On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. I. Proton shifts in the ribose ring of pyrimidine nucleosides as a function of the torsion angle about the glycosyl bond

Molecular orbital computations are performed on the different contributions to the variation of the chemical shifts of the non-exchangeable protons of the ribose ring in pyrimidine nucleosides as a function of the torsion angle X_CN about the glycosyl bond. They show that the ring current effects are negligible, that the contribution of the atomic diamagnetic anisotropy is important for protons which come at very short distances to the anisotropic group (C₂ = 0₂) and that the polarization effect may have a determining influence on the sign of the variation of the chemical shift. The theoretical results are discussed in relation to the experimental findings on the differences between the chemical shifts of the ribose protons of pyrimidine nucleosides methylated at C₅ and C₆.     

A proton magnetic resonance investigation of the glycosyl torsion angle of uracil nucleosides and nucleotides.

The use of line-shape decomposition techniques permitted the small 5-bond (5-J51') and 4-bond (4-J61') proton-proton coupling constants of a series of uracil nucleosides and nucleotides to be determined accurately. From an analysis of these coupling constants we have determined that the uracil base is in a predominantly anti conformation in aqueous solution and the mean position is not substantially altered by phosphate substitution at the 2', 3', or 5' positions, by changing the furanose stereochemistry from a ribose to a deoxyribose or an arabinose, or by an increase in temperature of 43 degree C.     

Ab-inito quantum mechanical calculations of NMR chemical shifts in nucleic acids constituents. II. Conformational dependence of the 1H and 13C chemical shifts in the ribose

The magnetic shielding constant of the different 13C and 1H nuclei of a deoxyribose are calculated for the C2' endo and C3' endo puckerings of the furanose ring as a function of the conformation about the C4'C5' bond. For the carbons the calculated variations are of several ppm, the C3' endo puckering corresponding in most cases to a larger shielding than the C2' endo one. For the protons the calculated variations of chemical shifts are all smaller than 1.3 ppm, that is of the order of magnitude of the variation of the geometrical shielding produced on these protons by the other units of a DNA double helix, with a change of the overall structure of the helix. The computations carried out on the deoxyribose-3' and 5' phosphates for several conformations of the phosphate group tend to show that the changes of conformation of the charged group of atoms produce chemical shift variations smaller than the two conformational parameters of the deoxyribose itself. The calculations carried out for a ribose do give the general features of the differences between the carbon and proton spectra of deoxynucleosides and nucleosides. The comparison of the measured and calculated phosphorylation shifts tend to show that the counterion contributes significantly, for some nuclei of the deoxyribose, to the shifts measured. The calculated magnitude of this polarization effect on carbon shifts suggests a tentative qualitative interpretation of carbon spectra of the ribose part of DNA double helices.     

Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.

Structural comparisons have led to the suggestion that the conformational rearrangement that would be required to change A-DNA into the TA-DNA form of DNA observed in the complex with the TATA box binding protein (TBP) could be completed by modifying only the value of the glycosyl bond chi by approximately 45 degrees. The lack of a high number of crystal structures of this type makes it difficult to conclude whether a smooth transition from A-DNA to TA-DNA can occur without disrupting at any point either the Watson-Crick base pairing or the A-DNA conformation of the backbone. To explore the possibility of such a smooth transition, constrained molecular dynamics simulations were carried out for the double-stranded dodecamer d(GGTATATAAAAC), in which a transition from A-DNA to TA-DNA was induced by modifying only the chi angle values. The results demonstrate the feasibility of a continuous path in the A-DNA to TA-DNA transition. Varying extents of DNA curvature are also attainable, by maintaining the A-DNA backbone structure and Watson-Crick hydrogen bonding while changing the chi angle value smoothly from that in A-DNA to one corresponding to B-DNA.     

Carbon-13 NMR in conformational analysis of nucleic acid fragments. 4. The torsion angle distribution about the C3''-O3'' bond in DNA constituents.

Carbon-13 and proton NMR spectra of a series of oligodeoxynucleotides (d(CT), d(CC), d(TA), d(AT), d(CG), d(GC), d(AG), d(AAA), d(TATA) and d(GGTAAT] were measured at various temperatures. The three coupling constants that are related to the magnitude of backbone angle epsilon (J(C4'-P), J(C2'-P) and J(H3'-P] are analyzed in terms of a three-state equilibrium about this bond. Two epsilon (trans) angles occur, which differ in magnitude depending on the conformation (N or S) of the adjoining deoxyribose ring. The S-type deoxyribose ring is associated with a smaller epsilon (trans) angle: epsilon (t,S) = 192 degrees. The N-type deoxyribose ring is associated with a larger epsilon (trans) angle epsilon (t,N) = 212 degrees. The third rotamer participating in the conformational equilibrium, is a gauche(-) (epsilon (-] conformer and occurs exclusively in combination with the S-type sugar ring (epsilon (-,S) = 266 degrees). Within the limits of experimental error, the magnitude of these three angles appears to be independent of the particular base sequence, except in the case of d(CG) where a slightly larger epsilon (t,S) angle (197 degrees) is indicated. A simple equation is proposed which may be used to calculate the population of epsilon (t,S) conformer in cases where only J(H3'-P) is known.     

Effect of temperature and protonation upon the conformation of 2'-o-methyladenosine. Correlation of conformational parameters in purine nucleosides.

Proton magnetic resonance studies of 2'-o-methyladenosine in 2H2O have been carried out at variable temperature and p2H. The chemical shifts and H-H coupling constants are discussed in terms of the molecular conformation. Comparison of the data with those of adenosine reveals that 2'-O-methylation has little influence on the conformation. At neutral p2H where the adenine base is not protonated, the molecules favor a 2' endo, gauche-gauche conformation. Protonation of the base at the N(1) position leads to a decrease in the 2' endo, gauche-gauche bias. The data for 2'-O-methyladenosine and adenosine, as well as for several other purine derivatives, reveal the presence of a correlation between the sugar pucker and the C(5')-C(4') conformer distribution which is the inverse of the correlation previously reported for pyrimidine derivatives.     

Specificity of the enzymes of Salmonella O-antigen biosynthesis. 6. Synthesis of sugar nucleotides with glycosyl phosphate activation. Analogs of guanosine diphosphate mannose modified at position 6 ofthe purine ring

Interaction of alpha-D-mannopyranosyl phosphate with diphenyl phosphochloridate gave the trisubstituted pyrophosphate which was converted through the reaction with nucleoside 5'-phosphates into nucleoside 5'-(alpha-D-mannopyranosyl)pyrophosphates. The method was used for preparation of guanosine diphosphate mannose analogs derived from adenine, purine, 2-aminopurine, 2-amino-6-methoxypurine, 2-amino-6-chloropurine, and 2-amino-6-mercaptopurine. These analogs are necessary for study on substrate specificity of mannosyltransferases of Salmonella O-specific polysaccharides biosynthesis.     

Variation of nonexchangeable proton resonance chemical shifts as a probe of aberrant base pair formation in DNA

Variation of nonexchangeable proton resonance chemical shifts for deoxycytidine and deoxy-adenosine as a function of protonation and imino tautomer formation has been determined. Protonation induces downfield shifts of proton resonances whereas formation of the rare imino tautomer induces upfield shifts. Titration curves are constructed on the basis of spectrophotometrically determined pK values. Excellent fit is obtained between theoretical titration curves and experimental data, which indicates that chemical shifts of base protons may be used to quantitatively determine the relative concentrations of either rare imino tautomeric conformations or protonated base forms. These data may be utilized as an aid in the elucidation of the nature of hydrogen bonding between mismatched base pairs in DNA oligomers containing cytosine or adenine residues. These data, in conjunction with the oligonucleotide study of Patel et al. [Patel, D. J., Kozlowski, S.A., Ikuta, S., & Itakura, K. (1984) Biochemistry 23, 3218-3226], have been used to rigorously argue the existence of a "protonated" adenine residue in the A-C mismatch. This structure allows reconciliation of the NMR solution data with crystallographic data [Hunter, W.N., Brown, T., Anand, N.N., & Kennard, O. (1986) Nature (London) 320, 552-555], which support the protonated base pair.     

Influence of the glycosidic torsion angle on 13C and 15N shifts in guanosine nucleotides: Investigations of G-tetrad models with alternating syn and anti bases

Summary The effect of the glycosidic torsion angle on ¹³C and ¹⁵N shifts of the sugar and base moieties of guanosine nucleotides was investigated by comparing the sites in two model G-tetrad oligodeoxynucleotides that contain guanosine residues alternately with syn and anti bases. The sugar puckering has been shown to be C2-endo for both cases. It was observed that, for the instances with syn bases, the C1 through C4 carbons showed shifts that may be distinguished from those normally found in B-DNA-like structures. C1, C3 and C4 moved to lower field, while C2 moved to higher field. Effects of the change in glycosidic torsion angle were also seen in the shifts of base carbons and nitrogens in the five-membered ring portion of the base. Characterization of the shift variation associated with this conformational change may be useful in developing the use of ¹³C shifts as a tool in conformational analysis of oligonucleotides.Part of the work reported here derives from the Ph.D. Thesis of Karen L. Greene, Emory University, Atlanta, GA, 1991.     

Proton polarizability and proton transfer in histidine-phosphate hydrogen bonds as a function of cations present: ir investigations

(L -His)_n- dihydrogen phosphate systems are studied by ir spectroscopy in the presence of various cations and as a function of the degree of hydration. Ir continua indicate that (I) OH … N ? O^?…H⁺N (IIR) hydrogen bonds are formed and that these bonds show high proton polarizability, which increases from the Li⁺ to the K⁺ system. In the K⁺?system, His-P_i-P_i chains are formed, showing particularly high proton polarizability due to collective proton motion within both hydrogen bonds. The OH N ? O^?…H^?N equilibria are determined from ir bands. With the Li⁺ system, 55% of the protons are present at the histidine residues; this percentage is smaller with the Na⁺ system (41%), and amounts to only 32% with the K⁺ system. With the increasing degree of hydration the removal of the degeneracy of ν_as?PO^2?₃ vanishes, indicating loosening of the cations from the phosphates. Nevertheless, the hydrogen bond acceptor O atom becomes more negative; a shift of the equilibrium to the right is observed in the OH… N ? O^?…H⁺N bond. This is explained by the strong interaction of the dipole of the hydrogen bonds with the water molecules. All these results show that protons can be shifted easily in these hydrogen bonds due to their high proton polarizability. The transfer equilibria can be controlled easily by local electrical fields. In addition, these results may be of significance when phosphates interact with proteins.     

On the pH dependence of amide proton exchange rates in proteins.

We have analyzed the pH dependencies of published amide proton exchange rates (kex) in three proteins: bovine pancreatic trypsin inhibitor (BPTI), bull seminal plasma proteinase inhibitor IIA (BUSI IIA), and calbindin D9K. The base-catalyzed exchange rate constants (kOH) of solvent exposed amides in BPTI are lower for residues with low peptide carbonyl exposure, showing that the environment around the carbonyl oxygen influences kOH. We also examined the possible importance of an exchange mechanism that involves formations of imidic acid intermediates along chains of hydrogen-bonded peptides in the three proteins. By invoking this "relayed imidic acid exchange mechanism," which should be essentially acid-catalyzed, we can explain the surprisingly high pHmin (the pH value at which kex reaches a minimum) found for the non-hydrogen-bonded amide protons in the beta-sheet in BPTI. The successive increase of pHmin along a chain of hydrogen-bonded peptides from the free amide to the free carbonyl, observed in BPTI, can be explained as an increasing contribution of the proposed mechanism in this direction of the chain. For BUSI IIA (pH 4-5) and calbindin D9K (pH 6-7) the majority of amide protons with negative pH dependence of kex are located in chains of hydrogen-bonded peptides; this situation is shown to be consistent with the proposed mechanism.     

Properties of a human liver ribonuclease. Inhibition by polynucleotides and specificity for phosphodiester bond cleavage to yield purine nucleosides at the 5' termini.

A ribonuclease, purified 2500-fold from human liver, was found to be inactive against synthetic homopolynucleotides, whereas synthetic co-polymers containing adenylic acid were rapidly degraded. The specificity of the RNase is unique in that only purine residues, in a 5:4 ratio of guanylic to adenylic acid, are found at the 5' termini of the degradation products of yeast RNA. No specificity was observed at the 3' termini of the fragments. When analyzed by DEAE-cellulose chromatography, approximately 80% of the oligonucletoides were 4 to 11 residues in length. The hydrolysis of RNA by the liver enzyme, when examined in low ionic strength buffer, could be increased severalfold over control levels by the addition of polyamines. The enzyme was found to exist as two distinct species on sucrose gradients, with molecular weights of 128,000 and 14,000. However, the addition of spermidine to the gradients resulted in the recovery of all the enzyme activity as the smaller species. The polyamines were also shown to reverse the inhibition of the enzyme by the ordered polynucleotides, polyguanylic acid and polyadenylic acid. Inhibition of enzyme activity by the polyadenylic acid segment of various mammalian mRNAs was also demonstrated.     

Regulation of purine utilization in bacteria. VII. Involvement of membrane-associated nucleoside phosphorylase in the uptake and the base-mediated loss of the ribose moiety of nucleosides by Salmonella typhimurium membrane vesicles.

Although uridine and adenosine are converted by membrane-associated nucleoside phosphorylases to ribose-1-phosphate (ribose-1-P) and the corresponding bases (uracil and adenine), only ribose -1-P is accumulated within Salmonella typhimurium LT2 membrane vesicles. In accordance with these observations, no uptake is observed when the vesicles are incubated with the bases or nucleosides labeled in their base moieties. The vesicles lack a transport system for ribos-1-P, since excess ribose-1-P does not inhibit the uptake of the ribose moiety of uridine. In addition, there is no exchange with preaccumulatedribose-1-P. Thus, uridine, rather than ribose-1-P, must serve as the initially transported substrate. The uptake of the ribose portion of uridine is coupled to electron transport, and the levels to which ribose-1-P are accumulated may be reduced by adding various bases to the reaction mixtures. The bases appear to inhibit the uridine phosphorylase reaction and/or cause an efflux of ribose-1-P from the vesicles. This loss of ribose-1-P reflects the accumulation of nucleosides in the external medium after being synthesized within the membranes. Synthesis of the nucleosides from intravesicular ribose-1-P and exogenous base proceeds even though the bases are not accumulated by the vesicles. Furthermore, ribose-1-P cannot significantly inhibit uridine phosphorylase activity unless the membranes are disrupted. These observations indicate that the membrane-associated nucleoside phosphorylases may have a transmembranal orientation with their base and ribose-1-P binding sites on opposite sides of the membranes. Such an asymmetric arrangement of these enzymes may facilitate the uptake of the ribosyl moiety of nucleosides by a group translocation mechanism. Thus, nucleosides may be cleaved during the membrane transport process, with the resultant bases delivered to the external environment while ribose-1-P is shunted to the intravesicular space.     

Proton stoichiometry of the cytochrome c peroxidase mechanism as a function of pH.

The proton stoichiometry for the oxidation of cytochrome c peroxidase (ferrocytochrome c: hydrogen-peroxide oxidoreductase, EC 1.11.1.5) to cytochrome c peroxidase Compound I by H2O2, for the reduction of cytochrome c peroxidase Compound I to cytochrome c peroxidase Compound II by ferrocyanide, and for the reduction of cytochrome c peroxidase Compound II to the native enzyme by ferrocyanide has been determined as a function of pH between pH 4 and 8. The basic stoichiometry for the reaction is that no protons are required for the oxidation of the native enzyme to Compound I, while one proton is required for the reduction of Compound I to Compound II, and one proton is required for the reduction of Compound II to the native enzyme. Superimposed upon the basic stoichiometry is a contribution due to the perturbation of two ionizable groups in the enzyme by the redox reactions. The pKa values for the two groups are 4.9 +/- 0.3 and 5.7 +/- 0.2 in the native enzyme, 4.1 +/- 0.4 and 7.8 +/- 0.2 in Compound I, and 4.3 +/- 0.4 and 6.7 +/- 0.2 in Compound II.     

Molecular conformational changes in the triglyceride and methyl ester of stearic acid as studied by temperature dependent carbon-13 chemical shifts

The temperature dependence of the ¹³C chemical shifts in tristearin and methyl stearate has been investigated in both the melt and solution phases. Intramolecular conformational changes dominate the observed behaviour and there is little evidence for intermolecular interactions even in the melt phase of tristearin. The terminal methyl carbons of methyl stearate and tristearin and the C17, C2, and glyceryl carbons of tristearin exhibit a temperature dependence consistent with there being only two rotamers of significant population. The calculated enthalpy difference between the terminal methyl and C17 rotamers is of the same order of magnitude as would be expected for tt and tg^± rotamers in hydrocarbon chains. For the glyceryl carbons the rotamer energy difference is very large and only one of the rotamers is significantly populated at room temperature. The remaining carbons (C16, C17, C15, C6, C4 and C3) show a general drift to high fields with increasing temperature but the observed temperature dependence requires the existence of more than two rotamers. In the absence of an acceptable mechanism for the chemical shifts of ¹³C nuclei in hydrocarbon chains it is not possible to use this data to investigate conformational changes along the hydrocarbon chain.