Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy

A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.     

Total Syntheses of (-)-Papuamine and (-)-Haliclonadiamine

The pentacyclic marine alkaloids (-)-papuamine (1) and (-)-haliclonadiamine (2) have been prepared by total synthesis. The synthesis began with (-)-8, which was converted into diester 20 by way of bis-mesylate 17, dinitrile 18, and diacid 19. Dieckmann cyclization of 20 provided keto ester 21, which was transformed into acetal 22. After hydrolysis of the acetal, ketone 25 was subjected to reductive amination with 1,3-propanediamine and sodium triacetoxyborohydride to obtain diamines 26 and 27 as a 71:29 mixture of diastereomers, favoring the symmetrical isomer having the papuamine relative configuration. After transformation of the diamines to their t-Boc derivatives, the benzyl ethers were cleaved and the resulting diol was oxidized to dialdehyde 30. Application of the Seyferth procedure for conversion of aldehydes to alkynes gave a mixture of diynes 31 and 32. After removal of the t-Boc protecting groups from 31, diamino diyne 15 was treated with tributylstannane and azoisobutyronitrile to obtain the bis-vinylstannane 34. Treatment of this compound with Pd(II) and Cu(I) in the presence of air produced (-)-papuamine (1). (-)-Haliclonadiamine (2) was obtained from the unsymmetrical isomer, 32. The NMR spectra of the synthetic alkaloids were identical to those of authentic samples of the natural alkaloids.     

Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin

High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D (13)C-(13)C correlation spectroscopy under magic angle spinning conditions. High-resolution (13)C spectra have been acquired from hydrated microcrystals of site-directed (13)C-enriched ubiquitin. Inter-residue carbon-carbon distance constraints defining the global protein structure have been evaluated from 'dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.     

Silicone-modified starch/protein microparticles: protecting biopolymers with a hydrophobic coating

Silicone-coated starch/protein (human serum albumin, HSA) microparticles were prepared by precipitation of a starch/HSA/DMSO/water (water-in-oil) emulsion into acetone containing a silicone: the silicone polymer was either unfunctionalized (SiMe₃ terminated, PDMS) or functionalized at its termini with Si(OEt)₃ groups (TES-PDMS). The microparticles of approximate diameter 2–7 μm were highly hydrophobic with advancing contact angles 115°. Over several minutes, however, the contact angle decreased to ca. 40–70°. Soxhlet extraction with water led to degradation of the microparticles, irrespective of the nature of their silicone coating, as evidenced by release of the protein from them. Intraperitoneal (IP) or gastric administration of the two different particles to mice, however, showed a clear difference between the two silicones. The microparticles coated with either PDMS or TES-PDMS led to very different immune responses. Oral administration of the microparticles prepared with functionalized silicone elicited a significant production of antibodies, whereas the particles prepared with the unfunctionalized silicone (PDMS) were only weakly active. By contrast, the IP results demonstrated that particles coated with PDMS elicited an immune response that was established much more rapidly than with the particles modified with TES-PDMS. It is proposed that the TES-PDMS forms a physically adhering film or covalent bond to the protein molecules, which serves to protect the microparticle from biological degradation in the gut and/or facilitates the microparticle/protein interaction with the immune system.     

Realisations of quantum GL p,q(2) and Jordanian GLh,h′(2)

The quantum group GL _p,q(2) is known to be related to the Jordanian GL_h,h(2) via a contraction procedure. It can also be realised using the generators of the Hopf algebra G _r,s. We contract the G _r,s quantum group to obtain its Jordanian analogue G _m,k, which provides a realisation of GL_h,h(2) in a manner similar to the q-deformed case.     

Templateless assembly of molecularly aligned conductive polymer nanowires: a new approach for oriented nanostructures

Although oriented carbon nanotubes, oriented nanowires of metals, semiconductors and oxides have attracted wide attention, there have been few reports on oriented polymer nanostructures such as nanowires. In this paper we report the assembly of large arrays of oriented nanowires containing molecularly aligned conducting polymers (polyaniline) without using a porous membrane template to support the polymer. The uniform oriented nanowires were prepared through controlled nucleation and growth during a stepwise electrochemical deposition process in which a large number of nuclei were first deposited on the substrate using a large current density. After the initial nucleation, the current density was reduced stepwise in order to grow the oriented nanowires from the nucleation sites created in the first step. The usefulness of these new polymer structures is demonstrated with a chemical sensor device for H(2)O(2), the detection of which is widely investigated for biosensors. Finally, we demonstrated that controlled nucleation and growth is a general approach and has potential for growing oriented nanostructures of other materials.     

Observation of ligand binding to cytochrome P450 BM-3 by means of solid-state NMR spectroscopy

A broad understanding of the binding modes of ligands and inhibitors to cytochrome P450 is vital for the development of new drugs. We investigated ligand binding in a site-specific fashion on cytochrome P450 BM-3 from Bacillus megaterium, a 119 kDa paramagnetic enzyme, using solid-state magic angle spinning nuclear magnetic resonance methods. Selective labeling and longitudinal relaxation effects were utilized to identify the peaks in a site-specific fashion and to provide evidence for binding. Well-resolved one-dimensional and two-dimensional NMR spectra of cytochrome P450 BM-3 reveal shifts upon binding of its substrate, N-palmitoylglycine. These data are consistent with the crystallographic result that a biochemically important amino acid residue, Phe87, moves upon ligation. This experimental scheme provides a tool for probing ligand binding for complex systems.     

1/f Flux noise in Josephson phase qubits

We present a new method to measure 1/f noise in Josephson quantum bits (qubits) that yields low-frequency spectra below 1 Hz. A comparison of the noise taken at positive and negative bias of a phase qubit shows the dominant noise source to be flux noise and not junction critical-current noise, with a magnitude similar to that measured previously in other systems. Theoretical calculations show that the level of flux noise is not compatible with the standard model of noise from two-level state defects in the surface oxides of the films.     

Locating hydrogen atoms in single crystal and uniaxially aligned amino acids by solid-state NMR

We demonstrate a novel method to locate hydrogen atoms in amino acids, which involves measuring the C(alpha)H(alpha) bond vector geometry through orientationally dependent dipolar coupling frequencies measured by Lee-Goldburg cross polarization (LGCP). A 2D LGCP experiment is used to measure the polar angle of the C(alpha)H(alpha) bond vector in a single crystal of the model compound L-alanine. It is also demonstrated that by coupling the 13C(alpha)1H(alpha) LGCP experiment to a 13C(alpha)15N REDOR experiment, one can determine the complete three-dimensional geometry of the C(alpha)H(alpha) and C(alpha)N vectors in a single crystal. These measurements allow for location of hydrogen atoms in crystalline biological macromolecules.