Phosphate catalyzed exchange rates of NH-N protons of DNA

We have studied the catalysis of the exchange of the hydrogen-bonded NH-N protons of the short DNA helix (d-CCAAGCTTGG)2 by phosphate addition. The NH exchange rates were monitored by the line widths of the corresponding NH resonances in the 1H nmr spectra. The exchange catalyst phosphate is most effective on the exchange rate of the terminal CG1 base pairs. However, all internal base pairs are also moderately affected by phosphate which suggests an exchange mechanism governed by a fast equilibrium between opened and closed states of the duplex. Within the limits of error the same effectiveness of phosphate on the exchange rate of all internal NH-N protons has been observed. With the exception of the terminal base pairs, no sequence and/or position specificity of the exchange rates of the NH-N protons of the base pairs has been found.     

Nuclear magnetic resonance study of muscle water protons in muscular dystrophy of chickens

Using the pulsed nuclear magnetic resonance (NMR) spectroscopy, the spin-lattice (T1) and the spin-spin (T2) relaxations times of water protons from samples of pectoralis major muscles of normal (line 412) and homozygous dystrophic (line 413) chickens were measured. Both the T1 and T2 were significantly increased (P less than 0.05) in the dystrophic muscles. The mean values of the relaxation times are given +/- S.D. The T1 values were 654 +/- 22 msec in normal and 692 +/- 41 msec in dystrophic muscles. The T2 values for normal and dystrophic muscles were 39 +/- 4 msec and 52 +/- 7 msec, respectively. Although the water content of dystrophic muscles (78.9 +/- 0.6%) determined by gravimetric methods was significantly higher than normal muscles (74.9 +/- 1.1%), this difference in tissue hydration could not explain quantitatively the increase of T1 and T2 values in the dystrophic muscles. The results of the measurements of the relaxation times seem to suggest that there are changes in the composition and/or conformational state of the proteins.     

Nuclear magnetic resonance studies on transfer ribonucleic acid: assignment of AU tertiary resonances.

The hydrogen-bonded ring NH nuclear magnetic resonance (NMR) spectra of several transfer ribonucleic acid (RNA) species have been examined with particular emphasis on the extreme low-field portion. Betwen --13.8 and --15 ppm there are two extra resonances which are not derived from cloverleaf base pairs. A combined approach involving undermodified tRNAs, chemical modification, and hairpin fragment studies has assigned the T54--A58 resonance at --14.3 ppm in yeast tRNAPhe and Escherichia coli tRNA1 Val., the U8--A14 resonance has been assigned at --14.3 ppm, and the s4U8--A14 resonance in bacterial tRNAs has been assigned at --14.9 ppm. The T54--A58 resonance shifts between --14.3. and --13.8 ppm depending on the surrounding nucleotide sequence in the ribothymidine loop.     

Nuclear magnetic resonance studies on the tertiary folding of transfer ribonucleic acid: assignment of the 7-methylguanosine resonance.

Analysis of the low-field nuclear magnetic resonance (NMR) spectra of several class 1 D4V5 transfer ribonucleic acid (tRNA) species containing 7-methylguanosine in their variable loops reveals a set of six to seven tertiary base pair resonances, one of which is always located at ca. --13.4 ppm. Other tRNA species which do not contain 7-methyl-guanosine do not contain the tertiary resonance at --13.4 ppm. Chemical removal of 7-methylguanosine from several tRNAs containing the same dihydrouridine (DHU) helix sequence as yeast tRNAPhe results in the loss of the --13.4-ppm tertiary resonance. In the initiator methionine tRNA, which contains a different DHU helix sequence, the 7-methylguanosine hydrogen bond has been assigned at --14.55 ppm by chemical removal of this residue. In these experiments the aromatic C8H proton of 7-methylguanosine was also assigned (--9.1 ppm). The unexpectedly low-field position of the 7-methylguanosine resonance is explained by the deshielding effect of the delocalized positive charge in this nucleoside.     

Conformation and interaction of short nucleic acid double-stranded helices. II. Proton magnetic resonance studies on the hydrogen-bonded NH-N protons of ribosyl ApApGpCpUpU helix.

A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1 degree C, 0.17 M Na+, pH 7.6 with 10 mM phosphate-0.1 mM EDTA in H2O, three proton resonances are found in the low-field region with the following chemical shifts and line widths at half-height: 13.2 ppm (80 Hz), 13.5 ppm (30 Hz), and 14.2 ppm (44 Hz). The existence of these resonances indicates the formation of a self-complementary, hydrogen-bonded duplex under these conditions. Upon elevation of temperature, these three resonances sequentially broaden and finally all disappear near 35 degrees C. Unambiguous assignments of these three resonances can be made to the terminal A(1)-U(6) pairs, interior A(2)-U(5) pairs, and to the middle G(3)-C(4) pairs. The assignments were based on (i) the differential sensitivities of the line widths of these resonances to thermal variation, as well as on (ii) a comparison of the computed chemical shifts with the observed chemical shifts. The quantitative aspects of the NH proton transfer between helix, coil, and water are discussed in relationship to the line widths of these resonances and the lifetime of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A'-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A'-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of (A2GCU2)2.     

Nuclear magnetic resonance spectra of lipoteichoic acid

Lipoteichoic acid acids with a range of chemical compositions have been studied using 1H; 13C- and 31P-nuclear magnetic resonance. Proton spectroscopy provided a rapid method for demonstrating whether alanine in a sample is covalently bound to the polyglycerophosphate chains and for monitoring hydrolysis of alanine. The nature of sugar substituents can be determined, with some limitations, from the 13C spectra, and the proportions of glycerol residues substituted by alanine and sugar can be measured. The 31P spectra of lipoteichoic acid provided information about both the degree of substitution and the distribution of the substituent along the polyglycerophosphate chain, except when the substituent was galactose. The polyglycerophosphate chains were shown to undergo rapid internal rotation and no evidence for tertiary structure was found either in the presence or absence of magnesium ions. Magnesium ions exchange rapidly between the bound and free state and the binding constant to lipoteichoic acid of 64 M-1 is typical for monophosphates in aqueous solution. There was no evidence that alanine substitution affects the binding constant for magnesium ions.     

Hydrogen--deuterium exchange kinetics of the amide protons of oxytocin studied by nuclear magnetic resonance

The contribution of intramolecular hydrogen bonding to the solution structure of oxytocin was evaluated by study of amide hydrogen exchange rates in D2O by Fourier transform 1H NMR spectroscopy. Resolution enhancement filtering was employed in the determination of individual pseudo-first-order rate constants. Apparent barriers to exchange of 0.5 and 0.6 kcal mol-1 were measured for Asn5 and Cys6 peptide NH, respectively. The slowing is best explained by steric hindrance to solvent access in the case of Asn5, while for the Cys6 participation in a weak intramolecular hydrogen bond is possible. Fourfold acceleration of base-catalyzed exchange was observed for Tyr2 NH; it is proposed that this is the result of electronic effects induced by hydrogen bonding of Cys1 C=0, either to Cys6 NH or to the N-terminal amino group. Exchange proceeds near the random coil limit for each of the remaining residues. Comparison with exchange data for the model tripeptide N-acetyl-L-prolyl-L-leucylglycinamide demonstrates no evidence of noncovalent association of the tocin ring with the tripeptide tail of the hormone.     

Nuclear magnetic resonance signal assignments of purified [13C]methyl-enriched yeast phenylalanine transfer ribonucleic acid

Yeast tRNA Phe, enriched in carbon-13 specifically at the naturally occurring methyl groups, has been produced through biosynthesis, then purified, and analyzed. Transfer RNA Phe was purified from the [13C]methyl-enriched, unfractionated tRNA that had been extracted from a methionine auxotroph of Saccharomyces cerevisiae [Agris, P. F., Kovacs, S. A. H., Smith, C., Kopper, R. H., & Schmidt, P. G. (1983) Biochemistry 22, 1402-1408]. The yeast had been grown in minimal medium supplemented with [13C]methylmethionine. Transfer RNA Phe purity and the full extent of nucleoside modification were confirmed by high-performance liquid chromatography of constituent nucleosides with simultaneous UV spectral identification and quantitation. Mass spectometry of [13C]methyl-enriched nucleosides and NMR of the tRNA indicated an enrichment of at least 70 atom %. Twelve resolved and prominent carbon-13 NMR signals from the tRNA were seen between 10 and 60 ppm. These have been assigned to 13 of the 14 naturally occurring methyl groups. However, the partially resolved signals assigned to the two 5-methylcytidines could not be assigned to their specific nucleoside positions of either 40 or 49 in the molecule. In addition, the partially resolved signals of the two methyl esters of wybutosine could not be distinguished. The methyl group found not to be enriched with 13C is bound to the ring carbon in the hypermodified nucleoside wybutosine (Y). A 13th enriched signal downfield (120.9 ppm) has been assigned to one of the two carbons added to guanosine to form the third ring in the biosynthesis of Y. The 13C enrichment of this ring carbon demonstrates its origin from the methionine methyl group.(ABSTRACT TRUNCATED AT 250 WORDS)     

Nuclear magnetic resonance study of sphingomyelin bilayers

Bilayers of D-erthro-(N-stearoylsphingosyl)-1-phosphocholine (C18-SPM), previously characterized by differential scanning calorimetry [Bruzik, K. S., & Tsai, M.-D. (1987) Biochemistry 26, 5364-5368] in various phases, were studied by means of wide-line 31P, 2H, high-resolution 13C CP-MAS, and 1H MAS NMR. The fully relaxed gel phase of C18-SPM at temperatures below 306 K displayed 31P NMR spectra characteristic of the rigid phase with frozen rotation of the phosphocholine head group. Three other gel phases existing in the temperature range 306-318 K displayed spectra with incompletely averaged axially symmetric powder line shapes and were difficult to differentiate on the basis of their 31P NMR spectra. The gel-to-gel transition at 306 K was found to be fully reversible. The main phase transition at 318 K resulted in the formation of the liquid-crystalline phase for which spectra with axially symmetric line shapes of uniform width were obtained, regardless of the nature of the starting gel phase. 13C CP-MAS NMR spectra revealed significant differences in the molecular dynamics of sphingomyelin in various phases. All carbon atoms of the polar head group in the liquid-crystalline phase gave rise to a separate resonance lines. Numerous carbon atom signals were doubled in the stable phase, demonstrating the existence of two slowly interconverting conformers.     

Nuclear magnetic resonance study of the isotope exchange of the proximal histidyl ring labile protons in hemoglobin A. The exchange rates and mechanisms of individual subunits in deoxy and oxy-hemoglobin

Proton nuclear magnetic resonance spectroscopy has been used to investigate the rates and mechanism of exchange with deuterium of the proximal histidyl imidazole labile ring proton in deoxy and oxy-hemoglobin A. The resolved signals for the two subunits indicate dynamic heterogeneity, with the exchange rate always faster in the alpha than the beta subunits, suggesting a lower dynamic stability for the alpha subunit. The activation energy for the exchange in both subunits (approximately 25 kcal; 1 cal = 4.184 J) indicates that exchange proceeds via an intermediate far from denaturation or global unfolding. The pH profiles for both hemoglobin states reflect the EX2 mechanism for both subunits. While the base catalysis expected for an iron-bound imidazole is observed in all cases, there are important differences in both rates and mechanisms between the subunits. In deoxy-hemoglobin, both base-catalyzed and water-assisted exchange contribute to the alpha subunit, but only the former to the beta subunit. For oxy-hemoglobin, the base-catalysis is retained for both subunits, but the slope is considerably less for the alpha relative to the beta subunit. Thus the two subunits in the two states of hemoglobin differ both in mechanisms and in the inherent dynamic stability reflected in any one mechanism. The relationships of the proximal histidyl ring NH exchange rates to previously characterized subsets of allosterically responsive protons in hemoglobin A is briefly discussed.     

Hydrogen exchange of individual amide protons in the E. coli lac repressor DNA-binding domain: a nuclear magnetic resonance study

Proton exchange in lac repressor headpiece was studied by COSY and 2D NOE spectroscopy. The exchange rates of amide protons, stabilized by the hydrogen bonds of the three alpha-helices of the headpiece, could be determined quantitatively. The exchange rates in these helices showed repetitive patterns of about three to four residues. A correlation with the position of the amide proton in the interior or the exterior of the alpha-helix of the protein was found. The exchange data strongly support the validity of the three-dimensional structure, as determined recently (Kaptein, R. et al., J. Mol. Biol. 182, 179-182 (1985)).     

Nuclear magnetic resonance studies of exchangeable protons. II. The solvent exchange rate of the indole nitrogen proton of tryptophan derivatives.

The exchange rate of the indole nitrogen proton with solvent water protons was measured as a function of pH and temperature for tryptophan, N-methyl tryptophan, glycyl tryptophan, tryptophanamide, tryptophylglycine, and tryptophylglycyl glycine. The nmr observation was by long-pulse Fourier transform methods, and kinetics were inferred from saturation recovery, H₂O transfer of saturation, and linewidth. There are observable differences between the rates of these compounds, but all are describable within a factor of two by specific acid and base-catalyzed rates k_H = 100 and k_OH = 10⁸ 1/mol-sec at 27°C. It is concluded that this behaviour is representative of this proton on the indole side chain in a random-chain peptide exposed to water.