The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using ¹⁵N-NMR and quantitative determination of ¹H-¹³C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH₂ and 0.18 for the CH₃ groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.     

Pulse FT NMR of non-equilibrium states of half-integer spin quadrupolar nuclei in single crystals

For quadrupolar nuclei with spin quantum numbers equal to 3/2, 5/2 and 7/2, the intensities of the NMR transitions in a single crystal are examined as a function of the rf excitation flip angle. Single-quantum NMR intensities are calculated using density matrix theory beginning under various non-equilibrium conditions and are compared with those determined experimentally. As a representative spin-3/2 system, the flip-angle dependence of the ²³Na NMR intensities of a single crystal of NaNO₃ was investigated beginning with the inversion of the populations associated with one of the satellite transitions. Subsequently, the populations of both satellite transitions were inverted using highly frequency-selective hyperbolic secant pulses. Calculated and experimental intensities are in good agreement. As an example of a spin-5/2 system, the flip-angle dependence of the ²⁷Al NMR transition intensities was determined using a single crystal of sapphire, Al₂O₃, starting under different nuclear spin population conditions. The experimental trends mimicked those predicted by the density matrix calculations but the agreement was not as good as for the spin-3/2 case. Some SIMPSON simulations were also carried out to confirm the results generated by our density matrix calculations. The theoretical flip-angle behavior of the NMR transition intensities obtained from a spin-7/2 spin system is also discussed.     

Density excitations of a harmonically trapped ideal gas

The dynamic structure factor S(q, ω) of a harmonically trapped Bose gas has been calculated well above the Bose-Einstein condensation temperature by treating the gas cloud as a canonical ensemble of non-interacting classical particles. The static structure factor is found to vanish s8 q ² in the long-wavelength limit. We also incorporate a relaxation mechanism phenomenologically by including a stochastic friction force to study S(q, ω). A significant temperature dependence of the density fluctuation spectra is found. The Debye-Waller factor has been calculated for the trapped thermal cloud as a function of q and the number N of atoms. A substantial difference is found for small- and large-N clouds.     

Geometrical analysis of cytochrome c unfolding

A geometrical model has been developed to study the unfolding of iso-1 cytochrome c. The model draws on the crystallographic data reported for this protein. These data were used to calculate the distance between specific residues in the folded state, and in a sequence of extended states defined by n?=?3, 5, 7, 9, 11, 13, and 15 residue units. Exact calculations carried out for each of the 103 residues in the polypeptide chain demonstrate that different regions of the chain have different unfolding histories. Regions where there is a persistence of compact structures can be identified, and this geometrical characterization is fully consistent with analyses of time-resolved fluorescence energy-transfer (TrFET) data using dansyl-derivatized cysteine side-chain probes at positions 39, 50, 66, 85, and 99. The calculations were carried out assuming that different regions of the polypeptide chain unfold synchronously. To test this assumption, lattice Monte Carlo simulations were performed to study systematically the possible importance of asynchronicity. Calculations show that small departures from synchronous dynamics can arise if displacements of residues in the main body of the chain are much more sluggish than near-terminal residues.     

Synthesis of tetraarylmethanes via a Friedel-Crafts cyclization/desulfurization strategy

Tetraarylmethanes are an important class of molecules that contain four aryl groups bonded to a central carbon atom. The shape/three-dimensionality of these molecules makes them suitable for organic light-emitting diodes (OLEDs), organic solar cells, hydrogen storage, and even drug-delivery. Despite their importance, there are only a few methods available for their preparation. Herein, we report a simple procedure for the preparation of tetraarylmethanes that involves a bismuth-catalyzed Friedel-Crafts cyclization followed by a desulfurization reaction mediated by Raney nickel.     

Stabilization of ketone and aldehyde enols by formation of hydrogen bonds to phosphazene enolates and their aldol products

Solution properties of enolates generated using the phosphazene (Schwesinger) base P4-tBu were investigated by NMR spectroscopy. With a full equivalent of base the benzyl ketones 1a and 1b, the acetophenone 2, the arylacetaldehyde 1c, and the methyl arylacetate 1d formed the expected "naked" (P4H+) enolates 3 and 7. However, at a half-equivalent of base the ketones 1a and 1b as well as the aldehyde 1c formed solutions of stable hydrogen-bonded dimeric (enol-enolate) structures (4). The acetophenone 2, on the other hand, forms only traces of the H-bonded dimer 8 during deprotonation of 2. The thermodynamic product was the isomeric self-aldol condensation product 12. The mechanism of this condensation was elucidated by low temperature rapid-injection (RI) NMR spectroscopy. Solutions of 8 stable enough for NMR characterization could be transiently generated by semiprotonation of the enolate 7 with HCl.OEt2 at -130 degrees C using RINMR. The ester enolate 1d gave no trace of 4d even on a time scale as short as a few seconds at -130 degrees C either during the semideprotonation of 1d, or during semiprotonation of the enolate 3d. Long-lived solutions of the enols derived from 1a, 1b, 1c, and 2 (but not 1d) could be produced by full protonation of the phosphazene enolates with HCl.OEt2 at low temperature.     

Acetylenic carbon-13 chemical shift tensors for diphenylacetylene and (eta2-Diphenylacetylene)Pt(PPh3)2: a solid-state NMR and theoretical study

The structure of (eta2-diphenylacetylene)Pt(PPh3) (2), as well as those of its dichloromethane and benzene solvates, is determined via X-ray crystallography. An investigation of the chemical shift (CS) tensors of the 13C-labeled carbons in Ph13C13CPh and (eta2-Ph13C13CPh)Pt(PPh3)2.(C6H6) is carried out via analysis of 13C NMR spectra from stationary solid samples. The principal components of the CS tensors as well as their orientations with respect to the 13C,13C internuclear vector are determined. DFT calculations of these CS tensors are in close agreement with the experimental values. For diphenylacetylene (tolane), the orientations and principal-component magnitudes of the alkynyl carbon CS tensors are comparable to those for other alkynyl carbons, although the CS tensor is not axially symmetric in this case. Coordination to platinum causes a change in the CS tensor orientation and a net increase in the isotropic chemical shift, resulting from a significant increase in two principal components (delta11 and delta33) while the third (delta22) decreases only slightly. The measured carbon CS tensors in the platinum complex bear a striking similarity to those of the alkenyl carbons in trans-Ph(H)C=C(H)Ph, and a short theoretical discussion of these observations is presented.     

In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors

There is a great demand for the discovery of new therapeutic molecules that combine the high specificity and affinity of biologic drugs with the bioavailability and lower cost of small molecules. Small, natural-product-like peptides hold great promise in bridging this gap; however, access to libraries of these compounds has been a limitation. Since ribosomal peptides may be subjected to in vitro selection techniques, the generation of extremely large libraries (>10(13)) of highly modified macrocyclic peptides may provide a powerful alternative for the generation and selection of new useful bioactive molecules. Moreover, the incorporation of many non-proteinogenic amino acids into ribosomal peptides in conjunction with macrocyclization should enhance the drug-like features of these libraries. Here we show that mRNA-display, a technique that allows the in vitro selection of peptides, can be applied to the evolution of macrocyclic peptides that contain a majority of unnatural amino acids. We describe the isolation and characterization of two such unnatural cyclic peptides that bind the protease thrombin with low nanomolar affinity, and we show that the unnatural residues in these peptides are essential for the observed high-affinity binding. We demonstrate that the selected peptides are tight-binding inhibitors of thrombin, with K(i)(app) values in the low nanomolar range. The ability to evolve highly modified macrocyclic peptides in the laboratory is the first crucial step toward the facile generation of useful molecular reagents and therapeutic lead molecules that combine the advantageous features of biologics with those of small-molecule drugs.     

Determination of arsenic and antimony in seawater by voltammetric and chronopotentiometric stripping using a vibrated gold microwire electrode

The oxidation potentials of As⁰/As^III and Sb⁰/Sb^III on the gold electrode are very close to each other due to their similar chemistry. Arsenic concentration in seawater is low (10–20 nM), Sb occurring at ∼0.1 time that of As. Methods are shown here for the electroanalytical speciation of inorganic arsenic and inorganic antimony in seawater using a solid gold microwire electrode. Anodic stripping voltammetry (ASV) and chronopotentiometry (ASC) are used at pH ≤ 2 and pH 8, using a vibrating gold microwire electrode. Under vibrations, the diffusion layer size at a 5 μm diameter wire is 0.7 μm. The detection limits for the As^III and Sb^III are below 0.1 nM using 2 min and 10 min deposition times respectively. As^III and Sb^III can be determined in acidic conditions (after addition of hydrazine) or at neutral pH. In the latter case, oxidation of As⁰ to As^III was found to proceed through a transient As^III species. Adsorption of this species on the gold electrode at potentials where Sb^III diffused away is used for selective deposition of As^III. Addition of EDTA removes the interfering effect of manganese when analysing As^III. Imposition of a desorption step for Sb^III analysis is required. Total inorganic arsenic (iAs = As^V + As^III) can be determined without interference from Sb nor mono-methyl arsenious acid (MMA) at 1.6 < pH < 2 using E_dep = −1 V. Total inorganic antimony (iSb = Sb^V + Sb^III) is determined at pH 1 using E_dep = −1.8 V without interference by As.