both photomodified 6S and 10S myosin with NaB3H4. Amino acid composition analyses identified [3H]serine as the only labeled residue(s), suggesting that the hydroxymethyl group of serine had been oxidized to an aldehyde as shown previously for photomodified skeletal myosin S1 [Cremo et al. (1989) J. Biol. Chem. 264, 6608-6611]. The 29-kDa NH2-terminal tryptic peptide from the heavy chain was found to contain essentially all of the [3H]serine. Preparations of 6S and 10S [3H]myosin were digested exhaustively with trypsin. An identical [3H]peptide was purified from each preparation and its sequence determined to be Glu169-Asp-Gln-Ser-Ile-Leu-(Cys)-Thr-Gly-[3H]Ser-Gly-Ala-Gly-Ly s183.(ABSTRACT TRUNCATED AT 250 WORDS)

Chiral recognition between dissymmetric Ln(dpa)33- and cobalt(III)-nucleotide complexes in aqueous solution. Enantioselective luminescence quenching as a probe of intermolecular chiral discrimination

Time-resolved chiroptical luminescence spectroscopy is used to investigate enantioselective excited-state quenching processes in solution samples that contain a racemic mixture of chiral luminophores and a small concentration of dissymmetric quencher molecules. The luminophores are Ln(dpa) 3 3- complexes (Ln≡Eu 3+ or Tb 3+ , dpa≡a dipicolinate dianion) that have tris(terdentate) chelate structures of D 3 symmetry with either left-handed (Λ) or right-handed (4) configurational chirality about the trigonal axis. The quenchers are 6-coordinate Co(III) complexes with the general stoichiometric formula Co(NH 3 ) 4 (ndp) or Co(NH 3 ) 4 (ntp), were ndp denotes a diphosphate nuceotide ligand and ntp denotes a triphosphate nucleotide ligand.

Simulation of the solution structure of the H-ras p21-GTP complex.

An unconstrained simulation of the GTP-bound form of the H-ras protein p21 is performed in an aqueous environment with charge-neutralizing counterions. The simulation is compared to the 1.35-A structure of Pai et al. [(1990) EMBO J. 9, 2351] and a proposed alternate structure, in which the loop at residues 60-65 is modeled into a form which may activate a water molecule for the GTP hydrolysis. The simulation suggests that some protein intermolecular H-bond contacts which are present in the crystal structure are lost in the solvation process and this loss may lead to localized refolding of the molecule. For instance, we find that the gamma-phosphate of the GTP has somewhat weaker contact with the protein in the simulation structure. The antiparallel beta-sheet (residues 38-57) partially melts. The 60-65 loop, which is hypervariable in the X-ray study, is initially relatively distant from the gamma-phosphate region. However, this loop moves so as to sample the space around the gamma-phosphate. For a significant fraction of the simulation time, forms similar to the alternate structure are observed, and a water molecule is localized near the hydrolytic site. The molecular dynamics simulations of p21-GTP in solution support a postulated hydrolysis mechanism for the biological inactivation of the nucleotide complex based on crystallographic data.

Thermodynamic study of dimethyltin(IV) complexes with nucleoside 5′-triphosphates

The complex formation of [SnMe2]2+ ion with guanosine 5′-triphosphate (GTP), inosine 5′-triphosphate (ITP), cytidine 5′-triphosphate (CTP) and tripolyphosphate(5–)(tpp) has been investigated by means of potentiometric and calorimetric measurements at 25 °C and I= 0.1 mol dm–3(KNO3). On the basis of the thermodynamic parameters, bonding details have been inferred for the main nucleotide complex species, using tpp as reference. The thermodynamic data show that the nitrogen atom [N(1)] of the bases interacts with dimethyltin in the [SnMe2L] species of GTP and ITP only.

25Mg NMR Studies of magnesium binding to erythrocyte constituents

The binding of Mg2+ ion to ATP, ADP, AMP, 2,3-bisphosphyoglycerate (DPG), and hemoglobin has been studied by 25Mg NMR spectroscopy at 9.4 T. Addition of any of these ligands to a solution of 2 mM 25MgCl2 at pH 7.2 caused a progressive increase in linewidth, with no discernible chemical shift. ATP and ADP, which form tight 1:1 complexes with Mg2+, did not cause maximal broadening until present in several-fold excess, implying that bis(nucleotide) complexes also form. The studies showed progressively weaker Mg2+ binding to ATP, ADP, DPG, and AMP, consistent with published binding constants. Hemoglobin cause fairly little broadening, consistent with its known weak affinity for Mg2+. Competition studies determined ATP affinities for Ca2+ and H+ that were also in good agreement with published values. 25Mg NMR spectra of 2 mM bound 25Mg2+ were obtained with good signal to noise in less than 1 hr. The technique may now be a practical means for studying the binding of Mg2+ within erythrocytes and other cells.

Interaction of La (III) and Tb (III) ions with purine nucleotides: evidence for metal chelation (N-7-M-PO3) and the effect of macrochelate formation on the nucleotide sugar conformation.

The interaction of the La (III) and Tb (III) ions with adenosine-5'-monophosphate (5'-AMP), guanosine-5'-monophosphate (5'-GMP), and 2'-deoxyguanosine-5'-monophosphate (5'-dGMP) anions with metal/nucleotide ratios of 1 and 2 has been studied in aqueous solution in acidic and neutral pHs. The solid complexes were isolated and characterized by Fourier transform ir and 1H-nmr spectroscopy. The lanthanide (III)-nucleotide complexes are polymeric in nature both in the solid and aqueous solutions. In the metal-nucleotide complexes isolated from acidic solution, the nucleotide binding is via the phosphate group (inner sphere) and an indirect metal-N-7 interaction (outer-sphere) with the adenine N-1 site protonated. In the complexes obtained from neutral solution, metal chelation through the N-7 and the PO3(2-) group is prevailing. In aqueous solution, an equilibrium between the inner and outer sphere metal-nucleotide interaction has been observed. The ribose moiety shows C2'-endo/anti pucker in the free AMP anion and in the lanthanide (III)-AMP complexes, whereas the GMP anion with C2'-endo/anti sugar conformation exhibits a mixture of the C2'-endo/anti and C3'-endo/anti sugar puckers in the lanthanide (III)-GMP salts. The deoxyribose has O4'-endo/anti sugar pucker in the free dGMP anion and a C3'-endo/anti, in the lanthanide (III)-dGMP complexes.

Functional consequences of single amino acid substitutions in calmodulin-activated adenylate cyclase of Bordetella pertussis.

Calmodulin-activated adenylate cyclase of Bordetella pertussis and Bacillus anthracis are two cognate bacterial toxins. Three short regions of 13-24 amino acid residues in these proteins exhibit between 66 and 80% identity. Site-directed mutagenesis of four residues in B. pertussis adenylate cyclase situated in the second (Asp188, Asp190) and third (His298, Glu301) segments of identity were accompanied by important decrease, or total loss, of enzyme activity. The calmodulin-binding properties of mutated proteins showed no important differences when compared to the wild-type enzyme. Apart from the loss of enzymatic activity, the most important change accompanying replacement of Asp188 by other amino acids was a dramatic decrease in binding of 3'-anthraniloyl-2'-deoxyadenosine 5'-triphosphate, a fluorescent analogue of ATP. From these results we concluded that the two neighbouring aspartic acid residues in B. pertussis adenylate cyclase, conserved in many other ATP-utilizing enzymes, are essential for binding the Mg(2+)-nucleotide complex, and for subsequent catalysis. Replacement of His298 and Glu301 by other amino acid residues affected the nucleotide-binding properties of adenylate cyclase to a lesser degree suggesting that they might be important in the mechanism of enzyme activation by calmodulin, rather than being involved directly in catalysis.

Crystal structure of a Barnase-d(GpC) complex at 1.9 Å resolution

The ribonuclease excreted by Bacillus amyloliquefaciens, Barnase, was co-crystallized with the deoxy-dinucleotide d(GpC). The crystal structure was determined by molecular replacement from a model of free Barnase previously derived by Mauguen et al. Refinement was carried out using data to 1.9 A resolution. The final model, which has a crystallographic R factor of 22%, includes 869 protein atoms, 38 atoms from d(GpC), a sulfate ion and 73 water molecules. Only minor differences from free Barnase are seen in the protein moiety, the root-mean-square C alpha movement being 0.45 A. The dinucleotide has a folded conformation. It is located near the active site of the enzyme, but outside the protein molecule and making crystal packing contacts with neighboring molecules. The guanine base is stacked on the imidazole ring of active site His102, rather than binding to the so-called recognition loop as it does in other complexes of guanine nucleotides with microbial nucleases. The deoxyguanosine is syn, with the sugar ring in C-2'-endo conformation; the deoxycytidine is anti and C-4'-exo. In addition to the stacking interaction, His102 hydrogen bonds to the free 5' hydroxyl, which is located near the position where the 3' phosphate group is found in other inhibitors of microbial ribonucleases. While the mode of binding observed with d(GpC) and Barnase would be non-productive for a dinucleotide substrate, it may define a site for the nucleotide product on the 3' side of the hydrolyzed bond.

Complexes of yeast adenylate kinase and nucleotides investigated by proton NMR

The role of one of the histidine residues present in many adenylate kinases (H36 in the porcine cytosolic enzyme) is highly disputed. We thus studied the yeast enzyme (AKye) containing this His residue. AKye is highly homologous to the Escherichia coli enzyme (AKec), a protein that is already well characterized by NMR [Vetter et al. (1990) Biochemistry 29, 7459-7467] and does not contain the His residue in question. In addition, discrepancies between solution structural and X-ray crystallographic studies on the location of the nucleotide binding sites of adenylate kinases are clarified. One- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy was used to investigate AKye and its complex with the bisubstrate analogue P1,P5-bis(5'-adenosyl)pentaphosphate (AP5A). The well-resolved spectra of AKye allowed identification of nearly all detectable resonances originating from aromatic side chain protons (12 out of 15 spin systems). From these studies, all aromatic residues of AKec involved in the binding of ATP.Mg2+ have functional analogues in AKye. The AMP site seems to make no contacts to aromatic side chains, neither in the AKye.AP5A.Mg2+ nor in the AKec.AP5A.Mg2+ complexes, so that it is presently not possible to localize this binding site by NMR. The ATP site of AKye is located near residues W210 and H143 in a position similar to the ATP site of the E. coli enzyme. In combination with the recent X-ray results on the AP5A complexes AKye and AKec and the GMP complex of guanylate kinase [Stehle, T., & Schultz, G. E. (1990) J. Mol. Biol. 221, 255-269], the latter one leading to the definition of the monophosphate site, the problem of the location of the nucleotide sites can be considered to be solved in a way contradicting earlier work [for a review, see Mildvan, A. S. (1989) FASEB J. 3, 1705-1714] and denying the His residue homologous to H36 in porcine adenylate kinase a direct role in substrate binding.

Two-state equilibria of myosin subfragment 1 and its complexes with ADP and actin

We previously reported that the nucleotide complex of myosin subfragment 1, S1.epsilon ADP, exists in two states on the basis of the temperature dependence of the fluorescence decay of bound 1,N6-ethenoadenosine diphosphate (epsilon ADP) [Aguirre, R., Lin. S.-H., Gonsoulin, F., Wang, C.-K., & Cheung, H.C. (1989) Biochemistry 28, 799-809]. We have extended the previous study of the equilibrium between the two states, S1L.ADP in equilibrium S1H.ADP, by using a fluorescently labeled myosin S1 (S1-AF). In S1 alkylated with IAF [5-(iodoacetamido)fluorescein], the decay of the label emission was biexponential both in the presence and absence of ADP and/or actin. In the presence of ADP, the two decay times were 4.30 (alpha 1 = 0.55) and 0.80 ns (alpha 2 = 0.45) at 12.4 degrees C, in a medium containing 60 mM KCl, 30 mM TES (pH 7.5), and 2 mM MgCl2. The steady-state fluorescence intensities of S1-AF, (S1-AF).ADP, acto.(S1-AF), and acto.(S1-AF).ADP were dependent on temperature over the range of 5-30 degrees C. By combining lifetime and steady-state intensity data, we obtained for the two-state transition (S1-AF)L.ADP in equilibrium (S1-AF)H.ADP the following parameters: delta H degrees = 16.1 kcal/mol (67.3 kJ/mol) and delta S degrees = 55.8 cal/(deg.mol) [233.5 J/(deg.mol)], in agreement with previous results obtained with epsilon ADP. The delta H degrees values for the two-state transition of S1-AF, acto.(S1-AF), and acto.(S1-AF).ADP are 13.0, 21.6, and 5.2 kcal/mol, respectively. The corresponding delta S degrees values are 46.9, 79.5, and 17.4 cal/(deg.mol).(ABSTRACT TRUNCATED AT 250 WORDS)

Site-directed mutagenesis of the RecA protein of Escherichia coli. Tyrosine 264 is required for efficient ATP hydrolysis and strand exchange but not for LexA repressor inactivation.

The role of Tyr264 in nucleotide binding and hydrolysis catalyzed by the RecA protein of Escherichia coli was investigated by constructing Gly, Ser, and Phe substitution mutations using oligonucleotide-directed mutagenesis. The corresponding mutant recA genes neither restored resistance to killing by ultraviolet irradiation nor increased homologous recombination in a recA strain. The purified RecA(Gly264) protein was unable to bind nucleotide, hydrolyze ATP, or form stable ternary complexes with adenosine 5'-O-thiotriphosphate and DNA although the mutant protein bound DNA normally in the absence of nucleotide. The RecA (Phe264) and RecA(Ser264) proteins hydrolyzed ATP poorly and the rates were reduced approximately 8- and 18-fold, respectively. Although capable of low levels of ATP hydrolysis, neither the RecA(Phe264) nor the RecA(Ser264) protein promoted DNA pairing or strand exchange reactions in vitro. Furthermore, these mutant RecA proteins were impaired in their ability to form salt-resistant ternary complexes with adenosine 5'-O-thiotriphosphate) and DNA as judged by filter binding. Nevertheless, nucleoprotein complexes formed with either RecA(Phe264) or RecA(Ser264) protein directed efficient cleavage of LexA repressor in vitro. These results demonstrate that Tyr264 is required for efficient ATP hydrolysis and for homologous pairing of DNA but does not participate in activating RecA protein for LexA repressor autodigestion.

Interaction of indole derivatives with biologically important aromatic compounds. Part 22. Importance of simultaneous co-operation of hydrogen-bond pairing and stacking interactions for recognition of guanine base by a peptide: X-ray crystal analysis of 7-methylguanosine-5′-phosphate–tryptophanylglutamic acid complex

As a model to investigate the mode of recognition of the base guanine by peptides and proteins, the crystal structure of the 7-methylguanosine-5′-phosphate–tryptophanylglutamic acid complex was analysed by X-ray diffraction; this is the first crystal structure determination of a peptide–nucleotide complex. The complex crystals are stabilized by extensive hydrogen-bond formation in which three independent water molecules per complex pair participate. Both molecules are joined by the coupled contributions of the triple hydrogen bonds between the guanine base and the peptide backbone chain and of the prominent stacking interactions between the guanine base and the tryptophan indole side-chain, suggesting the importance of the coupling of hydrogen bonding and stacking interactions for recognition of the base to occur.

Critical evaluation of stability constants for nucleotide complexes with protons and metal ions and the accompanying enthalpy changes

Critical evaluation of stability constants for nucleotide complexes with protons and metal ions and the accompanying enthalpy changes

Chromatographic behaviour of cyclodextrin complexes of nucleotides, nucleosides and their bases

Chromatographic behaviour of cyclodextrin complexes of nucleotides, nucleosides and their bases