1H NMR titrations of hydroxy protons in aqueous solution as a method of investigation of intramolecular hydrogen-bonding in phosphorylated compounds: examples of myo-inositol 2-phosphate and myo-inositol 1,2,6-tris(phosphates)

Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein

Hydroxyl proton resonances of uniformly ¹³C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man₃) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man₃ and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.

Cooperative hydrogen bonding in glyco-oligoamides: DNA minor groove binders in aqueous media

A strategy to create cooperative hydrogen-bonding centers by using strong and directional intramolecular hydrogen-bonding motifs that can survive in aqueous media is presented. In particular, glyco-oligoamides, a family of DNA minor groove binders, with cooperative and non-cooperative hydrogen-bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β-D-Man-Py-γ-Py-Ind (1; Ind=indole, Man=mannose, Py=pyrrole) and β-D-Tal-Py-γ-Py-Ind (2; Tal=talose), were chosen according to our design. These sugar molecules should present one- or two-directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco-oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco-oligoamides with non-cooperative hydrogen-bonding centers, that is, β-D-Glc-Py-γ-Py-Ind (3; Glc=glucose), β-D-Gal-Py-γ-Py-Ind (4; Gal=galactose), and the model compounds β-D-Man-Py-NHAc (5) and β-D-Tal-Py-NHAc (6) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH-π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf-thymus DNA and poly(dA-dT)2 by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar-oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen-bonding and CH-π interactions are present.

Selective induced polarization through electron transfer in acetone and pyrazole ester derivatives via C–H⋯OC interaction

A set of organic compounds (pyrazole ester derivatives,viz.5-[3-(substituted)-propoxy]-3-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid methyl ester and 5-[2-(substituted)-ethoxy]-3-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid methyl ester) was synthesized and their affinity and stability towards the acetone molecule were tested by NMR.

Biophysics and function of phosphatidic acid: a molecular perspective

Phosphatidic acid is the simplest (diacyl)glycerophospholipid present in cells and is now a well established second messenger with direct biological functions. It is specifically recognized by diverse proteins and plays an important role in cellular signaling and membrane dynamics in all eukaryotes. An important determinant of the biological functions of phosphatidic acid is its anionic headgroup. In this review we will focus on the peculiar ionization properties of phosphatidic acid and their crucial role in lipid-protein interactions. We will take a molecular approach focusing entirely on the physical chemistry of the lipid and develop a model explaining the ionization properties of phosphatidic acid, termed the electrostatic-hydrogen bond switch model. Diverse examples from recent literature in support of this model will be presented and the broader implications of our findings will be discussed.

NMR study of hydroxy protons of di- and trimannosides, substructures of Man-9

The chemical shifts, temperature coefficients and inter-residual rotating-frame Overhauser effect (ROE)s for the hydroxy protons of some alpha-(1,2)-, alpha-(1,3)- and alpha-(1,6)-linked di- and trimannosides have been measured for samples in 85% H2O/15% acetone-d6 solution. These mannosides, Manalpha(1-->2)ManalphaOMe (1) Manalpha(1-->3)ManalphaOMe (2), Manalpha(1-->6)ManalphaOMe (3), Manalpha(1-->2)Manalpha(1-->2)ManalphaOMe (4), Manalpha(1-->2)Manalpha(1-->3)ManalphaOMe (5), Manalpha(1-->2)Manalpha(1-->6)ManalphaOMe (6) and Manalpha(1-->3)[Manalpha1-->6]ManalphaOMe (7), are substructures of the N-glycan Man-9. The NMR data show that the hydration of each individual hydroxyl group in the di- and trisaccharides is very similar to the hydration of the corresponding hydroxyl in the monomeric methyl alpha-D-mannoside. No hydrogen-bond interactions were found to stabilize the conformations of the alpha-(1,2)- and alpha-(1,6)-linkages and the chemical shifts for the hydroxy proton resonances of the alpha-(1,6)-linkage indicated high-conformational flexibility. For the alpha-(1,3)-linkage, however, the downfield shift for the signal of O(2)H of the 3-substituted residue together with the ROE between this proton and H5' on the next residue suggest some weak inter-residue interactions.

Comparative 1H NMR and molecular modeling study of hydroxy protons of β-d-Galp-(1→4)-β-d-GlcpNAc-(1→2)-α-d-Manp-(1→O)(CH2)7CH3 analogues in aqueous solution

The (1)H chemical shifts, coupling constants, temperature coefficients, exchange rates, and inter-residual ROEs have been measured, in aqueous solution, for the hydroxy and amine/amide proton resonances of a set of beta-D-Galp-(1-->4)-beta-D-GlcpNAc-(1-->2)-alpha-D-Manp-(1-->O)(CH(2))(7)CH(3) analogues. From the structural data, a few significant structural features could be ascertained, such as a preferential anti-conformation for the amide protons of the N-acetyl and N-propionyl groups. The introduction of systematic modifications at Gal 2-C and Gal 6-C resulted in alterations of the Gal 4-OH, Gal 3-OH, and GlcNAc 3-OH areas, since variations in chemical shifts and temperature coefficient were observed. In order to verify the possibility of hydrogen bonds, molecular dynamics simulations in the gas phase and explicit solvent were performed and correlated with the experimental data. A network of hydrogen bonds to solvent molecules was observed, but no strong intramolecular hydrogen bonding was observed.

3-Hydroxybenzene 1,2,4-Trisphosphate, a Novel Second Messenger Mimic and unusual Substrate for Type-I myo-Inositol 1,4,5-Trisphosphate 5-Phosphatase: Synthesis and Physicochemistry

3-Hydroxybenzene 1,2,4-trisphosphate 4 is a new myo-inositol 1,4,5-trisphosphate analogue based on the core structure of benzene 1,2,4-trisphosphate 2 with an additional hydroxyl group at position-3, and is the first noninositol based compound to be a substrate for inositol 1,4,5-trisphosphate 5-phosphatase. In physicochemical studies on 2, when three equivalents of protons were added, the (31)P NMR spectrum displayed monophasic behaviour in which phosphate-1 and phosphate-2 behaved independently in most of the studied pH range. For compound 4, phosphate-2 and phosphate-4 interacted with the 3-OH group, which does not titrate at physiological pH, displaying complex biphasic behaviour which demonstrated co-operativity between these groups. Phosphate-1 and phosphate-2 strongly interacted with each other and phosphate-4 experienced repulsion because of the interaction of the 3-OH group. Benzene 1,2,4-trisphosphate 2 is resistant to inositol 1,4,5-trisphosphate type I 5-phosphatase catalysed dephosphorylation. However, surprisingly, 3-hydroxybenzene 1,2,4-trisphosphate 4 was dephosphorylated by this 5-phosphatase to give the symmetrical 2,3-dihydroxybenzene 1,4-bisphosphate 16. The extra hydroxyl group is shown to form a hydrogen bond with the vicinal phosphate groups at -15 degrees C, and (1)H NMR titration of the ring and hydroxyl protons in 4 shows the OH proton to be strongly stabilized as soon as the phosphate groups are deprotonated. The effect of the phenolic 3-OH group in compound 4 confirms a critical role for the 6-OH group of the natural messenger in the dephosphorylation mechanism that persists even in radically modified analogues.

Synergy of Intramolecular Hydrogen-Bonding Network in myo-Inositol 2-Monophosphate: Theoretical Investigations into the Electronic Structure, Proton Transfer, and pKa

This work demonstrates the pivotal role that an intramolecular hydrogen-bonding network (intra-HBN) plays in the determination of the conformation of myo-inositol 2-monophosphate (Ins(2)P1), a member of the inositol phosphate family of compounds, which are important participants in the role that phosphates play in biological and environmental chemistry. For biologically significant compounds that contain phosphate and hydroxyl groups, Ins(2)P1 is a model system for studying both the primary forces that determine their conformations and their chemical properties from the effect of phosphate group addition. We performed ab initio calculations to determine the intra-HBN within important thermally accessible conformations for neutral Ins(2)P1 and its anions, Ins(2)P1(1-) and Ins(2)P1(2-). The results show that the global minima prefer 1a/5e structures where the phosphate group is in the axial position with all -OH groups in the equatorial positions. The calculations of transition state structures for ring inversion at each ionization state predict an activation energy of 18.16 kcal/mol for the neutral species in water, while the activation energy is lower for the charged compounds, 15.62 kcal/mol for Ins(2)P1(1-) and 12.48 kcal/mol for Ins(2)P1(2-). The pK(a) values of Ins(2)P1 were calculated by modeling the solvent as a polarizable continuum medium (PCM) and as explicit solvent molecules. These values are in good agreement with experimental data. A novel four-center pattern of hydrogen bonding was found to stabilize the system. The intramolecular proton transfer across a low barrier hydrogen bond between the charged phosphate and hydroxyl groups was found to occur under standard conditions with an activation energy that is less than 0.5 kcal/mol.

Inframolecular Protonation Process of Norbadione A: Influence of the Ionic Environment and Stereochemical Consequences

The microscopic protonation mechanism, at an inframolecular level, of norbadione A, a pigment extracted from mushrooms and known to complex cesium cations, was determined by using 1H NMR titrations and the cluster expansion method. This study revealed a pH dependent Z to E isomer switch that occurs in both pulvinic moieties. As a consequence, norbadione A can exist in solution in four stereomeric forms (E-E, E-Z, Z-E, and Z-Z), which can be of interest in the development of molecular-level devices. In the presence of 0.15 M NaCl, the calculated microconstants showed an unusual apparent cooperativity between the enol groups, which results from the release of the sodium cations upon protonation of norbadione A.

2-O-(2-Aminoethyl)-myo-inositol 1,4,5-trisphosphate as a novel ligand for conjugation: physicochemical properties and synthesis of a new Ins(1,4,5)P(3) affinity matrix

2-O-(2-Aminoethyl)-Ins(1,4,5)P(3), (5), a novel derivative of the Ca(2+)-mobilising second messenger d-myo-inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)], was synthesised from myo-inositol. 5 was found to be a potent mobiliser of intracellular Ca(2+), and an Ins(1,4,5)P(3) affinity matrix synthesised from 5 was effective at selectively binding N-terminal fragments of the Ins(1,4,5)P(3) receptor containing the intact Ins(1,4,5)P(3) binding site. The microprotonation scheme for 5 was resolved and the related constants were determined in comparison with Ins(1,4,5)P(3) and another reactive Ins(1,4,5)P(3) analogue 1-O-(2-aminoethyl-1-phospho)-Ins(4,5)P(2), (2a), by potentiometric and NMR titration methods. The (31)P and (1)H NMR titration curves for compound 5 and Ins(1,4,5)P(3) are remarkably close, indicating analogous acid-base properties and intramolecular interactions for the two compounds. The 1-phosphate-modified Ins(1,4,5)P(3) derivative 2a, on the contrary, behaves as a bisphosphorylated rather than a trisphosphorylated inositol. Thus, 5 is a new reactive Ins(1,4,5)P(3) analogue of considerable potential for investigation of the chemical biology of Ins(1,4,5)P(3)-mediated cellular signalling.

Conformational and inframolecular studies of the protonation of adenophostin analogues lacking the adenine moiety

Four adenophostin analogues lacking the adenine moiety were subjected to 31P- and 1H-NMR titrations in order to determine the acid-base behaviour of the individual ionisable groups of the molecules and the complex interplay of intramolecular interactions resulting from the protonation process. For the two trisphosphorylated compounds, the curve pattern of the phosphorus nuclei corresponds to the superimposition of the titration curves of a monophosphorylated polyol and a polyol carrying two vicinal phosphates, suggesting that the two phosphate moieties behave independently. Also, the general shape of 1H-NMR titration curves of the studied compounds is very close to that of adenophostin A, indicating that the adenine moiety does not specifically interact with the phosphorylated sugar moieties. The curves show, however, that both trisphosphorylated compounds adopt slightly different preferential conformations which could contribute to explain the difference in their affinity for Ins(1,4,5)P3 receptor. Their macroscopic as well as the microscopic protonation constants are higher than those of adenophostin A, indicating that the adenine moiety plays a base-weakening effect on the phosphate groups. Further analysis of the microscopic protonation constants confirms that the compound whose conformation is the closest to that of adenophostin A also shows the highest biological activity. The two bisphosphorylated analogues studied behave very similarly, suggesting that the deletion of the hydroxymethyl group on the pentafuranosyl ring only weakly influences the protonation process of the phosphate groups that bear the glucopyranose moiety.