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PubMed1982

Formamide-induced dissociation and inactivation of Escherichia coli alkaline phosphatase. Metal-dependent reassociation and restoration of activity from isolated subunits.

Alkaline phosphatase from Escherichia coli has been reversibly dissociated by treatment with low concentrations of formamide. The monomer retains the capacity to bind metals and to regenerate catalytically active dimer that is identical with the native dimeric enzyme. The rate and extent of dissociation of dimer to monomer depend upon pH, ionic strength, temperature, formamide concentration, and enzyme-bound metal. Under appropriate experimental conditions, reassociation can be greatly slowed, allowing the properties of the monomer to be examined in solution. The formamide-induced apo monomer has a conformation distinct from that of the dimer and zinc- or cobalt-containing monomers. The monomer tightly binds 1 mol of zinc or cobalt in a metal-binding site altered from those of the dimer but is catalytically inactive. pH, ionic strength, and formamide concentration all influence reassociation. Hydrophobic forces are implicated as important in subunit interactions. The effect of metal content on the dissociation--reassociation process underscores the essential role that metals play in maintaining enzyme tertiary structure and reveals a new role in stabilizing the quaternary structure.

Alkaline Phosphatase↗
PubMed2006

Multiple isotope effect study of the hydrolysis of formamide by urease from jack bean (Canavalia ensiformis).

Multiple kinetic isotope effects have been measured for the urease-catalyzed hydrolysis of formamide at pH 6.0 and 25 degrees C. These kinetic isotope effects include the carbonyl-C ((13)k = 1.0241 +/- 0.0009), the carbonyl-O ((18)k = 0.9960 +/- 0.0009), the formyl-H ((D)k = 0.95 +/- 0.01), the leaving-N ((15)k= 1.0327 +/- 0.0006), and the nucleophile-O ((18)k = 0.9778 +/- 0.0005). In addition, the enzyme does not catalyze the exchange of oxygen from the solvent into the carbonyl-O of formamide or the product, formate ion. The isotope effects are consistent with the rate-determining collapse of the tetrahedral intermediate (i.e., C-N bond cleavage). The pH optimum for formamide is at pH 5.3, whereas for urea, it is near 8.0. This is best accommodated by the mechanism proposed by Hausinger and Karplus, in which an active site cysteine binds to the nonleaving nitrogen in urea. For urea, the preference is for the anionic form of the sulfhydryl; for formamide, the neutral form is preferred, leading to the lower pH optimum.

Canavalia↗
PubMed2000

Solution structure by NMR and molecular dynamics of a duplex containing a guanine opposite a N-(2-deoxy-beta-D-erythro-pentofuranosyl)formamide lesion.

One- and two-dimensional NMR spectroscopy has been used combined with molecular dynamics to determine the fine structure of the DNA duplex 5'-d(AGGAGCCACG).d(CGTGGFTCCT) where F is the N-(2-deoxy-beta-D-erythro-pentofuranosyl)formamide residue which is a ring fragmentation product of thymine. The formamide deoxyribose exists as two isomers with respect to the orientation about the peptide bond. The two isomers (trans and cis) are observed in a ratio 3:2 in solution. For both species, the oligonucleotide adopts a globally B form structure although conformational changes are observed around the mismatch site. The formamide residue, whatever the isomer, is intrahelical and can pair with the guanine on the opposite strand with one hydrogen bond. For the cis isomer, the residue adopts a syn orientation and is able to form a second hydrogen bond with the guanine on the 5' side on the same strand. Off-resonance ROESY experiments have been used to investigate the chemical exchange observed at low temperature of the duplex. Conformational exchange has only been found for the oligonucleotide with the formamide residue in the trans conformation.

DNA↗
PubMed1998

Inhibition of human alcohol dehydrogenases by formamides.

Human alcohol dehydrogenase (HsADH) comprises class I (alpha, beta, and gamma), class II (pi), and class IV (sigma) enzymes. Selective inhibitors of the enzymes could be used to prevent the metabolism of alcohols that form toxic products. Formamides are unreactive analogues of aldehydes and bind to the enzyme-NADH complex [Ramaswamy, S.; Scholze, M.; Plapp, B. V. Biochemistry 1997, 36, 3522-3527]. They are uncompetitive inhibitors against varied concentrations of alcohol, and this makes them effective even with saturating concentrations of alcohols. Molecular modeling led to the design and synthesis of a series of cyclic, linear, and disubstituted formamides. Evaluation of 23 compounds provided structure-function information and selective inhibitors for the enzymes, which have overlapping but differing substrate specificities. Monosubstituted formamides are good inhibitors of class I and II enzymes, and disubstituted formamides are selective for the alpha enzyme. Selective inhibitors, with Ki values at pH 7 and 25 degrees C of 0.33-0.74 microM, include N-cyclopentyl-N-cyclobutylformamide for HsADH alpha, N-benzylformamide for HsADH beta1, N-1-methylheptylformamide for HsADH gamma2, and N-heptylformamide for HsADH sigma and HsADH beta1.

Alcohol Dehydrogenase↗
PubMed1984

Formamide as a substrate of xanthine oxidase.

Formamide is a substrate of xanthine oxidase. At pH 8.2 and 1.14 mM-O2, Vmax.(app.) is 3.1 s-1 and Km (app.) is 0.7 M. Mo(V) e.p.r. signals obtained by treating the enzyme with formamide were studied, and these provide new information about the ligation of molybdenum in the enzyme and about the enzymic mechanism. The substrate is the first compound that is not a nitrogen-containing heterocycle to give a Very Rapid signal. This supports the hypothesis that the Very Rapid signal, though it is not detectable with all substrates, represents an essential intermediate in turnover. Formamide also gives the Inhibited signal and is the first non-aldehyde substrate to do so. The Rapid type 1 signal obtained in the presence of formamide was examined in H2O enriched with 2H or with 17O. The single oxygen atom detectable in the signal is shown to be strongly and anisotropically coupled. This indicates that this atom remains as an oxo ligand of molybdenum in this signal-giving species. Other structural features of this species are discussed.

Chemical Phenomena↗
PubMed1969

Immunochemistry of a formamide-extracted antigen from Clostridium perfringens cell walls.

The type-specific antigen of a strain of Clostridium perfringens involved in food poisoning was isolated from the cell wall by the use of hot formamide. The antigen appears to consist of polysaccharide or mucopeptide. The formamide extract was shown to be heterogeneous by gel filtration on Sephadex G-200. The serologically active fraction contained about 25% of the amount of protein present in the original formamide extract. Hexosamine, acetyl groups, and carbohydrate also were detected. The formamide extract showed a high degree of serological activity. The serological activity was increased twofold on Sephadex gel filtration.

Alkynes↗
PubMed1977

Oxalate, formate, formamide, and methanol metabolism in Thiobacillus novellus.

Thiobacillus novellus was able to grow with oxalate, formate, formamide, and methanol as sole sources of carbon and energy. Extensive growth on methanol required yeast extract or vitamins. Glyoxylate carboligase was detected in extracts of oxalate-grown cells. Ribulose bisphosphate carboxylase was found in extracts of cells grown on formate, formamide, and thiosulfate. These data indicate that oxalate is utilized heterotrophically in the glycerate pathway, and formate and formamide are utilized autotrophically in the ribulose bisphosphate pathway. Nicotinamide adenine dinucleotide-linked formate dehydrogenase was present in extracts of oxalate-, formate-, formamide-, and methanol-grown cells but was absent in thiosulfate- and acetate-grown cells.

Alcohol Oxidoreductases↗
PubMed1973

Hydroxyapatite chromatography and formamide denaturation of adenovirus DNA.

Denatured adenovirus DNA was retained by hydroxyapatite columns under conditions generally used for selective retention of double-stranded DNA, probably due to several partially complementary sequences within single-stranded DNA. It was found that addition of formamide reduced the fraction of sonically treated, denatured adenovirus DNA bound to hydroxyapatite from about 30% to less than 1%. This led to a study of the effect of formamide on the melting temperature (T(m)) of double-stranded DNA in solution or bound to hydroxyapatite. The T(m) of DNA decreases 0.56 C/1% formamide, a value determined in buffered solutions with purified formamide.

Adenoviridae↗
PubMedDate not supplied

The influence of formamide on thermal denaturation profiles of DNA and metaphase chromosomes in suspension.

Systematic photometric studies are presented to analyze the thermal denaturation behaviour with and without formamide of metaphase chromosome suspensions in comparison to DNA solutions. Temperature dependent hyperchromicity measurements at 256 nm and 313 nm were performed using an appropriately designed computer-controlled photometer device. Due to an upright optical axis, this allowed absorbance measurements with negligible sedimentation effects not only for solutions of pure DNA, but also for particle suspensions of isolated metaphase chromosomes. This device has a temperature resolution of +/- 0.5 degrees C and an optical sensitivity of 10(-3) to 10(-4) optical density. For calf thymus DNA the reduction of the melting point with the increase of formamide in the solution was measured at pH 7.0 and pH 3.2. The good correlation of the theoretical approximation to experimental data indicated the suitability of the apparatus to quantitatively describe DNA conformation changes induced by thermal denaturation. For metaphase chromosome preparations of Chinese hamster culture cells, absorbance changes were measured between 20 degrees C and 95 degrees C with a temperature gradient of 1 degrees C/min. These measurements were performed at pH 7.0 and at pH 3.2. The denaturation profiles (= first derivative of the absorbance curve) resulted in a highly variable peak pattern at 256 nm and 313 nm indicating complex conformation changes. A statistical evaluation of the temperature values of the peak maxima resulted in temperature ranges typical for chromosomal conformation changes during thermal treatment. Especially the range of highest temperature values was independent from pH modifications. For pH 3.2 the influence of formamide on the denaturation behaviour of metaphase chromosome preparations was analyzed. In contrast to pure DNA solutions, a reduction of the "melting point" (i.e. the maximum temperature at which a conformation change takes place) was not found. However, the denaturation behaviour depended on the duration of formamide treatment before the measurement.

Animals↗
PubMed1992

[Presynaptic effects induced by pretreatment with formamide of the neuromuscular junction of the mouse].

Some techniques to block muscular nerve evoked contraction involve pharmacological approaches using synaptic blocking agents. Such methods interfere with normal synaptic transmission, and could introduce artifacts making difficult the experimental interpretation. The method based on the use of formamide pre-treatment should not interfere with synaptic physiology, indeed previous works suggest that the mechanism involved in block of muscle activity could depend on the decrease in specific postsynaptic membrane capacitance, and on the disruption of the morphology of the transverse tubule system. To prove this assumption we evaluated before and after formamide pre-treatment, some pre and postsynaptic parameters related to the spontaneous quantal release (MEPC). By means of the Loose patch clamp technique, we demonstrated, that formamide pre-treatment increases in an irreversible manner the frequency of spontaneous quantal release. Morphology of MEPC appear not modified by formamide pretreatment, which does not interfere with postsynaptic cholinergic receptors activity.

Acetylcholine↗
PubMedDate not supplied

[Electron microscopic study of changes in chromosomal structural organization under the effect of formamide].

Isolated human metaphase chromosomes were treated with formamide at different (0-70%) concentrations and examined electronmicroscopically by protein monolayer technique. At increasing formamide concentration chromosomes gradually decondense, the scaffold becomes more clearly visible, the loops of chromatin fibres coming off the central part of chromosomes lose their nucleosomal appearance. Electrophoretic analysis of chromosomal proteins data show that formamide-treated chromosomes have approximately the same histone content as those before treatment, although chromosomes treated with 70% formamide look very similar to histone-depleted ones described elsewhere.

Chromosomes, Human↗
PubMed2005

Formamide tautomerization: catalytic role of formic acid.

Formic acid catalyzed tautomeric conversion of formamide to formamidic acid has been investigated by use of ab initio and density functional theoretical calculations. In a 1:1 dimeric complex between formamide and formic acid, the tautomeric conversion occurs via double-hydrogen transfer within an eight-member hydrogen-bonded cyclic network. The results predict that the energy barrier of the catalytic process is reduced by more than a factor of 4 compared to that in the isolated formamide molecule in the gas phase, and the tautomerization in the 1:1 complex is several kcal/mol less endothermic than that of the isolated molecule. The potential energy surface corresponding to this double hydrogen transfer process indicates that a concerted transfer of both the hydrogen atoms along the hydrogen bond directions is energetically favorable, and no minimum for an ionic intermediate, which may arise for stepwise transfer, was predicted. The unique configuration of the transition state has been identified by starting the reaction from both the tautomeric forms, and the transition state was subjected to IRC calculation.

Journal Article↗
PubMed1985

Methadone metabolism in the rat in vivo: identification of a novel formamide metabolite.

Deuterium-labelled methadone and metabolites were used for the g.l.c.-mass spectrometry detection and identification of biliary conjugated methadone metabolites in rats. After beta-glucuronidase hydrolysis the bile extract contained an unknown metabolite that was not ring hydroxylated and retained an intact keto group. Chemical oxidation of the methadone metabolite 2-ethylidene-N,5-dimethyl-3,3-diphenylpyrrolidine, perchlorate salt (EDDP) with m-chloroperbenzoic acid in chloroform, gave a compound identical by g.l.c.-mass spectrometry to the new metabolite. The chemical oxidation product was identified as 2-(4',4'-diphenylheptan-5'-one-2'-yl)oxaziridine by spectroscopic methods. The oxaziridine was shown to quantitatively isomerize to a secondary formamide (2-formamido-4,4-diphenyl-5-heptanone) during g.l.c.-mass spectrometry analysis. The formamide was also isolated by flash column chromatography after reflux of the oxaziridine in m-xylene, and then characterized by spectroscopy. The formamide and oxaziridine g.l.c.-mass spectrometry characteristics were identical. It was concluded on the basis of g.l.c.-mass spectrometry that the metabolite is the secondary formamide.

Animals↗
PubMed1965

THE ACTION OF HOT FORMAMIDE ON BACTERIAL CELL WALLS.

1. The cell walls of Corynebacterium tritici contain much carbohydrate and their mucopeptide contains diaminobutyric acid instead of lysine or diaminopimelic acid. They are resistant to lysozyme. 2. The residue after extraction with hot formamide contains only about 10% less carbohydrate but is attacked by lysozyme. Lysozyme also slowly attacks cell walls treated with fluorodinitrobenzene and more rapidly cell walls that have been N-acetylated. 3. All these processes block the free gamma-amino groups of diaminobutyric acid present in the untreated cell wall. Hot formamide introduces formyl groups, as shown by its ability to make formylglycine and diformyl-lysine under the same conditions. 4. N-Formyl groups are also introduced into the cell walls of Micrococcus lysodeikticus by hot formamide, but this change increases only slightly their already great sensitivity to lysozyme. N-Acetylation also increases sensitivity to lysozyme.

Bacillus megaterium↗
PubMed2005

The mechanism of formamide hydrolysis in water from ab initio calculations and simulations.

The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule. Its interaction with the bulk has been treated with the aid of a dielectric continuum model. Molecular dynamics simulations at the combined density functional/molecular mechanics level have been carried out in parallel to better understand the structure of the reaction intermediates in aqueous solution. Overall, the most favored mechanism predicted by our study involves two reaction steps. In the first step, the carbonyl group of the formamide molecule is hydrated to form a diol intermediate. The corresponding transition structure involves two water molecules. From this intermediate, a water-assisted proton transfer occurs from one of the hydroxy groups to the amino group. This reaction step may lead either to the formation of a new reaction intermediate with a marked zwitterionic character or to dissociation of the system into ammonia and formic acid. The zwitterionic intermediate dissociates quite easily but its lifetime is not negligible and it could play a role in the hydrolysis of substituted amides or peptides. The predicted pseudo-first-order kinetic constant for the rate-limiting step (the first step) of the hydrolysis reaction at 25 degrees C (3.9x10(-10) s(-1)) is in excellent agreement with experimental data (1.1x10(-10) s(-1)).

Computer Simulation↗
PubMed1992

Formamide modified polyacrylamide gels for DNA sequencing by capillary gel electrophoresis.

Compressions are occasionally found during the separation of DNA sequencing fragments, particularly in G/C-rich regions and in gels operated at room temperature. Addition of at least 10% formamide to urea/polyacrylamide sequencing gels improves the denaturing capacity of the gel, minimizing compressions. Addition of 20% or more formamide decreases the separation rate, theoretical plate count, and resolution for normally migrating fragments. An optimum concentration of 10% formamide improves resolution of compressed regions without degrading the other characteristics of the gel. Operation of gels at room temperature simplifies the engineering associated with automated sequencers based on capillary gel electrophoresis.

Base Sequence↗
PubMed2004

Formamide as solvent for capillary zone electrophoresis.

A comprehensive investigation of a number of aspects when using formamide as background electrolyte solvent in capillary zone electrophoresis was presented. It included (i) the change of the ion mobility with ionic strength, (ii) the influence of the ionic strength on diffusion coefficients, and (iii) on the separation efficiency expressed by the maximum reachable plate numbers (when only longitudinal diffusion contributed to zone broadening), (iv) the effect of the solvent on pKa values (taken from the literature) of neutral and cation acids, (v) the establishment of the a pH scale in formamide by dissolving acids with known pKa values and their salts at defined proportion (thus circumventing the problem of calibrating the pH meter), (vi) the agreement between the experimentally derived and the theoretical dependence of the effective mobility on pH, (vii) the uptake of water of this hygroscopic solvent from the humidity of the environment and its consequence to the ion mobilities, pKa values, and the chemical stability of the solvent (e.g., hydrolysis), and finally (viii) the use of conductivity and indirect UV absorption to enable detection of analytes below the optical cutoff of formamide.

Diffusion↗
PubMed1996

Cell-free extract(s) of Pseudomonas putida catalyzes the conversion of cyanides, cyanates, thiocyanates, formamide, and cyanide-containing mine waters into ammonia.

Our isolate, Pseudomonas putida, is known to be capable of utilizing cyanides as the sole source of carbon (C) and nitrogen (N) both in the form of free cells and cells immobilized in calcium alginate. In the present study, the cell-free extract(s) were prepared from the cells of P. putida grown in the presence of sodium cyanide. The ability of enzyme(s) to convert cyanides, cyanates, thiocyanates, formamide and cyanide-containing mine waters into ammonia (NH3) was studied at pH 7.5 and pH 9.5. The kinetic analysis of cyanide and formamide conversion into NH3 at pH 7.5 and pH 9.5 by the cell-free extract(s) of P. putida was also studied. The Km and Vmax values for cyanide/formamide were found to be 4.3/8 mM and 142/227 mumol NH3 released mg protein-1 min-1 respectively at pH 7.5 and 5/16.67 mM and 181/434 mumol NH3 released mg protein-1 h-1 respectively at pH 9.5. The study thus concludes that the cell-free extract(s) of P. putida is able to metabolize not only cyanides, cyanates, thiocyanates, and formamide but also cyanide-containing mine waters to NH3.

Ammonia↗