Analysis of tritium-labeled glycine and alanine using 3H-NMR

A method for analysis of three-component isotopic mixtures of tritium-labelled glycine and alanine in D2O solutions has been developed on the basis of high resolution 3H NMR spectra at 266.8 MHz. Determined were composition of the mixtures in molar per cent, as well as geminal and vicinal coupling constants (2JGly3H,H = -16.4 +/- 0.2 Hz; 2JAla3H,H = -14.0 +/- 0.5 Hz; 3JAla3H,H = 7.6 +/- 0.2 Hz) and isotopic shifts (0.21 +/- 0.001 ppm for glycine; 0.026 +/- 0.001 ppm for alanine).     

Secondary structure of histones in solution

The secondary structure of histones H2B and H3 from calf thymus has been quantitatively studied in heavy water solutions in a wide range of histone concentrations, pD, and concentrations of sodium chloride by an infrared spectroscopy method. Also, the interactions between molecules of different histones in equimolar mixtures H2A-H2B, H2A-H3, H2A-H4, H2B-H3, H2B-H4, H3-H4, and H2A-H2B-H3-H4 have been investigated using the same method. For H2B and H3 conditions favourable for aggregation have been shown to induce the formation of pleated sheet structure. When the pD and concentration of NaCl are in a physiological range, the secondary structure of H2B and H3 contains about 15% of alpha-helix, 4% of parallel pleated sheet structure, 14% of antipatallel pleated sheet structure in H2B and 18% in H3. For mixtures in all cases, except H2A-H4, there is an interaction between molecules of different histones followed by a reduction of the antiparallel pleated sheet structure content. The data on the secondary structure of histones in different states (under self-association, in mixtures, in nucleosomes, and in chromatin) have been discussed and it is suggested that: 1) the secondary structure of histones in chromatin is essentially similar to that in the state of self-association; 2) in the core nucleosome particle the quantity of DNA (in nucleotide pairs), and the quantities of alpha-helix and antiparallel pleated sheet structure (in peptide groups) satisfy the relation 1 : 1 : 1.     

Phage viability in organic media: insights into phage stability

The stability of the filamentous phages derived from phagemid pG8H6 has been examined in a range of solvents and solvent mixtures. The results show an enhanced capacity to infect E. coli after exposure to various organic solvent-water mixtures. The dependence of stability upon solvent hydrophobicity was demonstrated. Furthermore, conditions have been identified which should allow the application of phage display libraries based upon pG8H6 in organic media.     

Effect of H2S on the formation of organic compounds from C, N,H, S model atmospheres submitted to a glow discharge.

H2S has been often invoked as the initial source of sulfur in prebiotic evolution, and several sulfur-containing compounds have been proposed as intermediates in the primordial synthesis of biologically relevant sulfur-containing chemicals. The possibilities of synthesis of the principal key intermediates by glow discharges in CH4-N2-H2S mixtures is studied. It is shown that synthesis of important intermediates such as HCN, (CN)2, CHCCN and CH3SH is possible from such mixtures if the amount of H2S is not more than 10%. For higher amounts of H2S, the syntheses are strongly inhibited.     

Spontaneous vesiculation of aqueous lipid dispersions

The swelling properties of lipid mixtures consisting of phosphatidylcholine and a charged single-chain detergent have been studied. The work presented here is confined to lipid mixtures forming smectic lamellar phases in H2O. These mixtures exhibit continuous swelling with increasing water content, provided the surface charge density exceeds a threshold value of about 1-2 microC/cm2. In excess H2O, such mixtures undergo spontaneous vesiculation: unilamellar vesicles form spontaneously when excess H2O or salt solutions of moderate ionic strength (I less than 0.2) are added to the dried film of such lipid mixtures. The resulting dispersion of unilamellar vesicles is usually polydisperse. Its average size depends on the detergent/phospholipid mole ratio, decreasing with increasing detergent content. It is shown that in the phase diagram of three-component systems consisting of phosphatidylcholine, a charged single-chain detergent, and excess H2O there is a compositional range, though narrow, within which the small unilamellar vesicle (diameter less than 100 nm) is the thermodynamically most stable structure. This behavior is characteristic of charged, single-chain detergents of 14 and more C atoms. Many pharmacologically active compounds are amphiphilic and surface-active, and as such, they will orient at phospholipid-water interfaces, imparting a net surface charge to neutral lipid surfaces. It is shown that such drugs exhibit detergent-like action. Mixed films of phosphatidylcholine and a pharmacologically active compound behave similarly to phosphatidylcholine-detergent mixtures: they undergo spontaneous vesiculation when excess H2O or salt solutions of moderate ionic strength are added. In this case, the drug itself induces vesiculation; possible pharmacological implications of this finding are discussed.     

A kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues in DNA.

The kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues of DNAs with different G-C content as well as in corresponding dNMP mixtures have been carried out. The present results show that 1H--3H exchange in DNA is retarded (as compared to the exchange in dNMP mixtures) to a lesser extent (Kret =2.4-2.8) than in RNA (Kret=6-8). The degree of retardation in these polymers is practically independent of their nucleotide composition. Assuming the ylide mechanism of exchange reaction it is suggested that the lower rate of 1H leads to 3H exchange in C(8) H-groups of purinic residues in polynucleotides of A-form (RNA and other polyribonucleotides) as compared to those of B-form (DNA and other polydeoxyribonucleotides) might be accounted for by decreased availability of C(8) H-groups for OH-ions of the solvent due to a different microenviroment of these groups in A- and B-type helixes.     

Disturbing effect of perdeuterated fatty acids used as probes in phospholipid monolayers

Surface pressure-area per molecule isotherms have been obtained for tetradecanoic acid (C₁₄H) and perdeuterated tetradecanoic acid (C₁₄²H) and their mixtures at air/water interface. The perdeuterated fatty acid was then used as a probe to evaluate the consequent disturbing effect of perdeuteration in dimyristoyl (DMPC) and dipalmitoyl (DPPC) phosphatidylcholine monolayers used as model membranes. It appears from the analysis of the transition pressure variation versus mole fraction of the probe that C₁₄H/C₁₄²H mixtures behave ideally, whereas mixtures of DMPC-C₁₄²H or DMPC-C₁₄H and DPPC-C₁₄²H lead to negative azeotropic phase diagrams showing that the disturbing isotopic effect of the probe is really negligible with respect to the hydrocarbon chain structure as can be seen from the phase diagram analysis. According to these data, it seems that a perdeuterated lipid is suitable as a really almost non perturbing probe only if the latter constitutes the deuterated homologous of the system forming molecules under study.     

Development of field modulation in a split-field drift tube for high-throughput multidimensional separations

A field modulation approach for high-throughput ion mobility/time-of-flight analyses of complex mixtures has been developed using a split-field drift tube. In this approach, complex mixtures of peptides, such as those that arise from tryptic digestion of protein mixtures, are separated by nanocolumn liquid chromatography, ionized by electrospray ionization, and analyzed by ion mobility/time-of-flight techniques. The split-field drift tube allows parent ions to be separated based on differences in their low-field mobilities through the first-field region before entering the second region. For increased throughput, the magnitude of the field in the second region can be modulated throughout an LC separation in order to favor transmission of different types of ions: parent ions at low fields; fragments from primarily [M+3H]3+ peptides at moderate fields; or, fragmentation of [M+3H]3+ and [M+2H]2+ species at higher fields. We demonstrate the approach with two examples: a mixture of tryptic peptides from digestion of hemoglobin; and a complex mixture of tryptic peptides from digestion of human plasma.     

Effect of H(2)-CO(2) on Methanogenesis from Acetate or Methanol in Methanosarcina spp

Growth of Methanosarcina sp. strain 227 and Methanosarcina mazei on H(2)-CO(2) and mixtures of H(2)-CO(2) and acetate or methanol was examined. The growth yield of strain 227 on H(2)-CO(2) in complex medium was 8.4 mg/mmol of methane produced. Growth in defined medium was characteristically slower, and cell yields were proportionately lower. Labeling studies confirmed that CO(2) was rapidly reduced to CH(4) in the presence of H(2), and little acetate was used for methanogenesis until H(2) was exhausted. This resulted in a biphasic pattern of growth similar to that reported for strain 227 grown on methanol-acetate mixtures. Biphasic growth was not observed in cultures on mixtures of H(2)-CO(2) and methanol, and less methanol oxidation occurred in the presence of H(2). In M. mazei the aceticlastic reaction was also inhibited by the added H(2), but since the cultures did not immediately metabolize H(2), the duration of the inhibition was much longer.     

Analysis of membrane lipids by 500 MHz 1H NMR

A nondestructive method has been developed for rapid analysis of lipid content of membrane extracts based on high field proton NMR spectroscopy. Lipid extraction is done by stepwise sonication of purified membranes into chloroform:methanol:water mixtures, and 1H spectra are recorded at 35 degrees C on final preparations consisting of at least 1 mg dried lipid solubilized in 2:1 CD3OD:CDCl3. Spectral peaks of lipid mixtures are assigned to lipid classes using a data base of standard lipid characteristic resonances derived from purified single membrane lipids and known mixtures of them. Peak intensities of characteristic peaks yield ratios of various lipids such as cholesterol:phospholipid and phosphatidylcholine:phosphatidylethanolamine, degree of unsaturation, average acyl chain length, total glycerol lipid content, and presence or absence of particular lipids, such as glycolipids or lysolipids. This procedure of membrane lipid analysis has been verified using known mixtures of purified standard lipids.     

Polymorphism of pyridinium amphiphiles for gene delivery: influence of ionic strength, helper lipid content, and plasmid DNA complexation

Two double-tailed pyridinium cationic amphiphiles, differing only in the degree of unsaturation of the alkyl chains, have been selected for a detailed study of their aggregation behavior, under conditions employed for transfection experiments. The transfection efficiencies of the two molecules are remarkably different, especially when combined with 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) as helper lipid. The phase behavior of the cationic amphiphile/DOPE mixtures have been studied using (31)P- and (2)H-NMR (on deuterated cationic amphiphiles) as main techniques, to monitor independently the behavior of the two components. In water, the lamellar organization is dominant for both the surfactants in their mixtures with the helper lipid. In HEPES saline buffer (HBS), the mixtures of the unsaturated surfactant form inverted phases and, in particular, stable H(II) phases for DOPE contents > or =30 mol %. By contrast, the saturated surfactant does not form homogeneously mixed inverted phases in mixtures with DOPE at room temperature. However, mixed inverted phases are observed for this system at higher temperatures and, after mixing has been achieved by heating, the metastable mixed phases remain present for several hours at 5 degrees C. At 35 degrees C the dominant phase is the cubic phase. The lipoplex composed of equimolar mixtures of the unsaturated surfactant with DOPE and plasmid DNA was found to be organized in highly curved bilayers.     

Response of the phosphatidylcholine headgroup to membrane surface charge in ternary mixtures of neutral, cationic, and anionic lipids: a deuterium NMR study.

Deuterium nuclear magnetic resonance (2H NMR) spectroscopy was used to investigate the response of the phosphatidylcholine headgroup of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) to changes in surface electrostatic charge in membranes consisting of ternary mixtures of lipids. DMPC was deuterated at the choline alpha- and beta-methylene segments. The membrane surface charge was manipulated by the simultaneous addition of cationic didodecyldimethylammonium bromide (DDAB) and anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) to neutral DMPC. Addition of increasing amounts of DDAB caused a progressive decrease (increase) in the 2H NMR quadrupole splitting from DMPC-alpha-d2 (DMPC-beta-d2). Addition of increasing amounts of DMPG caused a progressive increase (decrease) in the quadrupole splitting from DMPC-alpha-d2 (DMPC-beta-d2). Qualitatively, the 2H NMR quadrupole splitting charge response exhibited the same main features for ternary mixtures of DDAB/DMPG/DMPC and binary mixtures of DDAB/DMPC or DMPG/DMPC. Quantitatively, however, the 2H NMR quadrupole splittings obtained from ternary mixtures did not coincide with those obtained from binary mixtures of nominally identical surface charge densities. Hence, the quadrupole splitting did not respond directly to the net membrane surface charge. Instead, the quadrupole splitting measured for a given ternary lipid composition could be reproduced by summing the individual effects of the charged lipids in binary mixtures, weighted according to their appropriate mole fractions.     

Carbon and energy yields in prebiotic syntheses using atmospheres containing CH4, CO and CO2

Yields based on carbon are usually reported in prebiotic experiments, while energy yields (moles cal-1) are more useful in estimating the yields of products that would have been obtained from the primitive atmosphere of the earth. Energy yields for the synthesis of HCN and H2CO from a spark discharge were determined for various mixtures of CH4, CO, CO2, H2, H2O, N2 and NH3. The maximum yields of HCN and H2CO from CH4, CO, and CO2 as carbon sources are about 4 X 10(-8) moles cal-1.     

An octamer of histones H3 and H4 forms a compact complex with DNA of nucleosome size.

Equimolar mixtures of histones H3 and H4 have been reconstituted onto DNA of nucleosome core size. Two distinct complexes are formed in a relative abundance that depends on the starting ratio of H3 + H4 to DNA. One of these complexes contains two H3-H4 dimers for each DNA molecule, and has a sedimentation coefficient of 7.5S. The other complex contains an octamer consisting of four H3-H4 dimers, and has a sedimentation coefficient of 10.4S. On the basis of these measurements, we conclude that the octamer complex (but not the tetramer complex) is a fully folded, compact structure resembling the nucleosome.     

An optical method for the determination of the isotopic composition of 1H2O/2H2O mixtures: Eu3+ luminescence lifetimes

A spectroscopic method employing pulsed dye laser instrumentation is described for the determination of the 1H2O/2H2O composition of aqueous solutions by the measurement of reciprocal excited state lifetimes of EuEDTA-. The reciprocal lifetimes, gamma-1, of the 1H2O/2H2O mixtures increase linearly with the mole fraction of 1H2O. For EuEDTA- the relationship between gamma-1 and the mole fraction, chi H, of 1H2O in 1H2O/2H2O mixtures is expressed by the equation chi H = 0.37 gamma-1-0.152, with a sensitivity in chi H of +/- 0.02. The reciprocal lifetimes are independent of pH in the range 5.1 to 10.5, changes in ionic strength, and the type of buffer used in EuEDTA- containing solutions.     

Differential scanning calorimetry and 2H NMR studies of the phase behavior of gramicidin-phosphatidylcholine mixtures

The extents of two-phase coexistence in the phase diagrams of mixtures of gramicidin with 1,2-bis(perdeuteriopalmitoyl)-sn-glycero-3-phosphocholine (DPPC-d62) and with 1,2-bis(perdeuteriomyristoyl)-sn-glycero-3-phosphocholine (DMPC-d54) mixtures have been explored with differential scanning calorimetry (DSC) and deuterium nuclear magnetic resonance (2H NMR). For both systems, increased gramicidin content causes a decrease in transition enthalpy and a broadening of the peak in excess heat capacity at the transition. In DMPC-d54-based mixtures, the broadening is roughly symmetric about the pure lipid transition temperature. Addition of gramicidin to DPPC-d62 extends the excess heat capacity peak on the low-temperature side, resulting in a slightly asymmetric scan. Deuterium NMR spectra showing a superposition of gel and liquid-crystalline components, observed for both mixtures, indicate the presence of two-phase coexistence. For the DPPC-d62-based mixtures, two-phase coexistence is restricted to an approximately 2 degrees C temperature range below the pure transition temperature. For DMPC-d54-based mixtures, the region of two-phase coexistence is even narrower. For both mixtures, beyond a gramicidin mole fraction of 2%, distinct gel and liquid-crystal contributions to the spectra cannot be distinguished. Along with the broad featureless nature of the DSC scan in this region, this is taken to indicate that the transition has been replaced by a continuous phase change. These results are consistent with the existence of a closed two-phase region having a critical concentration of gramicidin below 2 mol%.     

Application of tritium high resolution NMR spectroscopy to analysis of tritium-labelled amino acids and peptides

Summary A method has been developed for the qualitative and quantitative analysis of complex isotopic mixtures of tritium-labelled amino acids and peptides by using high resolution³H NMR spectroscopy at 266.8 MHz. Determined were tritium distribution in alanine, glycine, tryptophan and 4-hydroxyproline amino acids, as well as in glycine and valine residues of peptides. Approaches have been worked out for the determination of spin coupling constants and isotope chemical shifts for the strongly coupled nonequivalent atoms of the methylene groups.     

2D NMR studies of aminoglycoside antibiotics. Use of relayed coherence transfer for 1H resonance assignment and in situ structure elucidation of amikacin derivatives in reaction mixtures

Phase-sensitive 2D 1H/1H COSY spectra can be used to identify the structures of individual pure specimens of the aminoglycoside antibiotic amikacin and its N-hemisuccinyl derivatives. However, even at 500 MHz the 2D chemical shift dispersion does not allow for unambiguous assignment of all cross-peaks. By use of 2D relayed coherence transfer experiments (RELAY) optimized to detect two-step 1H/1H scalar interactions in which one of the J-values is small, sufficient additional correlations can be obtained from the frequency-isolated resonances to allow facile tracing of all scalar connectivities. Complete assignments of the 1H NMR spectra of amikacin, its 6'-N-hemisuccinamide, and a novel bis(acylate) [gamma-N-(p-vinylbenzoyl)amikacin 6'-N-hemisuccinamide] were obtained for aqueous media. The NMR spectrum of amikacin free base was also assigned in dimethyl sulfoxide solution. The RELAY experiment can be extended to the analysis of reaction mixtures, which allows for the identification and resonance assignment of regioisomeric amikacin haptens in the mixture state. All of the N-monohemisuccinyl isomers of amikacin have been identified in reaction mixtures through the RELAY experiment. The relative reactivities of the amino functions of amikacin toward acylating agents were found to be 6'-N greater than 3-N equal to or greater than 3"-N equal to or greater than gamma-N. However, this reactivity order is altered after the initial acylation event.     

Computer analysis of double-labeled two-dimensional electrophoresis gels

A computerized process for the automatic analysis of double-label autoradiography after two-dimensional polyacrylamide gel electrophoresis has been developed. Matching fluorographs and autoradiographs produced from gels containing 3H- and 14C-labeled proteins are digitized by a rotating drum densitometer and analyzed by the Man-computer Interactive Data Analysis System III. This system locates corresponding protein spots in the films with edge-detection algorithms, converts spot density readings to isotopic disintegrations by reference to standard curves, and computes a 3H:14C ratio for each spot in the gels. On the average, calculated ratios are accurate to approximately 9% for test strips of polyacrylamide gel containing uniform mixtures of 3H and 14C. Values obtained for two-dimensional gels containing n protein spots with a known 3H:14C ratio of 8.6 +/- 0.1 are as follows: 8.1 +/- 1.4 (n = 268), 8.8 +/- 2.1 (n = 278), 9.1 +/- 1.7 (n = 245), and 8.8 +/- 2.2 (n = 223). The computer process greatly reduces the time required to precisely compare two complex protein mixtures and has sufficient precision to detect a doubling in the biosynthesis of any individual protein.