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A S Mildvan

Publications and source records attributed to A S Mildvan.

At least 109 records · Page 6Linked to original sources
PubMed1985

Nuclear Overhauser effect studies of the conformations and binding site environments of deoxynucleoside triphosphate substrates bound to DNA polymerase I and its large fragment.

The conformations and binding site environments of Mg2+TTP and Mg2+dATP bound to Escherichia coli DNA polymerase I and its large (Klenow) fragment have been investigated by proton NMR. The effect of the large fragment of Pol I on the NMR line widths of the protons of Mg2+TTP detected one binding site for this substrate with a dissociation constant of 300 +/- 100 microM and established simple competitive binding of deoxynucleoside triphosphates at this site in accord with previous equilibrium dialysis experiments with whole Pol I [Englund, P. T., Huberman, J.A., Jovin, T.M., & Kornberg, A. (1969) J. Biol. Chem. 244, 3038]. Primary negative nuclear Overhauser effects were used to calculate interproton distances on enzyme-bound Mg2+dATP and Mg2+TTP. These distances established that each substrate was bound with an anti-glycosidic torsional angle (chi) of 50 +/- 10 degrees for Mg2+dATP and 40 +/- 10 degrees for Mg2+TTP. The sugar pucker of both substrates was predominantly O1'-endo, with a C5'-C4'-C3'-O3' exocyclic torsional angle (delta) of 95 +/- 10 degrees for Mg2+dATP and 100 +/- 10 degrees for Mg2+TTP. The consistency of these conformations with those previously proposed, on the basis of distances from Mn2+ at the active site [Sloan, D. L., Loeb, L. A., Mildvan, A.S., & Feldman, R.J. (1975) J. Biol. Chem. 250, 8913], indicates a unique conformation for each bound nucleotide. The chi and delta values of the bound substrates are appropriate for nucleotide units of B DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1985

On the fidelity of DNA replication: manganese mutagenesis in vitro.

Manganese is mutagenic in vivo and in vitro in studies with a variety of enzymes and templates. Using Escherichia coli DNA polymerase I with poly[d(A-T)] and phi X174 DNA templates, we analyzed the mechanism of manganese mutagenesis by determining the dependence of error rate on free Mn2+ concentration and comparing this to measured dissociation constants of Mn2+ from enzyme, template, and deoxynucleoside triphosphate substrates. This comparison suggests several conclusions: (1) At very low Mn2+ concentrations, the enzyme is activated at high fidelity. Thus, it is unlikely that activation with manganese per se significantly alters the conformation of the enzyme so as to affect nucleotide selection. (2) At low free Mn2+ concentrations (less than 100 microM), manganese causes errors in incorporation via its interaction with the DNA template. The concentration dependence of mutagenesis is determined by the strength of binding Mn2+ to the particular DNA template used. The data do not allow one to rule out the possibility that Mn2+-deoxynucleoside triphosphate interactions contribute to mutagenesis in selected situations. This range of free Mn2+ concentrations is the one of greatest relevance for in vivo mutagenesis. (3) At higher concentrations (between 500 microM and 1.5 mM), further mutagenesis by Mn2+ occurs. This mutagenesis probably is due either to binding of manganese to single-stranded regions within the DNA or to weak accessory sites on the enzyme.

DNA Polymerase I↗
PubMed1985

NMR studies of the MgATP binding site of adenylate kinase and of a 45-residue peptide fragment of the enzyme.

Proton NMR was used to study the interaction of beta,gamma-bidentate Cr3+ATP and MgATP with rabbit muscle adenylate kinase, which has 194 amino acids, and with a synthetic peptide consisting of residues 1-45 of the enzyme, which has previously been shown to bind MgepsilonATP [Hamada, M., Palmieri, R. H., Russell, G. A., & Kuby, S. A. (1979) Arch. Biochem. Biophys. 195, 155-177]. The peptide is globular and binds Cr3+ATP competitively with MgATP with a dissociation constant, KD(Cr3+ATP) = 35 microM, comparable to that of the complete enzyme [KI(Cr3+ATP) = 12 microM]. Time-dependent nuclear Overhauser effects (NOE's) were used to measure interproton distances on enzyme- and peptide-bound MgATP. The correlation time was measured directly for peptide-bound MgATP by studying the frequency dependence of the NOE's at 250 and 500 MHz. The H2' to H1' distance so obtained (3.07 A) was within the range established by X-ray and model-building studies of nucleotides (2.9 +/- 0.2 A). Interproton distances yielded conformations of enzyme- and peptide-bound MgATP with indistinguishable anti-glycosyl torsional angles (chi = 63 +/- 12 degrees) and 3'-endo/O1'-endo ribose puckers (sigma = 96 +/- 12 degrees). Enzyme- and peptide-bound MgATP molecules exhibited different C4'-C5' torsional angles (gamma) of 170 degrees and 50 degrees, respectively. Ten intermolecular NOE's from protons of the enzyme and four such NOE's from protons of the peptide to protons of bound MgATP were detected, which indicated proximity of the adenine ribose moiety to the same residues on both the enzyme and the peptide. Paramagnetic effects of beta,gamma-bidentate Cr3+ATP on the longitudinal relaxation rates of protons of the peptide provided a set of distances to the side chains of five residues, which allowed the location of the bound Cr3+ atom to be uniquely defined. Distances from enzyme-bound Cr3+ATP to the side chains of three residues of the protein agreed with those measured for the peptide. The mutual consistency of interproton and Cr3+ to proton distances obtained in metal-ATP complexes of both the enzyme and the peptide suggests that the conformation of the peptide is very similar to that of residues 1-45 of the enzyme. When this was assumed to be the case and when molecular models and a computer graphics system were used, MgATP could be fit into the X-ray structure of adenylate kinase in a unique manner such that all of the distances determined by NMR were accommodated.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenosine Triphosphate↗
PubMed1984

NMR and computer modeling studies of the conformations of glutathione derivatives at the active site of glyoxalase I.

The conformations of four derivatives of glutathione bound at the active site of the metalloenzyme glyoxalase I have been determined by NMR measurements and by computer model building using a distance geometry approach. Paramagnetic effects of Mn2+-glyoxalase I on the longitudinal relaxation rates of the carbon-bound protons of the substrate analog S-(acetonyl)-glutathione at three frequencies, the hydrophobic competitive inhibitor S-(propyl)glutathione at four frequencies, and the charged competitive inhibitor S-(carboxymethyl)glutathione at a single frequency were used to calculate Mn2+ to proton distances in each complex. These and previously determined distances from Mn2+ to the protons and 13C-enriched carbon atoms of the product S-(D-lactoyl)glutathione were used in a distance geometry program to compute the conformations of each enzyme-bound derivative which best fit the measured distances and other known constraints such as bond lengths, van der Waals radii, planar and trans-peptide bonds, and thioester linkages. The distance geometry program also provided a measure of the uniqueness of the conformations consistent with the experimental data. Extended Y-shaped conformations were detected for each of the bound glutathione derivatives, similar to the x-ray structure and the theoretically calculated conformation of glutathione itself, suggesting this to be a low energy form. Acceptable conformations of each enzyme-bound derivative fell into two classes with the metal either above or below the mean plane through the glutathione compound. The conformational uncertainty within each class was relatively small, ranging from deviations of 0.9-1.9 A in the average positions of each of the atoms. A small but significant difference in the conformation of the substrate analog as compared to the product was detected in the position of the reaction center carbon directly bonded to the glutathione sulfur atom. Unlike the second-sphere metal complexes formed by the bound substrate analog, the product, or the hydrophobic competitive inhibitor, the charged competitive inhibitor S-(carboxymethyl)glutathione binds farther from the metal, in the third coordination sphere.

Binding Sites↗
PubMed1984

NMR studies of the backbone protons and secondary structure of pentapeptide and heptapeptide substrates bound to bovine heart protein kinase.

The conformations of enzyme-bound pentapeptide (Arg-Arg-Ala-Ser-Leu) and heptapeptide (Leu-Arg-Arg-Ala-Ser-Leu-Gly) substrates of protein kinase have been studied by NMR in quaternary complexes of the type (Formula: see text). Paramagnetic effects of Mn2+ bound at the inhibitory site of the catalytic subunit on the longitudinal relaxation rates of backbone Ca protons, as well as on side-chain protons of the bound pentapeptide and heptapeptide substrates, have been used to determine Mn2+ to proton distances which range from 8.2 to 12.4 A. A combination of the paramagnetic probe-T1 method with the Redfield 2-1-4-1-2 pulse sequence for suppression of the water signal has been used to measure distances from Mn2+ to all of the backbone amide (NH) protons of the bound pentapeptide and heptapeptide substrates, which range from 6.8 to 11.1 A. Paramagnetic effects on the transverse relaxation rates yield rate constants for peptide exchange, indicating that the complexes studied by NMR dissociate rapidly enough to participate in catalysis. Model-building studies based on the Mn2+-proton distances, as well as on previously determined distances from Cr3+-AMPPCP to side-chain protons [Granot, J., Mildvan, A.S., Bramson, H. N., & Kaiser, E. T. (1981) Biochemistry 20, 602], rule out alpha-helical, beta-sheet, beta-bulge, and all possible beta-turn conformations within the bound pentapeptide and heptapeptide substrates. The distances are fit only by extended coil conformations for the bound peptide substrates with a minor difference between the pentapeptides and heptapeptides in the phi torsional angle at Arg3C alpha and in psi at Arg2C alpha. An extended coil conformation, which minimizes the number of interactions within the substrate, would facilitate enzyme-substrate interaction and could thereby contribute to the specificity of protein kinase.

Animals↗
PubMed1984

X-ray absorption studies of the Zn2+ site of glyoxalase I.

X-ray edge and extended absorption fine structure spectra of Zn2+ at the active site of glyoxalase I have been measured. The edge spectrum reveals a simple set of transitions consistent with a 7-coordinate or distorted octahedral Zn2+ model complex. Analysis of the fine structure rules out sulfur ligands to Zn2+ and yields a best fit complex with Zn2+-N (or Zn2+-O) distances of 2.04 and 2.10 A, which are too great for tetrahedral Zn2+ coordination but are appropriate for an octahedral or more highly coordinated complex. Peaks of electron density in the Fourier-transformed region of the higher order shells at distances of 3-4 A from the Zn2+-imidazole model similar to those found with known Zn2+-imidazole model complexes, including carbonic anhydrase [Yachandra, V., Powers, L., & Spiro, T.G. (1983) J. Am. Chem. Soc. 105, 6596-6604], indicating at least two imidazole ligands to Zn2+ on glyoxalase I. Binding of the heavy atom substrate analogue S-(p-bromobenzyl)glutathione did not significantly alter the number of atoms directly bonded to Zn2+ or their distances. No evidence for coordination of the cysteine sulfur of glutathione by the Zn2+ was obtained, and no heavy atom signal from bromine was detected, indicating this atom to be greater than or equal to 4 A from the Zn2+. However, conformational changes of the imidazole ligands of Zn2+ upon binding of the substrate analogue were suggested by changes in the relative intensity of the doublet peaks at 3-4 A from the Zn2+ and assignable to imidazole.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1984

Mechanistic studies of cAMP-dependent protein kinase action.

The details of the process by which protein kinase catalyzes phosphoryl group transfers are beginning to be understood. Early work that explored the primary specificity of cAMP-dependent protein kinase action enabled the synthesis of small peptide substrates for the enzyme. Enzyme-peptide interactions seem simpler to understand than protein-protein interactions, so peptide substrates have been used in most protein kinase studies. In most investigations the kinetics for the phosphorylation of small peptides have been interpreted as being consistent with mechanisms which do not invoke phospho-enzyme intermediates (see, for example, Bolen et al.). Protein kinase has been shown to bind two metal ions in the presence of a nucleotide. Using magnetic resonance techniques the binding of these ions has been utilized to elucidate the conformation of nucleotide and peptide substrates or inhibitors when bound in the enzymic active site. Also, two new peptides with the form Leu-Arg-Arg-Ala-Ser-Y-Gly, where Y was either Pro or (N-methyl)Leu, were synthesized and found not to be substrates, within the limits of detection, for protein kinase. The striking lack of affinity that protein kinase has for such peptides which are unlikely to form a beta 3-6 turn has not been reported before. Our results may indicate that this type of turn is a requirement for protein kinase catalyzed phosphorylation or that these peptides lack the ability to form a particular hydrogen bond with the enzyme. Magnetic resonance techniques have indicated that the distance between the phosphorous in the gamma-phosphoryl group of MgATP and the hydroxyl oxygen of serine in the peptide Leu-Arg-Arg-Ala-Ser-Leu-Gly is 5.3 +/- 0.7 A. This, together with certain kinetic evidence, suggests that the mechanism by which protein kinase catalyzes phosphoryl group transfer has considerable dissociative character. Chemical modifications, including one using a peptide-based affinity label, have identified two residues at or near the active site, lysine-72 and cysteine 199. While neither of these groups has been shown to be catalytically essential, similar studies may help to identify groups that are directly involved in the catalytic process. Finally, a spectrophotometric assay for cAMP-dependent protein kinase has been described. Using this assay the preliminary results of an in-depth study of the pH dependence of protein kinase catalyzed phosphoryl group transfer have been obtained. This study shall aid in the identification of active site residues and should contribute to the elucidation of the enzyme's catalytic mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenosine Triphosphate↗
PubMed1984

NMR studies of the mechanism of cyclic AMP-dependent protein kinase.

NMR has been used to study the role of the divalent cation, the conformations, arrangement, and exchange rates of the enzyme-bound metal-ATP and peptide substrates, the mechanism of the phosphoryl transfer, and the structure and role of the regulatory subunit on type II cyclic AMP (cAMP)-dependent protein kinase from bovine heart. The active complex consists of an enzyme-ATP-metal bridge in which the metal is beta, gamma coordinated, with delta chirality at P beta, and a torsional angle at the adenine-ribose bond in the high-anti range (x approximately 80 degrees). The bound heptapeptide substrate Leu-Arg-Arg-Ala-Ser-Leu-Gly is extended in conformation, forming either a coil or, less likely, a beta turn but not an alpha helix or beta sheet. The distance from the gamma-P of bound ATP analogs to the Ser-OH of the bound peptide (5.3 +/- 0.7 A) would permit a metaphosphate or an elongated phosphorane intermediate or transition state. The regulatory subunit (R2) blocks the peptide- or protein-binding site of the catalytic subunit. The 31P chemical shift of cAMP is not greatly altered on binding to R2, but the resonance is broadened to approximately 32 Hz, which indicates no chemical change but marked immobilization of bound cAMP. A narrower (approximately 7 Hz) 31P resonance at 4.44 ppm is assigned to P-serine-95 of R2 because it disappears with catalytic subunit, Mg2+, and an ADP-generating system.

Binding Sites↗
PubMed1983

13C NMR studies of the product complex of glyoxalase I.

The paramagnetic effects of Mn2+ . glyoxalase I on the 13C relaxation rates of the reaction product, S-(D-lactoyl)glutathione, separately enriched in the lactoyl carbonyl (C-1) and hydroxymethylene (C-2) carbons, have been measured at 62.8 MHz. The 1/fT1p values of C-1 (1100 +/- 120 s-1) and C-2 (712 +/- 290 s-1) and the previously determined tau c (0.74 ns) yield Mn2+ to carbon distances of 5.7 +/- 0.3 and 6.1 +/- 0.5 A, respectively. These distances, together with previously determined Mn2+-proton distances (Sellin, S., Rosevear, P.R., Mannervik, B., and Mildvan, A.S. (1982) J. Biol. Chem. 257, 10023-10029) constrain the thioester carbonyl group of the product to point toward the metal, with the oxygen positioned to accept a hydrogen bond from a water ligand, in a kinetically competent, second sphere complex. Model-building studies indicate that any averaging of multiple second sphere complexes would require as a major contributor at least one conformation with the lactoyl carbonyl oxygen within hydrogen-bonding distance of an intervening water ligand. Such a structure would facilitate polarization of the carbonyl group in the reverse glyoxalase reaction.

Erythrocytes↗
PubMed1983

Metal content of DNA polymerase I purified from overproducing and wild type Escherichia coli.

DNA polymerase I purified from both E. coli strain B, and from an overproducing E. coli stain lysogenized with a lambda pol A phage were analyzed for metal content. After gel filtration to remove loosely bound metals, DNA polymerase I from both strains contained less than or equal to 0.2 gm atoms Zn2+/mole enzyme and 0.09 to 0.7 Mg2+/mole enzyme. Substoichiometric amounts of Fe, Co, Ni (less than or equal to 0.2 gm atoms), and Mn (less than or equal to 0.1 gm atoms) were detected. Since the metal content does not correlate with enzymatic activity, we conclude that DNA polymerase I is not a metalloenzyme.

Chemical Phenomena↗
PubMed1982

Nuclear magnetic resonance studies of the nucleotide binding sites of porcine adenylate kinase.

The alpha, beta, gamma-tridentate complex of CrATP, a paramagnetic competitive inhibitor of porcine adenylate kinase, increases the longitudinal [1/(fT1p)] and transverse [1/(fT2p)] relaxation rates of a resonance of the enzyme previously assigned by McDonald et al. [McDonald, G.G., Cohn, M., & Noda, L. (1975) J. Biol. Chem. 250, 6947-6954] to the C2 proton of histidine-36. These paramagnetic effects are diminished upon the addition of the substrate MgATP by an amount consistent with the simple displacement of CrATP. The 1/(fT2p) value sets a lower limit of 400 s-1 on the rate constant for dissociation of CrATP from the enzyme. The 1/(fT1p) value at 250 MHz and the correlation time for water protons in the same complex are used to calculate a distance of 12.9 +/- 1.0 A from Cr(III) to the C2 proton of histidine-36. A primary, negative nuclear Overhauser effect is detected on the adenine H2 resonance of enzyme-bound MgATP upon preirradiation of the C2 proton of histidine-36, indicating that these protons are approximately less than 5 A apart. These distances and negative intramolecular Overhauser effects from the ribose protons to adenine H8 of MgATP indicate an extended structure for bound MgATP with an anti conformation about the glycosidic bond. These findings require a different orientation or location of the bound metal-ATP substrate from that proposed based on X-ray studies of the binding of salicylate [Pai, E. F., Sachsenheimer, W., & Schirmer, R.H. (1977) J. Mol. Biol. 114, 37-45]. Other nuclear Overhauser effects from resonances of the protein at 1.8 and 0.9 ppm to both adenine H2 and ribose H1' of bound MgATP indicate the proximity to the substrate of at least one Arg C beta proton (at 1.8 ppm), C gamma proton (at 1.7 ppm), Lys C delta proton (at 1.7 ppm), or Leu C beta proton (at 1.6 ppm) and one or more Leu, Ile, or Val methyl groups (at 0.9 ppm). Entirely different Overhauser effects are observed from the enzyme to the adenine protons of AMP consistent with a distinct site for the other substrate.

Adenosine Monophosphate↗