SEPT9 negatively regulates ubiquitin-dependent downregulation of EGFR.

Septins constitute a family of GTP-binding proteins that are involved in a variety of biological processes. Several isoforms have been implicated in disease, but the molecular mechanisms underlying pathogenesis are poorly understood. Here, we show that depletion of SEPT9 decreases surface levels of epidermal growth factor receptors (EGFRs) by enhancing receptor degradation. We identify a consensus motif within the SEPT9 N-terminal domain that supports its association with the adaptor protein CIN85 (also known as SH3KBP1). We further show CIN85-SEPT9 to be localized exclusively to the plasma membrane, where SEPT9 is recruited to EGF-engaged receptors in a CIN85-dependent manner. Finally, we demonstrate that SEPT9 negatively regulates EGFR degradation by preventing the association of the ubiquitin ligase Cbl with CIN85, resulting in reduced EGFR ubiquitylation. Taken together, these data provide a mechanistic explanation of how SEPT9, though acting exclusively at the plasma membrane, impairs the sorting of EGFRs into the degradative pathway.

Site-specific analysis of heteronuclear Overhauser effects in microcrystalline proteins.

Relaxation parameters such as longitudinal relaxation are susceptible to artifacts such as spin diffusion, and can be affected by paramagnetic impurities as e.g. oxygen, which make a quantitative interpretation difficult. We present here the site-specific measurement of [(1)H](13)C and [(1)H](15)N heteronuclear rates in an immobilized protein. For methyls, a strong effect is expected due to the three-fold rotation of the methyl group. Quantification of the [(1)H](13)C heteronuclear NOE in combination with (13)C-R 1 can yield a more accurate analysis of side chain motional parameters. The observation of significant [(1)H](15)N heteronuclear NOEs for certain backbone amides, as well as for specific asparagine/glutamine sidechain amides is consistent with MD simulations. The measurement of site-specific heteronuclear NOEs is enabled by the use of highly deuterated microcrystalline protein samples in which spin diffusion is reduced in comparison to protonated samples.

The mechanism of denaturation and the unfolded state of the α-helical membrane-associated protein Mistic.

In vitro protein-folding studies using chemical denaturants such as urea are indispensible in elucidating the forces and mechanisms determining the stability, structure, and dynamics of water-soluble proteins. By contrast, α-helical membrane-associated proteins largely evade such approaches because they are resilient to extensive unfolding. We have used optical and NMR spectroscopy to provide an atomistic-level dissection of the effects of urea on the structure and dynamics of the α-helical membrane-associated protein Mistic as well as its interactions with detergent and solvent molecules. In the presence of the zwitterionic detergent lauryl dimethylamine oxide, increasing concentrations of urea result in a complex sequence of conformational changes that go beyond simple two-state unfolding. Exploiting this finding, we report the first high-resolution structural models of the urea denaturation process of an α-helical membrane-associated protein and its completely unfolded state, which contains almost no regular secondary structure but nevertheless retains a topology close to that of the folded state.

Hydrogen bonding involving side chain exchangeable groups stabilizes amyloid quarternary structure.

The amyloid ß-peptide (Aß) is the major structural component of amyloid fibrils in the plaques of brains of Alzheimer's disease patients. Numerous studies have addressed important aspects of secondary and tertiary structure of fibrils. In electron microscopic images, fibrils often bundle together. The mechanisms which drive the association of protofilaments into bundles of fibrils are not known. We show here that amino acid side chain exchangeable groups like e.g. histidines can provide useful restraints to determine the quarternary assembly of an amyloid fibril. Exchangeable protons are only observable if a side chain hydrogen bond is formed and the respective protons are protected from exchange. The method relies on deuteration of the Aß peptide. Exchangeable deuterons are substituted with protons, before fibril formation is initiated.

Characterization of membrane proteins in isolated native cellular membranes by dynamic nuclear polarization solid-state NMR spectroscopy without purification and reconstitution.

Membrane proteins in their native cellular membranes are accessible by dynamic nuclear polarization magic angle spinning solid-state NMR spectroscopy without the need of purification and reconstitution (see picture). Dynamic nuclear polarization is essential to achieve the required gain in sensitivity to observe the membrane protein of interest.

Structure calculation from unambiguous long-range amide and methyl 1H-1H distance restraints for a microcrystalline protein with MAS solid-state NMR spectroscopy.

Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane proteins and amyloid fibrils. Extensive deuteration of the protein allows multidimensional experiments with exceptionally high sensitivity and resolution to be obtained. Here we present an experimental strategy to measure highly unambiguous spatial correlations for distances up to 13 Å. Two complementary three-dimensional experiments, or alternatively a four-dimensional experiment, yield highly unambiguous cross-peak assignments, which rely on four encoded chemical shift dimensions. Correlations to residual aliphatic protons are accessible via synchronous evolution of the (15)N and (13)C chemical shifts, which encode valuable amide-methyl distance restraints. On average, we obtain six restraints per residue. Importantly, 50% of all restraints correspond to long-range distances between residues i and j with |i - j| > 5, which are of particular importance in structure calculations. Using ARIA, we calculate a high-resolution structure for the microcrystalline 7.2 kDa α-spectrin SH3 domain with a backbone precision of ∼1.1 Å.

Bacterial inclusion bodies of Alzheimer's disease ß-amyloid peptides can be employed to study native-like aggregation intermediate states.

The structures of oligomeric intermediate states in the aggregation process of Alzheimer's disease ß-amyloid peptides have been the subject of debate for many years. Bacterial inclusion bodies contain large amounts of small heat shock proteins (sHSPs), which are highly homologous to those found in the plaques of the brains of Alzheimer's disease patients. sHSPs break down amyloid fibril structure in vitro and induce oligomeric assemblies. Prokaryotic protein overexpression thus mimics the conditions encountered in the cell under stress and allows the structures of Aß aggregation intermediate states to be investigated under native-like conditions, which is not otherwise technically possible. We show that IB40/IB42 fulfil all the requirements to be classified as amyloids: they seed fibril growth, are Congo red positive and show characteristic ß-sheet-rich CD spectra. However, IB40 and IB42 are much less stable than fibrils formed in vitro and contain significant amounts of non-ß-sheet regions, as seen from FTIR studies. Quantitative analyses of solution-state NMR H/D exchange rates show that the hydrophobic cores involving residues V18-F19-F20 adopt ß-sheet conformations, whereas the C termini adopt α-helical coiled-coil structures. In the past, an α-helical intermediate-state structure has been postulated, but could not be verified experimentally. In agreement with the current literature, in which Aß oligomers are described as the most toxic state of the peptides, we find that IB42 contains SDS-resistant oligomers that are more neurotoxic than Aß42 fibrils. E. coli inclusion bodies formed by the Alzheimer's disease ß-amyloid peptides Aß40 and Aß42 thus behave structurally like amyloid aggregation intermediate states and open the possibility of studying amyloids in a native-like, cellular environment.

Assignment of dynamic regions in biological solids enabled by spin-state selective NMR experiments.

Structural investigations are a prerequisite to understand protein function. Intermediate time scale motional processes (ns-micros) are deleterious for NMR of biological solids and obscure the detection of amide moieties in traditional CP based solid-state NMR approaches as well as in regular scalar coupling based experiments. We show that this obstacle can be overcome by using TROSY type techniques in triple resonance experiments, which enable the assignment of resonances in loop regions of a microcrystalline protein. The presented approach provides an exemplified solution for the analysis of secondary structure elements undergoing slow dynamics that might be particularly crucial for understanding protein function.

Identification of hydroxyl protons, determination of their exchange dynamics, and characterization of hydrogen bonding in a microcrystallin protein.

Heteronuclear correlation experiments employing perdeuterated proteins enable the observation of all hydroxyl protons in a microcrystalline protein by MAS solid-state NMR. Dipolar-based sequences allow magnetization transfers that are >50 times faster compared to scalar-coupling-based sequences, which significantly facilitates their assignment. Hydroxyl exchange rates were measured using EXSY-type experiments. We find a biexponential decay behavior for those hydroxyl groups that are involved in side chain-side chain C-O-H...O horizontal lineC hydrogen bonds. The quantification of the distances between the hydroxyl proton and the carbon atoms in the hydrogen-bonding donor as well as acceptor group is achieved via a REDOR experiment. In combination with X-ray data and isotropic proton chemical shifts, availability of (1)H,(13)C distance information can aid in the quantitative description of the geometry of these hydrogen bonds. Similarly, correlations between backbone amide proton and carbonyl atoms are observed, which will be useful in the analysis of the registry of beta-strand arrangement in amyloid fibrils.

Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solid-state.

HNCO/HNCACO type correlation experiments are an alternative for assignment of backbone resonances in extensively deuterated proteins in the solid-state, given the fact that line widths on the order of 14-17 Hz are achieved in the carbonyl dimension without the need of high power decoupling. The achieved resolution demonstrates that MAS solid-state NMR on extensively deuterated proteins is able to compete with solution-state NMR spectroscopy if proteins are investigated with correlation times tau(c) that exceed 25 ns.

Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.

We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual (15)N-T (1) timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s(-1). Backbone amide (15)N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D(2)O is employed as a solvent for sample preparation. Due to the intrinsically long (15)N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

The Surface Distributions of the Production of the Major Volatile Species, H2O, CO2, CO and O2, from the Nucleus of Comet 67P/Churyumov-Gerasimenko throughout the Rosetta Mission as Measured by the ROSINA Double Focusing Mass Spectrometer.

The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) suite of instruments operated throughout the over two years of the Rosetta mission operations in the vicinity of comet 67P/Churyumov-Gerasimenko. It measured gas densities and composition throughout the comet's atmosphere, or coma. Here we present two-years' worth of measurements of the relative densities of the four major volatile species in the coma of the comet, H2O, CO2, CO and O2, by one of the ROSINA sub-systems called the Double Focusing Mass Spectrometer (DFMS). The absolute total gas densities were provided by the Comet Pressure Sensor (COPS), another ROSINA sub-system. DFMS is a very high mass resolution and high sensitivity mass spectrometer able to resolve at a tiny fraction of an atomic mass unit. We have analyzed the combined DFMS and COPS measurements using an inversion scheme based on spherical harmonics that solves for the distribution of potential surface activity of each species as the comet rotates, changing solar illumination, over short time intervals and as the comet changes distance from the sun and orientation of its spin axis over long time intervals. We also use the surface boundary conditions derived from the inversion scheme to simulate the whole coma with our fully kinetic Direct Simulation Monte Carlo model and calculate the production rates of the four major species throughout the mission. We compare the derived production rates with revised remote sensing observations by the Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) as well as with published observations from the Microwave Instrument for the Rosetta Orbiter (MIRO). Finally we use the variation of the surface production of the major species to calculate the total mass loss over the mission and, for different estimates of the dust/gas ratio, calculate the variation of surface loss all over the nucleus.

Accurate determination of order parameters from 1H,15N dipolar couplings in MAS solid-state NMR experiments.

A reliable site-specific estimate of the individual N-H bond lengths in the protein backbone is the fundamental basis of any relaxation experiment in solution and in the solid-state NMR. The N-H bond length can in principle be influenced by hydrogen bonding, which would result in an increased N-H distance. At the same time, dynamics in the backbone induces a reduction of the experimental dipolar coupling due to motional averaging. We present a 3D dipolar recoupling experiment in which the (1)H,(15)N dipolar coupling is reintroduced in the indirect dimension using phase-inverted CP to eliminate effects from rf inhomogeneity. We find no variation of the N-H dipolar coupling as a function of hydrogen bonding. Instead, variations in the (1)H,(15)N dipolar coupling seem to be due to dynamics of the protein backbone. This is supported by the observed correlation between the H(N)-N dipolar coupling and the amide proton chemical shift. The experiment is demonstrated for a perdeuterated sample of the alpha-spectrin SH3 domain. Perdeuteration is a prerequisite to achieve high accuracy. The average error in the analysis of the H-N dipolar couplings is on the order of +/-370 Hz (+/-0.012 A) and can be as small as 150 Hz, corresponding to a variation of the bond length of +/-0.005 A.

Probing surface accessibility of proteins using paramagnetic relaxation in solid-state NMR spectroscopy.

Paramagnetic Relaxation Enhancement (PRE) can be used to accelerate NMR data acquisition by reducing the longitudinal proton relaxation time T(1) in the solid state. We show that the presence of paramagnetic compounds in the bulk solvent induces a site-specific relaxation in addition to local dynamics, which is dependent on the surface accessibility of the respective amide proton in the protein. Differentiation between paramagnetic relaxation and dynamics was achieved by a comparison of (1)H T(1) times obtained from microcrystalline protein samples prepared with different concentrations of the Cu(II)(edta) chelate. We find that relaxation can in addition be mediated by hydroxyl groups, which transfer relaxation by their ability to exchange with the quickly relaxing bulk solvent. Furthermore, relaxation seems to be transferred by water molecules which diffuse into the protein structure and yield an efficient difference PRE in flexible regions of the protein. The experiments are demonstrated using a perdeuterated sample of the alpha-spectrin SH3 domain, which was microcrystallized from a buffer containing 90% D(2)O. Deuteration is a prerequisite to avoid spin diffusion which would otherwise compromise site specific resolution.

Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy.

We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include (15)N T (1) relaxation times measured at two different magnetic fields as well as (1)H-(15)N dipole, (15)N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T (2) in the solid-state. In addition, global order parameters are included from a (1)H,(15)N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 degrees for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken alpha-spectrin SH3 domain.

MAS solid-state NMR studies on the multidrug transporter EmrE.

We study the uniformly 13C,15N isotopically enriched Escherichia coli multidrug resistance transporter EmrE using MAS solid-state NMR. Solid-state NMR can provide complementary structural information as the method allows studying membrane proteins in their native environment as no detergent is required for reconstitution. We compare the spectra obtained from wildtype EmrE to those obtained from the mutant EmrE-E14C. To resolve the critical amino acid E14, glutamic/aspartic acid selective experiments are carried out. These experiments allow to assign the chemical shift of the carboxylic carbon of E14. In addition, spectra are analyzed which are obtained in the presence and absence of the ligand TPP+.

Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins.

Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the (15)N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken alpha-spectrin, which was re-crystallized in H(2)O/D(2)O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu(II) to enable rapid data acquisition.

Structural properties of EGCG-induced, nontoxic Alzheimer's disease Aß oligomers.

The green tea compound epigallocatechin-3-gallate (EGCG) inhibits Alzheimer's disease ß-amyloid peptide (Aß) neurotoxicity. Solution-state NMR allows probing initial EGCG-Aß interactions. We show that EGCG-induced Aß oligomers adopt a well-defined structure and are amenable for magic angle spinning solid-state NMR investigations. We find that EGCG interferes with the aromatic hydrophobic core of Aß. The C-terminal part of the Aß peptide (residues 22-39) adopts a ß-sheet conformation, whereas the N-terminus (residues 1-20) is unstructured. The characteristic salt bridge involving residues D23 and K28 is present in the structure of these oligomeric Aß aggregates as well. The structural analysis of small-molecule-induced amyloid aggregates will open new perspectives for Alzheimer's disease drug development.