Carole Gardiennet

3D Structure Determination of the Crh Protein from Highly Ambiguous Solid-State NMR Restraints

In a wide variety of proteins, insolubility presents a challenge to structural biology, as X-ray crystallography and liquid-state NMR are unsuitable. Indeed, no general approach is available as of today for studying the three-dimensional structures of membrane proteins and protein fibrils. We here demonstrate, at the example of the microcrystalline model protein Crh, how high-resolution 3D structures can be derived from magic-angle spinning solid-state NMR distance restraints for fully labeled protein samples. First, we show that proton-mediated rare-spin correlation spectra, as well as carbon-13 spin diffusion experiments, provide enough short, medium, and long-range structural restraints to obtain high-resolution structures of this 2 x 10.4 kDa dimeric protein. Nevertheless, the large number of 13C/15N spins present in this protein, combined with solid-state NMR line widths of about 0.5-1 ppm, induces substantial ambiguities in resonance assignments, preventing 3D structure determination by using distance restraints uniquely assigned on the basis of their chemical shifts. In the second part, we thus demonstrate that an automated iterative assignment algorithm implemented in a dedicated solid-state NMR version of the program ARIA permits to resolve the majority of ambiguities and to calculate a de novo 3D structure from highly ambiguous solid-state NMR data, using a unique fully labeled protein sample. We present, using distance restraints obtained through the iterative assignment process, as well as dihedral angle restraints predicted from chemical shifts, the 3D structure of the fully labeled Crh dimer refined at a root-mean-square deviation of 1.33 A.

Methyl Proton Contacts Obtained Using Heteronuclear Through-Bond Transfers in Solid-State NMR Spectroscopy

A two-dimensional proton-mediated carbon-carbon correlation experiment that relies on through-bond heteronuclear magnetization transfers is demonstrated in the context of solid-state NMR of proteins. This new experiment, dubbed J-CHHC by analogy to the previously developed dipolar CHHC techniques, is shown to provide selective and sensitive correlations in the methyl region of 2D spectra of crystalline organic compounds. The method is then demonstrated on a microcrystalline sample of the dimeric protein Crh (2 x 10.4 kDa). A total of 34 new proton-proton contacts involving side-chain methyl groups were observed in the J-CHHC spectrum, which had not been observed with the conventional experiment. The contacts were then used as additional distance restraints for the 3D structure determination of this microcrystalline protein. Upon addition of these new distance restraints, which are in large part located in the hydrophobic core of the protein, the root-mean-square deviation with respect to the X-ray structure of the backbone atom coordinates of the 10 best conformers of the new ensemble of structures is reduced from 1.8 to 1.1 A.

Probing molecular geometry of solids by nuclear magnetic resonance spin exchange at the n=0 rotational-resonance condition

Exploration of the molecular geometry in rotating powder solids on the basis of magnetization exchange between spins with identical isotropic chemical shifts but differing chemical shielding tensor orientations is demonstrated experimentally. For this we take advantage of the potential of the ODESSA (one-dimensional exchange spectroscopy by sidebands alternation) experiment for the accurate measurement of spin exchange rate constants. We also report the observation of oscillatory behavior of the rotor-driven magnetization exchange at this so-called n=0 rotational-resonance condition which, in contrast to n=1,2,3,… rotational-resonance conditions, takes place at nearly arbitrary magic-angle spinning frequencies. The sensitivity of the longitudinal exchange decays to the relevant physical parameters of the spin system under conditions of rotor-driven and proton-driven magnetization exchange is discussed theoretically and demonstrated experimentally. Several 13C and 31P spin-exchange measurements have been p...

Determining the geometry of strongly hydrogen-bonded silanols in a layered hydrous silicate by solid-state nuclear magnetic resonance.

High-resolution solid-state NMR spectroscopy is exploited to obtain structural constraints involving strongly hydrogen-bonded silanols in octosilicate, a prominent member of the layered hydrous sodium silicates. Proton-silicon cross-polarization dynamics reveals that octosilicate contains two types of Q(3) silicons present in hydrogen-bonded -Si-O-Hcdots, three dots, centeredO-Si- and -Si-O(-)-type sites which can only be distinguished by their different abilities to cross polarize and the different mobilities of neighboring hydrous species. The theoretical analysis of the oscillating components of the polarization transfer buildup curves suggests that the model of heteronuclear pairs is an adequate description of the quantum spin system within hydrogen-bonded -Si-O-Hcdots, three dots, centeredO-Si- fragments. We also show that dipolar modulated, slow speed magic-angle (29)Si NMR spectrum provides unique geometric information on strongly hydrogen-bonded silanols. The dipolar modulated spinning sidebands contain all the information necessary to determine the internuclear Sicdots, three dots, centeredH distances as well as the magnitude and orientation of the principal elements of the (29)Si chemical shielding tensor in the molecular frame. The data provide definite proof of the intralayer character of strongly hydrogen-bonded silanol groups in a bridging, albeit not symmetric, position between neighboring tetrahedra. The approach developed in this work may be useful to obtain structural information on related layered alkali metal silicates, silica gels as well as on other classes of microporous materials.

Straightforward detection of the secondary ionisation of the phosphate group and pK determinations by high-resolution solid-state 31P NMR

The suitability of high-resolution solid-state 31P NMR for a straightforward determination of the protonation state of phosphate groups as well as of their pK2 values extracted from solid state mono : dianionic ratios has been demonstrated.