Interrelation between glycosidic torsion, sugar pucker, and backbone conformation in 5'-beta-nucleotides. A 1H and 31P fast Fourier transform nuclear magnetic resonance investigation of the conformation of 8-aza-5'-beta-adenosine monophosphate and 8-aza-5'-beta-guanosine monophosphate

Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs

The 5'-nucleotide of small RNAs associates directly with the MID domain of Argonaute (AGO) proteins. In humans, the identity of the 5'-base is sensed by the MID domain nucleotide specificity loop and regulates the integrity of miRNAs. In Arabidopsis thaliana, the 5'-nucleotide also controls sorting of small RNAs into the appropriate member of the AGO family; however, the structural basis for this mechanism is unknown. Here, we present crystal structures of the MID domain from three Arabidopsis AGOs, AtAGO1, AtAGO2 and AtAGO5, and characterize their interactions with nucleoside monophosphates (NMPs). In AtAGOs, the nucleotide specificity loop also senses the identity of the 5'-nucleotide but uses more diverse modes of recognition owing to the greater complexity of small RNAs found in plants. Binding analyses of these interactions reveal a strong correlation between their affinities and evolutionary conservation.

Structural insight into the substrate specificity of phosphodiesterases

Cyclic nucleotide phosphodiesterases (PDEs) share a highly conserved catalytic domain that hydrolyzes cAMP, cGMP, or both nucleotides. However, the mechanism that allows the PDE catalytic sites to specifically recognize these nucleotides and distinguish between their subtle differences is still unclear. An early model, called the "glutamine switch", proposed that the side chain of an invariant glutamine adopts two different conformations to allow for formation of two hydrogen bonds with cAMP and cGMP, thereby differentiating these nucleotides. However, the structure of PDE4D2 in complex with cAMP shows that Gln369 forms only one hydrogen bond with the substrate. In addition, the structures of PDE10A in complex with cAMP and cGMP reveal that cAMP and cGMP bind to the active site in different orientations and have different interactions with PDE10A residues. These structures suggest that the invariant glutamine does not appear to be a key residue to differentiate between cAMP and cGMP, although it is important for substrate binding. The structure-based sequence alignment shows that most of the active site residues change across PDE families. These residues may not only contribute differently to the substrate specificity, but also generate slightly different shapes and sizes of the active sites in different PDE families. Therefore, the substrate specificity of PDEs is likely to be determined jointly by multiple elements at the active site, yet the detailed mechanism needs further study.

Structural insight into substrate specificity of phosphodiesterase 10

Phosphodiesterases (PDEs) hydrolyze the second messengers cAMP and cGMP. It remains unknown how individual PDE families selectively recognize cAMP and cGMP. This work reports structural studies on substrate specificity. The crystal structures of the catalytic domains of the D674A and D564N mutants of PDE10A2 in complex with cAMP and cGMP reveal that two substrates bind to the active site with the same syn configuration but different orientations and interactions. The products AMP and GMP bind PDE10A2 with the anti configuration and interact with both divalent metals, in contrast to no direct contact of the substrates. The structures suggest that the syn configurations of cAMP and cGMP are the genuine substrates for PDE10 and the specificity is achieved through the different interactions and conformations of the substrates. The PDE10A2 structures also show that the conformation of the invariant glutamine is locked by two hydrogen bonds and is unlikely to switch for substrate recognition. Sequence alignment shows a potential pocket, in which variation of amino acids across PDE families defines the size and shape of the pocket and thus determines the substrate specificity.

Interaction energy studies of an antimetabolite 8-azaguanine during transcription

The possible incorporation of 8-azaguanine during transcription has been examined in the light of the model of transcription developed earlier by Sanyal et al. Electrostatic energy of interaction has been calculated for the nucleoside analogue (8-azaguanine) base for the entire space inside the deep groove of the DNA double helix. The interaction energy values and the location of the possible sites of association are compared with the recommended configurations of RNA transcription. It is concluded that 8-azaguanine is capable of replacing guanine during transcription. These conclusions are in general agreement with the experimental results.

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.

Alternate g-g- conformation for dinucleoside phosphates in solution

An alternative g-g- conformation (conformer I') for dinucleosides in solution has been deduced, based on potential energy calculations and nuclear magnetic resonance spectroscopy. This conformation is characterized by larger glycosidic torsional angles (chi = 94-111 degrees) than those of conformer I (chi = 8-35 degrees), although the other torsional angles are similar. There are thus four stable conformers (I, I', II and III) for dinucleosides in equilibrium with the open forms. The structure of conformer I' supports that of the 'vertical' double helix constructed by Olson (W.K. Olson, Proc. Natl. Acad. Sci. U.S.A. 74, (1977) 1775). Our data may suggest the possibility of interconversion between the vertical double helix and the regular double helix of A-form DNA, RNA or A'-form RNA.

The interactions between nucleic acids and polyamines. I. High resolution carbon-13 and hydrogen-1 nuclear magnetic resonance studies of spermidine and 5'-AMP

In 0.5 M solution at pH 7.6, interaction of spermidine and 5'-AMP is demonstrated by downfield proton NMR shifts. Shifts of ribose and adenine protons support a model in which triprotonated spermidine engages the phosphate anion with the C-3 diamine segment in a conformation to maximize interaction and the C-4 amino segment extended to interact with adenine N-7 (base anti, 2' endo, g'g' and gg nucleoside conformation). Changes in carbon-13 chemical shifts fro ribose C-5' (downfield), C-2' C-3', and C-4' (upfield) and for adenine C-6 and C-8 (upfield) support this model. In 0.006 M solution no significant changes in proton shifts and therefore no evidence for interaction was found. Spermidine and 5' -UMP (0.006 M) showed interaction at pH 10.5 (small upfield shifts in the proton nmr) interpreted as changing conformation by solvent interaction. In 0.00l M 3'-UMP at pH 10.5 small downfield proton shifts induced by spermidine are attributed to interactions with phosphate anion.

A conformational basis for the antiviral inactivity of tetrazole ribonucleosides

The antiviral activity of ribavirin has been associated with its inhibition of the enzyme, IMP dehydrogenase. The ability of ribavirin to inhibit this enzyme has previously been shown to be related to its stability in the high anti glycosidic conformation. The antiviral effectiveness of several analogs of ribavirin have been investigated recently. The evidence indicates their antiviral effectiveness is related to their stability in the high anti conformation. Recently the disposition of purine analogs that pass through the inosine monophosphate branch point has been investigated. The results of these studies are consistent with the concept that the conversion of IMP to XMP requires the high anti conformation and that the conversion of IMP to adenylosuccinate requires some other conformation, possibly the anti conformation.

Molecular orbital studies on the structure of nucleoside analogs. I. Conformation of 8-azapurine nucleosides

PCILO (perturbative configuration interaction using localized orbitals) computations have been carried out for the conformational properties of 8-azapurine nucleosides. The results indicate an anti conformation for Xcn and a gg conformation for phiC(4')-C(5') for C(2')-endo 8-aza analogs compared to the syn and gg conformation for the corresponding purine nucleosides. For C(3')-endo sugar puckering, both molecules prefer the syn conformation due to intramolecular hydrogen bonding between O(5')-H of the sugar and N(3) of the base, the preference being more profound in 8-aza analogs. The crystallographic conformation 8-azaadenosine has been attributed to crystal forces. The available NMR data on 8-azapurine nucleosides are in agreement with the PCILO predictions.

Proton NMR and spin lattice relaxation study of nucleoside di- and triphosphates in neutral aqueous solutions

The average conformations of adenosine, inosine and guanosine di- and triphosphates in neutral aqueous solution have been investigated by 1H vicinal couplings, chemical shifts and T1 relaxation time measurements at 250 MHz. Comparison of chemical shifts with those of the corresponding nucleotide monophosphates suggests that the beta-phosphate group is in all cases oriented towards the base and close to H3'. The vicinal coupling constants indicate that the proportion of the S conformer of the ribose moiety is 55--60% and that the gauche-gauche rotamer of the CH2-OP exocyclic group is predominant. The preferential orientations of the base have been determined by minimization of the standard deviation about the mean of the molecular reorientation correlation times derived from the H8, H1', H2' and H3' relaxation times and computed interproton distances. The problem of the correlation between the syn-anti equilibrium and the N equilibrium S interconversion has been examined. Typical magnetization recovery curves after a 180 degree pulse have been simulated in the case of ATP, taking into account cross relaxation effects. It is shown that in most of the molecules under consideration the syn orientation of the base is predominant whereas for ATP the syn and anti are equivalent.

Intramolecular hydrogen bonding and molecular conformations of nucleosides. N (6)-dimethyl-2',3'-isopropylidene adenosine

The physical properties of an adenosine derivative, N(6)-dimethyl-2',3'-O-isopropylidene adenosine, Derivative 1, which is capable of intramolecular hydrogen bond formation between base-ring and sugar exocyclic hydroxymethyl group, have been studied in solution by infrared, circular dichroic and nuclear magnetic resonance spectroscopy. Analysis of the 220 MHZ 1H NMR spectrum of Derivative 1 in C2HCl2 solution indicated an overwhelming preference for the gg conformation for rotation about the C(4')--C5') bond and a predominant conformation for rotation about the C(5')--O(5') bond in which OH(5') projects towards the base ring. The purine base ring was shown to be in a predominant syn conformation with respect to the sugar ring by 100 MHZ 1H nuclear Overhauser experiments, by analysis of 3J(13C,H1') magnitudes observed in proton-coupled 13C NMR experiments and by CD measurements. Combination of each conformation feature of Derivative 1 in non-polar solvents is consistent with the overall molecular conformation observed in the solid state in which intramolecular hydrogenbonding exists between purine N(3) and the sugar CH2OH group; the presence of a strong intramolecular hydrogen bond was observed by infrared spectroscopy. The sugar ring conformations of 2',3'-O-isopropylidene ribonucleosides were analysed in terms of the pseudorotational properties of the ring; the N and S conformations tend toward to C(2')-exo and C(3')-'exo conformations, respectively, compared to normal ribonucleosides (C(3')-endo and C(2')-endo, respectively). The presence of the hydrogen bond in the derivative is sufficient to promote the S-type conformations (approx. 80%--90%) compared to cases where such a strong hydrogen bond is unlikely to be present approx. 40--50%).

Adenosine-5'-d: rotational conformation of the 5'-carbinol group

A synthesis of adenosine-5'-d (4), and its p.m.r. spectral characteristics, are described. The presence of deuterium in 4 gives rise to a 2:1 mixture of R and S configurations at C-5, thereby permitting specific assignments for the resonances of the residual 5'-protons. From the observed spin-spin coupling between the latter and H-4', an estimate has been made of the rotamer population of the exocyclic 5'-carbinol group. It is shown that the gauche-gauche rotamer is preponderant (approximately 70%) and the gauche-trans one of minor importance (approximately 20%) in aqueous solution, which contrasts markedly with the preference for the latter rotamer exhibited by adenosine in the solid state.

Phosphorus-31 Fourier transform nuclear magnetic resonance study of mononucleotides and dinucleotides. 1. Chemical shifts

A phosphorus-31 nuclear magnetic resonance (NMR) study of adenine, uracil, and thymine mononucleotides, their cyclic analogues, and the corresponding dinucleotides is reported. From the pH dependence of phosphate chemical shifts, pKa values of 6.25-6.30 are found for all 5'-mononucleotides secondary phosphate ionization, independently from the nature of the base and the presence of a hydroxyl group at the 2' position. Conversely, substitution of a hydrogen atom for a 2'-OH lowers the pKa of 3'-monoribonucleotides from 6.25 down to 5.71-5.85. This indication of a strong influence of the 2'-hydroxyl group on the 3'-phosphate is confirmed by the existence of a 0.4 to 0.5 ppm downfield shift induced by the 2'-OH on the phosphate resonance of 3'-monoribonucleotides, and 3',5'-cyclic nucleotides and dinucleotides with respect to the deoxyribosyl analogues. Phosphate chemical shifts and titration curves are affected by the ionization and the type of the base. Typically, deviations from the theoretical Henderson-Hasselbalch plots are observed upon base titration. In addition, purine displays a more deshielding influence than pyrimidine on the phosphate groups of most of the mononucleotides (0.10 to 0.25 ppm downfield shift) with a reverse situation for dinucleotides. These effects together with the importance of stereochemical arrangement (furanose ring pucker, furanose-phosphate backbone conformation, O-P-O bond angle) on the phosphate chemical shifts are discussed.

Nucleotide rigidity

It is show that in aqueous solution the backbone conformation of adenosine is as much flexible as that of 3'-AMP, 5'-AMP and 3', 5'-ADP indicating that nucleotides are not any more rigid than nucleosides. The flexible conformation of the monomeric components is conserved in the nucleotidyl units of destacked ApA, ApApA and poly(A), but it is not conserved in base stacked conditions. The findings are extended to guanosine, uridine and cytidine systems. It is projected that in aqueous solution, conformations of the individual nucleotidyl units of yeast tRNAhe are confined to the classically stable domains in the base stacked region and non-rigid flexible structures populate in the unstacked region comprising D16, D17, G20, U47 and A76.

Properties of the ribose-ring-opened adenine nucleotide, 2,2'(1-(9-adenyl)-1'-(tri-,diphosphoryl-oxymethyl))-dihydroxydiethylether in mitochondrial adenine-nucleotide translocation

(Adenine-14C) or (gamma-32P)-labelled 2,2'[1-(9-adenyl)-1'-(tri-, diphosphoryl-oxymethyl]-dihydroxydiethylether (rroANP) was obtained from ANP by cleavage of the C-2--C-3' bond by sodium periodate oxidation and subsequent borohydride reduction. Binding of rroANP to rat liver mitochondria revealed carrier-linked (atractyloside-sensitive) and unspecific (atractyloside-insensitive) binding but no transfer across the inner mitochondrial membrane. Kinetic data indicate rroANP as a competitive inhibitor for ANP uptake with Ki = 9.3 X 10(-5) M. Experimental rroANP confirmed that an intact adenine base and three anio.nic charges of the phosphate chain are essential for the recognition between ANP-carrier and nucleotide but insufficient for the induction of a transmembrane ANP exchange. In addition mobilisation of the carrier-nucleotide complex requires an intact ribofuranoside ring system.