A simple NMR analysis of the protonation equilibrium that accompanies aminoglycoside recognition: dramatic alterations in the neomycin-B protonation state upon binding to a 23-mer RNA aptamer

A complete characterisation of the protonation equilibrium that accompanies the molecular recognition of neomycin-B by a specific RNA receptor has been achieved by employing simple NMR measurements.     

Single-molecule observation of the catalytic subunit of cAMP-dependent protein kinase binding to an inhibitor peptide

An engineered version of the staphylococcal alpha-hemolysin protein pore, bearing a peptide inhibitor near the entrance to the beta barrel, interacts with the catalytic (C) subunit of cAMP-dependent protein kinase. By monitoring the ionic current through the pore, binding events are detected at the single-molecule level. The kinetic and thermodynamic constants governing the binding interaction and the synergistic effect of MgATP are comparable but not identical to the values in bulk solution. Further, the values are strongly dependent on the applied membrane potential. Additional exploration of these findings may lead to a better understanding of the properties of enzymes at the lipid/water interface. Despite the complications, we suggest that the engineered pore might be used as a sensor element to screen inhibitors that act at either the substrate or ATP binding sites of the C subunit.     

Solid-state NMR evidence for a protonation switch in the binding pocket of the H1 receptor upon binding of the agonist histamine

G protein coupled receptors (GPCRs) represent a major superfamily of transmembrane receptor proteins that are crucial in cellular signaling and are major pharmacological targets. While the activity of GPCRs can be modulated by agonist binding, the mechanisms that link agonist binding to G protein coupling are poorly understood. Here we present a method to accurately examine the activity of ligands in their bound state, even at low affinity, by solid-state NMR dipolar correlation spectroscopy and confront this method with the human H1 receptor. The analysis reveals two different charge states of the bound agonist, dicationic with a charged imidazole ring and monocationic with a neutral imidazole ring, with the same overall conformation. The combination of charge difference and pronounced heterogeneity agrees with converging evidence that the active and inactive states of the GPCR represent a dynamic equilibrium of substates and that proton transfer between agonist and protein side chains can shift this equilibrium by stabilizing the active receptor population relative to the inactive one. In fact, the data suggest a global functional analogy between H1 receptor activation and the meta I/meta II charge/discharge equilibrium in rhodopsin (GPCR). This corroborates current ideas on unifying principles in GPCR structure and function.     

Direct observation of a doubly excited state of pleiadene

Evidence is presented that the second excited state of pleiadene (I) is of doubly excited nature. Such states are of interest in discussions of excited state and ground state reactivities and for further development of calculational methods.     

Synthesis of selenium analogues of the naturally occurring glycosidase inhibitor salacinol and their evaluation as glycosidase inhibitors

The syntheses of two selenium analogues (10 and 11) of the naturally occurring sulfonium ion, salacinol (3), are described. Salacinol is one of the active principles in the aqueous extracts of Salacia reticulata that are traditionally used in Sri Lanka and India for the treatment of diabetes. The synthetic strategy relies on the nucleophilic attack of a 2,3,5-tri-O-benzyl-1,4-anhydro-4-seleno-D-arabinitol at the least hindered carbon of benzyl- or benzylidene-protected D- or L-erythritol-1,3-cyclic sulfate. The use of 1,1,1,3,3,3-hexafluoro-2-propanol as a solvent in the coupling reaction proves to be beneficial. Enzyme inhibition assays indicate that 10 is a better inhibitor (K(i) = 0.72 mM) of glucoamylase than 3, which has a K(i) value of 1.7 mM. In contrast, 11 showed no significant inhibition of glucoamylase. Compounds 10 and 11 showed no significant inhibition of barley-alpha-amylase or porcine pancreatic-alpha-amylase.     

Divergent approach to imino sugar C-glycosides using imino glycals: application to the stereocontrolled synthesis of (+)-deoxoprosophylline

Tri-O-acetyl imino glucal 2 is readily made and shown to undergo a variety of Lewis acid mediated carbon-carbon bond forming reactions at C-1 of the piperidine nucleus. In all the reactions studied, the beta-anomer is predominant.     

Direct observation of an intermediate state for a surface photochemical reaction initiated by hot electron transfer

The photoinduced charge transfer that had been suggested to result in the dissociation of phenol on Ag(111) was investigated by two-photon photoemission spectroscopy. An unoccupied intermediate state was positively identified, which was found to be located 3.22 eV above the Fermi level. From the photoelectron energy dispersion, the effective mass of the intermediate state was determined to be (15 +/- 10)m(e) for a 1 ML coverage of phenol. This implies that the excited electron is localized mainly on the adsorbed phenol, forming a molecular resonance state. Polarization dependence of the photoelectron intensity suggested that the initial photoexcitation of the substrate produces hot electrons that scatter into the molecular resonance state, leading ultimately to the dissociation of the adsorbate. These results are the first two-photon photoemission study to characterize the transient anionic state involved in photodissociation of a molecule adsorbed on a metal surface.     

Synthesis of a sulfonium ion analogue of the glycosidase inhibitor swainsonine

The synthesis of a bicyclic sulfonium ion analogue of a naturally occurring indolizidine alkaloid, swainsonine, in which the bridgehead nitrogen atom is replaced by a sulfonium ion, has been achieved by a multistep synthesis starting from (2S,3S,4R)-2,3-dibenzyloxy-4-formaldehyde-thiolane. The synthetic strategy relies on the intramolecular displacement of a leaving group on a pendant acyclic chain by a cyclic thioether. This bicyclic sulfonium salt provides a candidate with which to further probe the hypothesis that a sulfonium salt carrying a permanent positive charge would be an effective glycosidase inhibitor.     

Direct observation of weak state mixing in highly vibrationally excited acetylene

A pulsed-laser double-resonance technique probes the mixing of zero-order states in the 3ν_CH vibrational overtone (ε_vib ≈ 9640 cm⁻¹) of acetylene (C₂H₂), where the calculated vibrational state density is about three states/cm⁻¹. Vibrational overtone excitation populates and laser induced fluorescence via the ùA_u electronic state detects the molecular eigenstates, which have slightly mixed vibrational character because of weak interactions between the zero-order optically bright C---H stretching state and optically dark background states. Observing the interacting states at low state density in the weak perturber limit dramatically simplifies the assignment and interpretation of the spectra. A two-state model recovers the important features of the experimental data including our prior observations of surprisingly intense electronic transitions originating from 3ν_CH, the anomalous rotational-level dependence of the electronic absorption cross sections, and small perturbations in the 3ν_CH line positions. A multi-state deperturbation analysis gives coupling matrix elements of 0.01–0.05 cm⁻¹ that are consistent with those measured for weak interactions in other polyatomic molecules at higher state densities.     

Efficient synthesis of the glucosidase inhibitor blintol, the selenium analogue of the naturally occurring glycosidase inhibitor salacinol

An efficient synthesis of blintol, the selenium congener of the naturally occurring glycosidase inhibitor salacinol, and a potent glucosidase inhibitor itself, is described. Unlike our previously reported synthesis, this improved route makes use of p-methoxybenzyl ether protecting groups in the synthesis of one of the two key intermediates, 2,3,5-tri-O-p-methoxybenzyl-1,4-anhydro-4-seleno-D-arabinitol, from L-xylose. The other key intermediate, 2,4-O-benzylidene-L-erythritol-1,3-cyclic sulfate, was successfully prepared from D-glucose instead of the expensive L-glucose. All protecting groups in the resulting adducts were removed with trifluoroacetic acid to yield a mixture of stereoisomers, thereby obviating the problematic deprotection of benzyl ethers by hydrogenolysis. The major stereoisomer, blintol, was then obtained by fractional crystallization.     

Total synthesis of hyacinthacine A1, a glycosidase inhibitor

A practical and enantioselective total synthesis of hyacinthacine A1 is achieved involving syn allylic epoxide opening with retention using Pd catalysis and "domino" hydrogenation (five steps in one pot) sequences.     

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.     

Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study

The detailed mechanism of metal-cysteine binding is still poorly understood. It is not clear if every metal cation can induce cysteine deprotonation, how the dielectric medium affects this process, and the extent to which other ligands from the metal's first and second coordination shell influence cysteine ionization. It is also not clear if the zinc cation, with its positive charge reduced by charge transfer from the first two bound cysteinates, could still assist deprotonation of the next one or two cysteines in Cys3His and Cys4 zinc-finger cores. Here, we elucidate the factors governing the cysteine protonation state in metal-binding sites, in particular in Zn.Cys4 complexes, using a combined ab initio and continuum dielectric approach. Transition metal dications such as Zn2+ and Cu2+ and trivalent cations such as Al3+ with pronounced ability to accept charge from negatively charged Cys- are predicted to induce cysteine deprotonation, but not "hard" divalent cations such as Mg2+. A high dielectric medium was found to favor cysteine deprotonation, while a low one favored the protonated state. Polarizable ligands in the metal's first shell that can competitively donate charge to the metal cation were found to lower the efficiency of the metal-assisted cysteine deprotonation. The calculations predict that the zinc cation could assist deprotonation of all the cysteines during the folding of Cys4 zinc-finger cores and the [Zn.(Cys-)4]2- state is likely to be preserved in the final folded conformation of the protein provided the binding site is tightly encapsulated by backbone peptide groups or lysine/arginine side chains, which stabilize the ionized cysteine core.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.     

Design and divergent synthesis of aza nucleosides from a chiral imino sugar

Several novel nucleoside analogues as potential inhibitors of glycosidases and purine nucleoside phosphorylase (PNP) have been synthesized via selective coupling of an appropriate nucleobase at different positions of an orthogonally protected imino sugar as a common precursor. This synthetic strategy offers a straightforward protocol for the assembly of imino sugar containing nucleosides, establishing a new repertoire of molecules as potential therapeutics.     

Geometry,basis set,and correlation energy dependence of computed protonation energies of imino bases

The nitrogen protonation energies of the imino bases HN?CHR, where R is H, CH₃, NH₂, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HN?CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O?CHR.     

Stereoselective synthesis of the glycosidase inhibitor australine through a one-pot, double-cyclization strategy

[reaction: see text] A stereocontrolled, convergent synthesis of the alkaloid australine, a glycosidase inhibitor of the pyrrolizidine class, is described. The chiral starting materials were ketone 3, derived from L-erythrulose, and alpha-alkoxy aldehyde 4, prepared from L-malic acid. A key step of the synthesis was the highly stereoselective aldol reaction between 4 and a Z boron enolate derived from 3. Another key step was the one-pot construction of the bicyclic pyrrolizidine system by means of a three-step sequence of SN2 displacements induced by benzylamine on a trimesylate precursor.