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PubMed1994

The effects of pH and cations on the spectral and kinetic properties of methylamine dehydrogenase from Thiobacillus versutus.

The catalytic parameters of Thiobacillus versutus methylamine dehydrogenase (MADH) with the physiological substrates methylamine and amicyanin show a pH profile that is quite different from the one found in commonly used assays with artificial electron acceptors. The optimum at pH 7.5, observed for kcat in the latter case, is absent with amicyanin as the reoxidizing substrate. With amicyanin kcat scarcely depends on pH; the same is true for the maximal rate of reduction of MADH by methylamine (kred). Conversely, both the specificity constant (kcat/Km) of MADH for amicyanin and the apparent second-order rate constant for the reduction of MADH by methylamine (kassocapp) increase very sharply with pH. MADH has a high- and a low-affinity binding site for monovalent cations. Cation binding to the high-affinity site, which only binds the larger cations (Cs+, Rb+, and NH4+), is accompanied by a red shift in the absorbance spectrum, whereas cation binding to the low-affinity site, which, less specifically, favors binding of the smaller cations, leads to a bleaching of the visible spectrum with a concomitant increase in the near-UV. Cation binding to either site strongly affects the reactivity of MADH. The reduction of MADH by methylamine is inhibited by monovalent cations, whereas the oxidation of reduced MADH by amicyanin is strongly stimulated. For the former reaction it was established that cations affect only kassocapp, not kred. Some speculations about the molecular basis for the effects of pH and cations are presented.

Bacterial Proteins↗
PubMed1983

Acridine-psoralen amines and their interaction with deoxyribonucleic acid.

A series of novel compounds in which a 9-acridinyl nucleus is linked to a psoralen nucleus in the 5- or 8-position via polyamines was prepared and examined. Their reversible binding to DNA and their irreversible binding to DNA and DNA cross-linking upon irradiation with UV-A light were examined. It was found that they were all less efficiently photoreactive than 8-methoxypsoralen (8-MOP), both in cross-linking and photobinding to DNA, whereas the ratio between their photobinding and cross-linking was 40-400 times that of 8-MOP. Compounds in which the linker was attached to the 5-position in psoralen showed smaller cross-linking and photobinding efficiencies and larger ratios between photobinding and cross-linking than those of psoralens attached in the 8-position. This strongly indicates that the 9-substituents of the acridines are oriented toward the minor groove. Flow linear dichroism studies showed that the compounds were DNA intercalating with the acridine moiety, whereas the psoralen moiety in no case was clearly intercalating. This conclusion was further supported by viscometry which also strongly indicated monointercalation.

Acridines↗
PubMed1984

Poly(8-bromodeoxyadenylic acid): properties of the polymer and contrast with the ribopolynucleotide analogue.

Introduction of the bulky 8-bromo substituent into adenine residues of polynucleotides has strikingly different consequences in the deoxy- and ribopolynucleotide series. Poly(r8BrA) was found in earlier studies to form a very stable double-helical self-structure but not to undergo interaction with potentially complementary polynucleotides. We find that poly(d8BrA), in contrast, does not form an ordered self-structure in 0.1 M Na+ but appears to exist as an electrostatically expanded rigid rod with unusual circular dichroism (CD) properties at very low ionic strength. The deoxy polymer, moreover, readily forms double helices with either deoxy or ribo pyrimidine polynucleotides, studied by UV, CD, and IR spectroscopy. These complexes are destabilized, relative to those formed by poly(dA), possibly because energy is needed to convert the purine residues from a more stable syn to an anti conformation, required for heteroduplex formation. The CD spectrum of (d8BrA)n X (dT)n is similar to that of B DNA. The deoxy-ribo hybrids (d8BrA)n X (rU)n and (d8BrA)n X (rBrU)n have CD spectra resembling those of A DNA or RNA. Unlike other deoxy-deoxy pairs (d8BrA)n X (dBrU)n, however, has a CD spectrum resembling RNA and other helices having the A form.

Chemical Phenomena↗
PubMed1988

Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy.

The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694], appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase [Sachsenheimer, W., & Schulz, G.E. (1977) J. Mol. Biol. 114, 23-26], with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of beta-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% alpha-helix, 38% beta-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possibly due to disorder, it can be fit by using methods developed on well-characterized globular proteins. On this basis, the peptide consists of 35 +/- 10% beta-structure, 60 +/- 12% turns and aperiodic structure, and not more than 10% alpha-helix. The CD spectrum is best fit by assuming the presence of at most 13% alpha-helix in the peptide, 24 +/- 2% beta-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformational changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assessed by CD. Detailed assignments of resonances in the peptide spectrum and intermolecular NOEs between protons of bound MgATP and those of the peptide, as well as chemical shifts of peptide resonances induced by the binding of MgATP, are consistent with the previously proposed binding site for MgATP on adenylate kinase.

Adenosine Triphosphate↗
PubMed1976

Synthesis and properties of carbonylbis(methionyl)insulin, a proinsulin analogue which is convertible to insulin by cyanogen bromide cleavage.

The preparation and use of carbonylbis (L-methionine p-nitrophenyl ester) as a reversible cross-linking reagent for insulin are described. The reaction of 1 equiv of reagent with zinc insulin in dimethylformamide in the presence of triethylamine yields as one of the products NalphaA1, NepsilonB29-carbonylbis(methionyl)insulin, (CBM-insulin). The CBM-insulin was characterized by end group analysis and by the products formed on tryptic and chymotryptic cleavage. It possessed 91% of the immunological and 6.5% of the hormonal activity of insulin. Treatment of CBM-insulin with cyanogen bromide (CNBr) in 70% formic acid for 1 h resulted in nearly complete removal of the methionine bridge to yield insulin. A small amount of a side product was removed on DEAE-cellulose at pH 7.2 to give an overall recovery of insulin of 70-80%. Oxidative sulfitolyses of CBM-insulin gave the hexa(S-sulfonate) which was reduced with dithiothreitol to yield reduced CBM-insulin. The latter compound, containing 6 sulfhydryls, exhibited a pH-dependent circular dichroic spectrum. The form at pH 10 exhibited a spectrum typical of random coil which was converted to a form at pH 7.8 which was characterized by a negative extremum at 213 nm. The change in the spectrum at 213 nm with pH was characterized by an apparent pKa of 8.5. Studies on the reoxidation of reduced CBM-insulin were performed at pH values between 7.8 and 10 and at protein concentrations of 0.01-1 mg/ml. The best yields (ca. 85%) of the correctly paired disulfide bonds were obtained in reoxidations at pH 9.5-10 at protein concentration of 0.01-0.1 mg/ml. CBM-insulin, which had been isolated from reoxidation at high pH of the reduced CBM-insulin, was cleaved by CNBr to yield a fully active insulin in an overall yield of 60% from the reduced CBM-insulin.

Adipose Tissue↗
PubMed1975

Stepwise enzymatic oligoribonucleotide synthesis including modified nucleotides.

A method has been developed for the routine synthesis of 2'(3')-o-monoacyl ribonucleoside 5'-diphosphates for stepwise synthesis of oligoribonucleotides with Escherichia coli polynucleotide phosphorylase. The use of triethyl orthoisovalerate allows the facile preparation of 2'(3')-o-isovaleryl-UDP, -CDP, -ADP, -GDP, -IDP, -EPLISON-APD, eplison-CDP, and N6-isopentenyl-ADP. The synthesis of N6-isopentenyl-ADP from ADP by N1-alkylation and the Dimroth rearrangement to N6 is reported. The effects of several factors including the nature of the divalent cation, pH, SALT CONCENTRATION, AND TIME ON THE EFFICIENCY OF THE POLYNUCLEOTIDE PHPSPHORYLASE CATALYZED SINGLE ADDITIONS OF THE 2'(3')-O-ISOVALERYL RIBONUCLEOSIDE 5'-DIPHOSPHATES TO AN OLIGORIBONUCLEOTIDE PRIMER ARE REPORTED. The syntheses of many tetranucleoside triphosphates and two pentanucleoside tetraphosphates in yields of 20-75 per cent are reported. The 2'(3')-o-isovaleryl derivatives of IDP, eplison-ADP, eplison-CDP, and N6-isopentenyl-ADP were all accepted by polynucleotide phosphorylase as substrates for the monoaddition reaction. The extension of the method to include the syntheses of oligoribonucleotides containing modified nucleosides offers a means of studying the role s of these modification by the use of relatively simple model compounds.

Cytosine Nucleotides↗
PubMed1975

Synthesis properties of the naturally occurring N-[(9-beta-D-ribofuranosylpurin-6-yl)-N-methylcarbamoyl]-L-threonine (mt-6A) and other related synthetic analogs.

The naturally occurring modified nucleoside, N-[(9-beta-D-ribofuranosylpurin-6-yl)-N-methylcarbamoyl]-L-threonine (mt6A), and the corresponding glycine analog mg6A were synthesized from N6-methyl-2',3',5'-tri-O-acetyladenosine and the appropriately blocked isocyanates derived from threonine and glycine. The natural mt6A isolated from Escherichia coli tRNA (F. Kimura-Harada et al. (1972), Biochemistry 11, 3910), from wheat embryo tRNA (R. Cunningham and M. W. Gray (1974), Biochemistry 13, 543), and from rat liver tRNA (Rogg et al. (1975), Eur. J. Biochem. 53, 115) was found to be identical with the synthetic mt6A in paper and thin-layer chromatography and electrophoresis. Several analogs of the parent 6-ureidopurine ribonucleoside, N-[(9-beta-D-ribofuranosylpurin-6-yl)carbamoyl]-L-thronine (t6A), were also prepared. Starting from 2',3',5'-tri-O-acetylguanosine and 2',3',5'-tri-O-acetylcytidine and the above isocyanates, the t6A analogs, N-[(9-beta-D-ribofuranosyl-6-oxo-1H-purin-2-yl)carbamoyl]-L-threonine (t2G) and N-[(1-beta-D-ribofuranosyl-2-oxypyrimidin-4-yl)carbamoyl]-L-threonine (t4C), were prepared. Also synthesized were the corresponding glycine analogs, g2G and g4C, from guanosine and cytidine, respectively. The 2'-deoxyribosyl analog, N-[(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)carbamoyl]-L-threonine (2'-deoxy-t6A), and the arabinosyl derivative, N-[(9-beta-D-arabinofuranosylpurin-6-yl)carbamoyl]-L-threonine (t6AraA), were synthesized from the appropriate urethane and the requisite amino acid. The ureido group in mt6A could not be hydrolyzed by the enzymes urease, peptidase, and protease. Various chemical and biological properties of the naturally occurring mt6A and the related analogs are discussed.

Chromatography, Paper↗
PubMed1975

Ionic strength induced structure in histone H4 and its fragments.

The salt-induced folding and self-association of histone H4 and its fragments (1-23), (25-67), (69-84), and (69-102) have been studied at the same molar concentration (1 mM) by nuclear magnetic resonance (NMR), circular dichroism (CD), and ir spectroscopy. Byeach of these techniques intact histone H4 exhibited a fast structural change, involving the formation of alphaR helix and aggregation, and also a slow change involving beta-structure formation. Fragment (25-67) was found to behave in a manner similar to the intact molecule for the fast change, showing both helix formation and aggregation but exhibited no time-dependent effects. All the other fragments were found to be essentially noninteracting. It is concluded that (25-67) contains the rgion critical for the folding and self-association of histone H4. On the basis of these results a model is proposed for the self-association of histone H4 in which helix is located between residues 49 and 73, while the beta structure lies between 74 and the C-terminus.

Amino Acid Sequence↗
PubMed1975

The mechanism of formylation of five-membered cyclic phosphorodiamidates.

Cyclic N,N'-diphenylethylenephosphorodiamidates, 1, have been found to yield up to 70% of the N-formyldiphenylethylenediamines when reacted in 1 M formate buffers (50 degrees, 25% v/v dioxane-H2O, mu = 1.0). The mechanism proposed for formylation on the basis of kinetic, product ratio, and 18O-labeling studies apparently involves cyclization of a formyl phosphoramidate-amine adduct derived from formate attack on 1H+, the process probably being catalyzed by intramolecular proton transfer between the phosphoryl moiety and aniline nitrogen. An oxygen is transferred from formate to inorganic phosphate in the net reaction. The initial site of formylation with dissymmetric 1 (p-CH3O, p-Cl) was shown by 18O incorporation studies to be the p-anisidine nitrogen, which also corresponds to the isomer of thermodynamic control. Attack by formate on 1H+, therefore, results in expulsion of the more basic nitrogen. Certain mechanistic aspects of the reaction might occur in the enzyme-catalyzed ATP-dependent formylation of tetrahydrofolic acid.

Chemical Phenomena↗
PubMed1975

Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid).

Poly(8-aminoguanylic acid) has in neutral solution a novel ordered structure of high stability. The 8-amino group permits formation of three hydrogen bonds between two residues along the "top", or long axis, of the purines. The usual hydrogen bonding protons and Watson-Crick pairing sites are not involved in the association. The bonding scheme has a twofold rotation axis and is hemiprotonated at N(7). Poly(8NH2G) is converted by alkaline titration (pK = 9.7) to a quite different ordered structure, which is the favored form over the range approximately pH 10-11. The bonding scheme appears to be composed of a planar, tetrameric array of guanine residues, in which the 8-amino group does not participate in interbase hydrogen bonding. Poly (8NH2G) does not interact with poly(C) in neutral solution because of the high stability of the hemiprotonated G-G self-structure. Titration to the alkaline plateau, however, permits ready formation of a two-stranded Watson-Crick helix. In contrast to the monomer 8NH2GMP, poly(8NH2G) does not form a triple helix with poly(C) under any conditions. The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH.

Binding Sites↗