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.     

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.     

B-MWW Zeolite: The Case Against Single-Site Catalysis

Boron-containing materials have recently been identified as highly selective catalysts for the oxidative dehydrogenation (ODH) of alkanes to olefins. It has previously been demonstrated by several spectroscopic characterization techniques that the surface of these boron-containing ODH catalysts oxidize and hydrolyze under reaction conditions, forming an amorphous B₂(OH)_xO_(3−x/2) (x=0–6) layer. Yet, the precise nature of the active site(s) remains elusive. In this Communication, we provide a detailed characterization of zeolite MCM-22 isomorphously substituted with boron (B-MWW). Using ¹¹B solid-state NMR spectroscopy, we show that the majority of boron species in B-MWW exist as isolated BO₃ units, fully incorporated into the zeolite framework. However, this material shows no catalytic activity for ODH of propane to propene. The catalytic inactivity of B-MWW for ODH of propane falsifies the hypothesis that site-isolated BO₃ units are the active site in boron-based catalysts. This observation is at odds with other traditionally studied catalysts like vanadium-based catalysts and provides an important piece of the mechanistic puzzle.     

B‐MWW Zeolite: The Case Against Single‐Site Catalysis

Boron‐containing materials have recently been identified as highly selective catalysts for the oxidative dehydrogenation (ODH) of alkanes to olefins. It has previously been demonstrated by several spectroscopic characterization techniques that the surface of these boron‐containing ODH catalysts oxidize and hydrolyze under reaction conditions, forming an amorphous B₂(OH)_xO_(3?x/2) (x=0–6) layer. Yet, the precise nature of the active site(s) remains elusive. In this Communication, we provide a detailed characterization of zeolite MCM‐22 isomorphously substituted with boron (B‐MWW). Using ¹¹B solid‐state NMR spectroscopy, we show that the majority of boron species in B‐MWW exist as isolated BO₃ units, fully incorporated into the zeolite framework. However, this material shows no catalytic activity for ODH of propane to propene. The catalytic inactivity of B‐MWW for ODH of propane falsifies the hypothesis that site‐isolated BO₃ units are the active site in boron‐based catalysts. This observation is at odds with other traditionally studied catalysts like vanadium‐based catalysts and provides an important piece of the mechanistic puzzle.     

Why Boron Nitride is such a Selective Catalyst for the Oxidative Dehydrogenation of Propane

Boron‐containing materials, and in particular boron nitride, have recently been identified as highly selective catalysts for the oxidative dehydrogenation of alkanes such as propane. To date, no mechanism exists that can explain both the unprecedented selectivity, the observed surface oxyfunctionalization, and the peculiar kinetic features of this reaction. We combine catalytic activity measurements with quantum chemical calculations to put forward a bold new hypothesis. We argue that the remarkable product distribution can be rationalized by a combination of surface‐mediated formation of radicals over metastable sites, and their sequential propagation in the gas phase. Based on known radical propagation steps, we quantitatively describe the oxygen pressure‐dependent relative formation of the main product propylene and by‐product ethylene. Free radical intermediates most likely differentiate this catalytic system from less selective vanadium‐based catalysts.     

Measurement of interfluorine distances in solids

(19)F homonuclear dipolar recoupling methods were used to measure internuclear distances ranging from 5 to 12 A in fluorinated organic compounds in the solid state. Magic-angle-spinning-based high-resolution techniques were utilized. Trifluoromethyl and aromatic fluorine groups were separated by rigid aromatic spacers; these compounds were diluted into nonfluorinated host molecule matrices to give isolated homonuclear spin pairs with known internuclear distances. Radiofrequency-driven recoupling (RFDR) was used to elicit magnetization exchange between the spin pairs in 1D and 2D experiments. Simulation of the exchange was accomplished using a Monte Carlo-type algorithm to search the parameter space. These methods allow the determination of distances with an accuracy of 1 A at shorter distances and 2 A at longer distances, with the assumption of no prior knowledge of T(2)(ZQ).     

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.     

Dipolar interactions in molecules aligned by strong AC electric fields

We observed magnetization transfer and spectroscopic splittings due to dipolar couplings in the solution NMR spectra of neat nitrobenzene aligned using AC electric fields. Weak dipolar splittings have been previously observed for nitrobenzene in a DC electric field (T. M. Plantenga, et al., Chem. Phys. 66, 1-9, 1982); the use of homogeneous pulsed AC fields has allowed us to establish stable experimental conditions, which were more tolerable to sample impurities and required no sample purification, and to carry out multidimensional experiments. A pulse sequence is discussed in which the electric field is present only for the indirect dimension: this sequence records the dipolar splittings for each proton in the indirect dimension; the direct dimension presents the isotropic chemical shift. Another pulse sequence is discussed that uses the applied electric field only in the mixing period to produce cross peaks between dipolar coupled pairs and correlate their isotropic chemical shifts. The order parameter describing molecular alignment was in good agreement with that previously determined from deuterium quadrupolar measurements of deuterated nitrobenzene in a similar range of electric fields: S(mol) approximately 0.025% for a field strength of 7.0 MV/m (rms). The dipolar splittings for ortho-meta, meta-para, and ortho-para protons were in qualitative agreement with the known geometry. Copyright 2000 Academic Press.