The determination of a representative set of protein structures is a chief aim in structural genomics. Solid-state NMR may have a crucial role in structural investigations of those proteins that do not easily form crystals or are not accessible to solution NMR, such as amyloid systems or membrane proteins. Here we present a protein structure determined by solid-state magic-angle-spinning (MAS) NMR. Almost complete (13)C and (15)N resonance assignments for a micro-crystalline preparation of the alpha-spectrin Src-homology 3 (SH3) domain formed the basis for the extraction of a set of distance restraints. These restraints were derived from proton-driven spin diffusion (PDSD) spectra of biosynthetically site-directed, labelled samples obtained from bacteria grown using [1,3-(13)C]glycerol or [2-(13)C]glycerol as carbon sources. This allowed the observation of long-range distance correlations up to approximately 7 A. The calculated global fold of the alpha-spectrin SH3 domain is based on 286 inter-residue (13)C-(13)C and six (15)N-(15)N restraints, all self-consistently obtained by solid-state MAS NMR. This MAS NMR procedure should be widely applicable to small membrane proteins that can be expressed in bacteria.

The aryl hydrocarbon receptor (AhR) is a highly conserved ligand-dependent transcription factor that senses environmental toxins and endogenous ligands, thereby inducing detoxifying enzymes and modulating immune cell differentiation and responses. We hypothesized that AhR evolved to sense not only environmental pollutants but also microbial insults. We characterized bacterial pigmented virulence factors, namely the phenazines from Pseudomonas aeruginosa and the naphthoquinone phthiocol from Mycobacterium tuberculosis, as ligands of AhR. Upon ligand binding, AhR activation leads to virulence factor degradation and regulated cytokine and chemokine production. The relevance of AhR to host defence is underlined by heightened susceptibility of AhR-deficient mice to both P. aeruginosa and M. tuberculosis. Thus, we demonstrate that AhR senses distinct bacterial virulence factors and controls antibacterial responses, supporting a previously unidentified role for AhR as an intracellular pattern recognition receptor, and identify bacterial pigments as a new class of pathogen-associated molecular patterns.

Slim peaks: Using a perdeuterated protein recrystallized from a 10:90 H2O:D2O mixture in magic‐angle spinning (MAS) solid‐state NMR spectroscopy experiments gives small 1H line widths at moderate spinning frequencies without application of homonuclear decoupling. This labeling strategy opens new perspectives for assignment of large protein spin systems.

In this paper, a three-dimensional (3D) NMR-based approach for the determination of the fold of moderately sized proteins by solid-state magic-angle spinning (MAS) NMR is presented and applied to the R-spectrin SH3 domain. This methodology includes the measurement of multiple 13 C- 13 C distance restraints on biosynthetically site-directed 13 C-enriched samples, obtained by growing bacteria on [2-13 C]glycerol and [1,3-13 C]glycerol. 3D 15 N-13 C-13 C dipolar correlation experiments were applied to resolve overlap of signals, in particular in the region where backbone carbon-carbon correlations of the C R -C R , CO-CO, C R -CO, and CO-C R type appear. Additional restraints for confining the structure were obtained from φ and ψ backbone torsion angles of 29 residues derived from C R , C , CO, NH, and H R chemical shifts. Using both distance and angular restraints, a refined structure was calculated with a backbone root-mean-square deviation of 0.7 Å with respect to the average structure.Many biological systems, such as membrane proteins and amyloid fibrils, remain a challenge in structural biology because of difficulties with crystallization and solubility. In the past years, solid-state NMR 1 has become a promising method for obtaining structural information about these systems, via the measurement of accurate distances (1-7), φ and backbone torsion angles (8-10), and chemical shift anisotropy (11,12). In these studies, samples labeled only in the positions of interest were investigated. For the determination of the complete protein folds, however, a different approach that allows the collection of a large number of structural restraints from a small number of samples has to be followed. The quality of the structures increases with the number of restraints, and the more that are measured, the lower the accuracy of the individual restraints may be. From a close analysis of the topology of helical and -sheet structures, it transpires that carboncarbon distances are very important in defining the fold of a protein. For example, distances between backbone carbons, i.e., R-carbons and carbonyl carbons, define the secondary structure of a protein (Table 1). Distances between backbone and side chain carbons or between side chain and side chain carbons provide information about the tertiary structure. The detection of structure-defining long-range carbon-carbon restraints is only possible when so-called dipolar truncation effects are suppressed (13,14). This can be accomplished by employing a reduced labeling scheme, in which chemically bonded carbons are not simultaneously labeled and hence the number of strong dipolar couplings between connected nuclei is reduced. For proteins expressed in bacterial systems, this can be achieved by using [2-13 C]glycerol or [1,3-13 C]glycerol as the only carbon source in the media (15)(16)(17). In combination with this labeling pattern, long-range 13 C-13 C distance restraints may be collected by using a broad-band recoupling method like the proton-driven spindiffusion (PDSD...

SignificanceUnderstanding the formation and structure of protective bacterial biofilms will help to design and identify antimicrobial strategies. Our experiments with the secreted major biofilm protein TasA characterize on a molecular level in vivo the transition of a folded protein into protease-resistant biofilm-stabilizing fibrils. Such conformational changes from a globular state into fibrillar structures are so far not seen for other biofilm-forming proteins. In this context, TasA can serve as a model system to study functional fibril formation from a globular state.

We present a systematic study of the effect of the level of exchangeable protons on the observed amide proton linewidth obtained in perdeuterated proteins. Decreasing the amount of D 2 O employed in the crystallization buffer from 90 to 0%, we observe a fourfold increase in linewidth for both 1 H and 15 N resonances. At the same time, we find a gradual increase in the signal-to-noise ratio (SNR) for 1 H-15 N correlations in dipolar coupling based experiments for H 2 O concentrations of up to 40%. Beyond 40%, a significant reduction in SNR is observed. Scalarcoupling based 1 H-15 N correlation experiments yield a nearly constant SNR for samples prepared with B30% H 2 O. Samples in which more H 2 O is employed for crystallization show a significantly reduced NMR intensity. Calculation of the SNR by taking into account the reduction in 1 H T 1 in samples containing more protons (SNR per unit time), yields a maximum SNR for samples crystallized using 30 and 40% H 2 O for scalar and dipolar coupling based experiments, respectively. A sensitivity gain of 3.8 is obtained by increasing the H 2 O concentration from 10 to 40% in the CP based experiment, whereas the linewidth only becomes 1.5 times broader. In general, we find that CP is more favorable compared to INEPT based transfer when the number of possible 1 H, 1 H interactions increases. At low levels of deuteration (C60% H 2 O in the crystallization buffer), resonances from rigid residues are broadened beyond detection. All experiments are carried out at MAS frequency of 24 kHz employing perdeuterated samples of the chicken a-spectrin SH3 domain.

Channelrhodopsins (ChR) are light-gated ion channels of green algae that are widely used to probe the function of neuronal cells with light. Most ChRs show a substantial reduction in photocurrents during illumination, a process named "light adaptation". The main objective of this spectroscopic study was to elucidate the molecular processes associated with light-dark adaptation. Here we show by liquid and solid-state nuclear magnetic resonance spectroscopy that the retinal chromophore of fully dark-adapted ChR is exclusively in an all-trans configuration. Resonance Raman (RR) spectroscopy, however, revealed that already low light intensities establish a photostationary equilibrium between all-trans,15-anti and 13-cis,15-syn configurations at a ratio of 3:1. The underlying photoreactions involve simultaneous isomerization of the C(13)═C(14) and C(15)═N bonds. Both isomers of this DAapp state may run through photoinduced reaction cycles initiated by photoisomerization of only the C(13)═C(14) bond. RR spectroscopic experiments further demonstrated that photoinduced conversion of the apparent dark-adapted (DAapp) state to the photocycle intermediates P500 and P390 is distinctly more efficient for the all-trans isomer than for the 13-cis isomer, possibly because of different chromophore-water interactions. Our data demonstrating two complementary photocycles of the DAapp isomers are fully consistent with the existence of two conducting states that vary in quantitative relation during light-dark adaptation, as suggested previously by electrical measurements.

Previously, Ishii et al., could show that chelated paramagnetic ions can be employed to significantly decrease the recycle delay of a MAS solid-state NMR experiment [N.P. Wickramasinghe, M. Kotecha, A. Samoson, J. Past, Y. Ishii, Sensitivity enhancement in C-13 solid-state NMR of protein microcrystals by use of paramagnetic metal ions for optimizing H-1 T-1 relaxation, J. Magn. Reson. 184 (2007) 350-356]. Application of the method is limited to very robust samples, for which sample stability is not compromised by RF induced heating. In addition, probe integrity might be perturbed in standard MAS PRE experiments due to the use of very short duty cycles. We show that these deleterious effects can be avoided if perdeuterated proteins are employed that have been re-crystallized from D 2 O:H 2 O = 9:1 containing buffer solutions. The experiments are demonstrated using the SH3 domain of chicken a-spectrin as a model system. The labeling scheme allows to record proton detected 1 H, 15 N correlation spectra with very high resolution in the absence of heteronuclear dipolar decoupling. Cu-edta as a doping reagent yields a reduction of the recycle delay by up to a factor of 15. In particular, we find that the 1 H T 1 for the bulk H N magnetization is reduced from 4.4 s to 0.3 s if the Cu-edta concentration is increased from 0 mM to 250 mM. Possible perturbations like chemical shift changes or line broadening due to the paramagnetic chelate complex are minimal. No degradation of our samples was observed in the course of the experiments.