Non-equilibrium hydrogen exchange for determination of H-bond strength and water accessibility in solid proteins.

We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1.3 mm rotor. Tracking of the HN peak intensities for 2 weeks reports on site-specific hydrogen bond strength and also likely reflects water accessibility in a qualitative manner. H/D exchange can be directly determined for hydrogen-bonded amides using 1H detection under fast magic angle spinning. This approach complements existing methods and provides the means to elucidate interesting site-specific characteristics for protein functionality in the solid state.

Cholesterol-mediated allosteric regulation of the mitochondrial translocator protein structure.

Cholesterol is an important regulator of membrane protein function. However, the exact mechanisms involved in this process are still not fully understood. Here we study how the tertiary and quaternary structure of the mitochondrial translocator protein TSPO, which binds cholesterol with nanomolar affinity, is affected by this sterol. Residue-specific analysis of TSPO by solid-state NMR spectroscopy reveals a dynamic monomer-dimer equilibrium of TSPO in the membrane. Binding of cholesterol to TSPO's cholesterol-recognition motif leads to structural changes across the protein that shifts the dynamic equilibrium towards the translocator monomer. Consistent with an allosteric mechanism, a mutation within the oligomerization interface perturbs transmembrane regions located up to 35 Å away from the interface, reaching TSPO's cholesterol-binding motif. The lower structural stability of the intervening transmembrane regions provides a mechanistic basis for signal transmission. Our study thus reveals an allosteric signal pathway that connects membrane protein tertiary and quaternary structure with cholesterol binding.

Access to side-chain carbon information in deuterated solids under fast MAS through non-rotor-synchronized mixing.

We demonstrate the accessibility of aliphatic (13)C side chain chemical shift sets for solid-state NMR despite perdeuteration and fast MAS using isotropic, non-rotor-synchronized (13)C-(13)C mixing. Combined with amide proton detection, we unambiguously and sensitively detect whole side chain to backbone correlations for two proteins using around 1 mg of sample.

Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR.

Interactions within proteins, with their surrounding, and with other molecules are mediated mostly by hydrogen atoms. In fully protonated, inhomogeneous, or larger proteins, however, aliphatic proton shifts tend to show little dispersion despite fast Magic-Angle Spinning. 3D correlations dispersing aliphatic proton shifts by their better resolved amide N/H shifts can alleviate this problem. Using inverse second-order cross-polarization (iSOCP), we here introduce dedicated and improved means to sensitively link site-specific chemical shift information from aliphatic protons with a backbone amide resolution. Thus, even in cases where protein deuteration is impossible, this approach may enable access to various aspects of protein functions that are reported on by protons.

Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli.

Type 1 pili are filamentous protein assemblies on the surface of Gram-negative bacteria that mediate adhesion to host cells during the infection process. The molecular structure of type 1 pili remains elusive on the atomic scale owing to their insolubility and noncrystallinity. Herein we describe an approach for hybrid-structure determination that is based on data from solution-state NMR spectroscopy on the soluble subunit and solid-state NMR spectroscopy and STEM data on the assembled pilus. Our approach is based on iterative modeling driven by structural information extracted from different sources and provides a general tool to access pseudo atomic structures of protein assemblies with complex subunit folds. By using this methodology, we determined the local conformation of the FimA pilus subunit in the context of the assembled type 1 pilus, determined the exact helical pilus architecture, and elucidated the intermolecular interfaces contributing to pilus assembly and stability with atomic detail.

Asynchronous through-bond homonuclear isotropic mixing: application to carbon-carbon transfer in perdeuterated proteins under MAS.

Multiple-bond carbon-carbon homonuclear mixing is a hurdle in extensively deuterated proteins and under fast MAS due to the absence of an effective proton dipolar-coupling network. Such conditions are now commonly employed in solid-state NMR spectroscopy. Here, we introduce an isotropic homonuclear (13)C-(13)C through-bond mixing sequence, MOCCA, for the solid state. Even though applied under MAS, this scheme performs without rotor synchronization and thus does not pose the usual hurdles in terms of power dissipation for fast spinning. We compare its performance with existing homonuclear (13)C-(13)C mixing schemes using a perdeuterated and partially proton-backexchanged protein. Based on the analysis of side chain carbon-carbon correlations, we show that particularly MOCCA with standard 180-degree pulses and delays leading to non-rotor-synchronized spacing performs exceptionally well. This method provides high magnetization transfer efficiency for multiple-bond transfer in the aliphatic region compared with other tested mixing sequences. In addition, we show that this sequence can also be tailor-made for recoupling within a selected spectral region using band-selective pulses.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments.

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common (13)C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

Carbene supported dimer of heavier ketenimine analogue with p and si atoms.

A cyclic alkyl(amino) carbene (cAAC) stabilized dimer [(cAAC)Si(P-Tip)]2 (2) (Tip = 2,4,6-triisopropylphenyl) is reported. 2 can be considered as a dimer of the heavier ketenimine (R2C═C═N-R) analogue. The dark-red rod-shaped crystals of 2 were synthesized by reduction of the precursor, cAAC-dichlorosilylene-stabilized phosphinidene (cAAC)SiCl2→P-Tip with sodium napthalenide. The crystals of 2 are storable at room temperature for several months and stable up to 215 °C under an inert atmosphere. X-ray single-crystal diffraction revealed that 2 contains a cyclic nonplanar four-membered SiPSiP ring. Magnetic susceptibility measurements confirmed the singlet spin ground state of 2. Cyclic voltammetry of 2 showed a quasi-reversible one-electron reduction indicating the formation of the corresponding radical anion 2(•-), which was further characterized by EPR measurements in solution. The electronic structure and bonding of 2 and 2(•-) were studied by theoretical calculations. The experimentally obtained data are in good agreement with the calculated values.

A soluble molecular variant of the semiconducting silicondiselenide.

Silicondiselenide is a semiconductor and exists as an insoluble polymer (SiSe2) n which is prepared by reacting elemental silicon with selenium powder in the temperature range of 400-850 °C. Herein, we report on the synthesis, isolation, and characterization of carbene stabilized molecular silicondiselenide in the form of (cAAC)2Si2Se4 (3) [cAAC = cyclic alkyl(amino)carbene]. 3 is synthesized via reaction of diatomic silicon(0) compound (cAAC)2Si2 (2) with black selenium powder at -78 °C to room temperature. The intensely orange colored compound 3 is soluble in polar organic solvents and stable at room temperature for a month under an inert atmosphere. 3 decomposes above 245 °C. The molecular structure of 3 has been confirmed by X-ray single crystal diffraction. It is also characterized by UV-vis, IR, Raman spectroscopy and mass spectrometry. The stability, bonding, and electron density distributions of 3 have been studied by theoretical calculations.

Electron-induced conversion of silylones to six-membered cyclic silylenes.

A silicon atom in the zero oxidation state stabilized by two carbene ligands is known as siladicarbene (silylone). There are two pairs of electrons on the silicon atom in silylone. This was recently confirmed by both experimental and theoretical charge density investigations. The silylone is stable up to 195 °C in an inert atmosphere. However, a substoichiometric amount (33 mol%) of potassium metal triggers the activation of the unsaturated C:Si:C backbone, leading to a selective reaction with a tertiary C-H bond in an atom-economical approach to form a six-membered cyclic silylene with three-coordinate silicon atom. Cyclic voltammetry shows that this reaction proceeds via the formation of a silylone radical anion intermediate, which is further confirmed by EPR spectroscopy.

BSH-CP based 3D solid-state NMR experiments for protein resonance assignment.

We have recently presented band-selective homonuclear cross-polarization (BSH-CP) as an efficient method for CO-CA transfer in deuterated as well as protonated solid proteins. Here we show how the BSH-CP CO-CA transfer block can be incorporated in a set of three-dimensional (3D) solid-state NMR (ssNMR) pulse schemes tailored for resonance assignment of proteins at high static magnetic fields and moderate magic-angle spinning rates. Due to the achieved excellent transfer efficiency of 33 % for BSH-CP, a complete set of 3D spectra needed for unambiguous resonance assignment could be rapidly recorded within 1 week for the model protein ubiquitin. Thus we expect that BSH-CP could replace the typically used CO-CA transfer schemes in well-established 3D ssNMR approaches for resonance assignment of solid biomolecules.

Atomic structure and handedness of the building block of a biological assembly.

Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.

Full quadrupolar tensor determination by NMR using a micro-crystal spinning at the magic angle.

An implementation of rotor-synchronised Magic Angle Spinning (MAS) NMR is presented to determine the quadrupolar coupling tensor values from a single crystal study for half-integer quadrupolar nuclei. Using a microcoil based probehead for studying micro crystals with superior sensitivity, we successfully determine the full quadrupolar tensor of (23)Na using a micro crystal of dimensions 210 x 210 x 700 mum of NaNO(3) as a model system. A two step simulation procedure is used to obtain the orientation of the quadrupolar tensor information from the experimental spectra and is verified by XRD analysis.