Showing papers by "Christian Griesinger published in 2012"

Atomic model of the type III secretion system needle

Abstract: The structure of the needle of the type III secretion system of Salmonella typhimurium, used to inject virulence proteins into host cells during infection, has been resolved by a combination of in vitro needle production, solid-state nuclear magnetic resonance, electron microscopy and Rosetta modelling at atomic resolution. The 'type-III' secretion system is used by many pathogenic bacteria to inject virulence proteins into host cells during infection. Using a combination of solid-state nuclear magnetic resonance imaging, electron microscopy and Rosetta modelling, the structure of the secretion needle at atomic resolution has now been resolved. The resulting atomic model reveals clearly defined supramolecular interfaces, an extended amino-terminal domain positioned on the surface of the needle, and a carboxy terminus pointing towards the lumen. Pathogenic bacteria using a type III secretion system (T3SS)1,2 to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells3,4,5,6. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies7,8,9,10,11,12, resulting in low-resolution and medium-resolution models13,14,15,16,17. However, such approaches cannot deliver atomic details, especially of the crucial subunit–subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be α-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.

β-sheet core of Tau paired helical filaments revealed by solid-state NMR

Abstract: One of the hallmarks of Alzheimer’s disease is the self-assembly of the microtubule-associated protein tau into fibers termed “paired helical filaments” (PHFs). However, the structural basis of PHF assembly at atomic detail is largely unknown. Here, we applied solid-state nuclear magnetic resonance (ssNMR) spectroscopy to investigate in vitro assembled PHFs from a truncated three-repeat tau isoform (K19) that represents the core of PHFs. We found that the rigid core of the fibrils is formed by amino acids V306 to S324, only 18 out of 99 residues, and comprises three β-strands connected by two short kinks. The first β-strand is formed by the well-studied hexapeptide motif VQIVYK that is known to self-aggregate in a steric zipper arrangement. Results on mixed [15N:13C]-labeled K19 fibrils show that β-strands are stacked in a parallel, in-register manner. Disulfide bridges formed between C322 residues of different molecules lead to a disturbance of the β-sheet structure, and polymorphism in ssNMR spectra is ...

Is Enantiomer Assignment Possible by NMR Spectroscopy Using Residual Dipolar Couplings from Chiral Nonracemic Alignment Media?—A Critical Assessment

Abstract: The discovery of Jean-Baptiste Biot in 1815 that optical activity is not a property bound to a certain aggregation state of matter but a property of the constituting molecules themselves, has had an enormous influence on the structural models that chemists developed at the end of the 19th century, long before the description of the chemical bond was based on quantum mechanics. Pasteur achieved the first separation of enantiomers in 1847, namely by crystallization of a racemic tartrate mixture that separated the two enantiomers into enantiomorphic crystals, solutions of which rotated the plane of linearly polarized light in opposite directions. Not until 1951, when Bijvoet used anomalous X-ray diffraction, it was possible to assign the absolute configuration to a specific enantiomer. However, anomalous X-ray diffraction has not put the problem of assigning absolute configurations to rest, because many chemical compounds cannot be crystallized. Moreover, anomalous X-ray diffraction of molecules that consist exclusively of lightweight atoms commonly lacks the needed accuracy to allow unambiguous assignment of absolute configurations. An alternative method for resolving enantiomers is to convert them to diastereoisomers, either by chemical derivatization with chiral nonracemic moieties or by intermolecular coordination with chiral nonracemic reagents. In this way it is possible to determine absolute configuration from NMR observables, most commonly chemical shifts. The use of chiroptical spectroscopies such as optical rotatory dispersion, and electronic or vibrational circular dichroism is well established, sometimes in combination with ab initio calculations. Further methods are conceivable but impractical momentarily. Yet, there is currently not a simple and universally applicable approach to determine the absolute configuration of molecules with few stereogenic centers. Two recent papers published in 2007 and 2011 have therefore created a lot of excitement in the chemistry and NMR spectroscopy communities. Their titles are: “Stereochemical Identification of (R)and (S)-Ibuprofen Using Residual Dipolar Couplings, NMR, and Modeling”, henceforth called “article 1”, and more recently: “Spin-Selective Correlation Experiment for Measurement of Long-Range J Couplings and for Assignment of (R/S) Enantiomers from the Residual Dipolar Couplings and DFT”, henceforth called “article 2”. Both articles describe the assignment of the absolute configuration of the chiral molecules, ibuprofen 1 (article 1) and 4-methyl-1,3-dioxolan-2-one 2 (article 2), using NMR spectroscopy in chiral nonracemic alignment media (Figure 1). Under chiral nonracemic conditions, the authors measured residual dipolar couplings (RDCs), a NMR parameter only visible in oriented samples, such as in liquid crystals, but not in isotropic solvents. The interaction of the enantiomers with the chiral nonracemic alignment medium gives rise to diastereomorphic associates for which reason the authors indeed found different sets of anisotropic parameters for each enantiomer, in total

Determining the absolute configuration of (+)-mefloquine HCl, the side-effect-reducing enantiomer of the antimalaria drug Lariam.

Abstract: Even though the important antimalaria drug rac-erythro-mefloquine HCl has been on the market as Lariam for decades, the absolute configurations of its enantiomers have not been determined conclusively. This is needed, since the (−) enantiomer is believed to cause adverse side effects in malaria treatment resulting from binding to the adenosine receptor in the human brain. Since there are conflicting assignments based on enantioselective synthesis and anomalous X-ray diffraction, we determined the absolute configuration using a combination of NMR, optical rotatory dispersion (ORD), and circular dichroism (CD) spectroscopy together with density functional theory calculations. First, structural models of erythro-mefloquine HCl compatible with NMR-derived 3 JHH scalar couplings, 15 N chemical shifts, rotational Overhauser effects, and residual dipolar couplings were constructed. Second, we calculated ORD and CD spectra of the structural models and compared the calculated data with the experimental values. The experimental results for (−)-erythro-mefloquine HCl matched our calculated chiroptical data for the 11R,12S model. Accordingly, we conclude that the assignment of 11R,12S to (−)-erythro-mefloquine HCl is correct.

Relative and Absolute Configuration of Vatiparol (1 mg): A Novel Anti-inflammatory Polyphenol

Abstract: Bioactive natural products offer multiple opportunities for the discovery of novel chemical entities with potential pharmaceutical, nutraceutical and agrochemical applications. Many new organic compounds with novel scaffolds are isolated in small quantities and established methods often fail to determine the structure and bioactivity of such novel natural products. To meet this challenge, we present here a new methodology combining RDC (residual dipolar coupling)-based NMR spectroscopy in microtubes, with a motif-inspired biological assessment strategy. Using only one milligram (ca. 1.5 μmol) of sample, the new protocol established the bioactivity as well as the relative and absolute configuration of vatiparol obtained from Vatica parvifolia. Vatiparol is unique in its unprecedented carbon skeleton and selective inhibitory effect on the expression of monocyte chemo-attractant protein-1 (MCP-1, also known as CCL2). The plausible biosynthetic pathway of vatiparol is briefly discussed. The approach introduced here promises to be widely applicable to the determination of the structure and bioactivity of structurally unknown organic samples available in very limited amounts.

Thermal coefficients of the methyl groups within ubiquitin

Abstract: Physiological processes such as protein folding and molecular recognition are intricately linked to their dynamic signature, which is reflected in their thermal coefficient. In addition, the local conformational entropy is directly related to the degrees of freedom, which each residue possesses within its conformational space. Therefore, the temperature dependence of the local conformational entropy may provide insight into understanding how local dynamics may affect the stability of proteins. Here, we analyze the temperature dependence of internal methyl group dynamics derived from the cross-correlated relaxation between dipolar couplings of two CH bonds within ubiquitin. Spanning a temperature range from 275 to 308 K, internal methyl group dynamics tend to increase with increasing temperature, which translates to a general increase in local conformational entropy. With this data measured over multiple temperatures, the thermal coefficient of the methyl group order parameter, the characteristic thermal coefficient, and the local heat capacity were obtained. By analyzing the distribution of methyl group thermal coefficients within ubiquitin, we found that the N-terminal region has relatively high thermostability. These results indicate that methyl groups contribute quite appreciably to the total heat capacity of ubiquitin through the regulation of local conformational entropy.

Chiral discrimination of amines by anisotropic NMR parameters using chiral polyacrylamide-based gels.

Abstract: A new chiral alignment medium for dimethyl sulfoxide, methanol, and water as solvents was developed. Because both enantiomers of the gel are available, it is possible to enantiodiscriminate natural products such as strychnine HCl that naturally occurs as single enantiomer. With the two methods of achieving anisotropy, namely stretching and confinement, the degree of alignment can be adjusted, and the director changed from horizontal to vertical. This increases the applicability. Three compounds were enantiodiscriminated on the basis of residual dipolar coupling data: mefloquine HCl, strychnine HCl, and menthylamine HCl.

Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima.

Abstract: Barleria alluaudii and Diospyros maritima were both investigated as part of an ongoing search for synergistic TRAIL (tumor necrosis factor-α-related apoptosis-inducing ligand) sensitizers. As a result of this study, two naphthoquinone epoxides, 2,3-epoxy-2,3-dihydrolapachol (1) and 2,3-epoxy-2,3-dihydro-8-hydroxylapachol (2), both not previously isolated from natural sources, and the known 2-methylanthraquinone (3) were identified from B. alluaudii. Time-dependent density functional theory (TD-DFT) calculations of electronic circular dichroism (ECD) spectra were utilized to establish the absolute configuration of 1 and 2. Additionally, five known naphthoquinone derivatives, maritinone (4), elliptinone (5), plumbagin (6), (+)-cis-isoshinanolone (7), and ethylidene-6,6′-biplumbagin (8), were isolated from D. maritima. Compounds 1, 2, and 4–6 showed varying levels of synergy with TRAIL. Maritinone (4) and elliptinone (5) showed the highest synergistic effect, with more than a 3-fold increase in activity obse...

An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude

Abstract: Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns.

Evaluation of a Shuttle DNP Spectrometer by Calculating the Coupling and Global Enhancement Factors of l -Tryptophan

Abstract: A liquid state shuttle dynamic nuclear polarization (DNP) spectrometer is presented, featuring several technical modifications that increase stability and improve reproducibility. For the protons of l-tryptophan, the signal enhancement and the DNP spin properties, such as relaxation, were measured and compared with each other. The calculated coupling factors suggest that the proton accessibility for the polarizer molecule has an important influence on the DNP enhancement. In general, short proton spin longitudinal relaxation times without radical reduce the detectable enhancement by decreasing the leakage factor and increasing the relaxation losses during the course of the sample transfer. The usage of a global enhancement factor gives a more complete overview of the capabilities for the described experimental setup. Global enhancements of up to −4.2 for l-tryptophan protons are found compared to pure Boltzmann enhancements of up to −2.4.

Standard tensorial analysis of local ordering in proteins from residual dipolar couplings.

Abstract: Residual dipolar couplings (RDCs) in proteins arise from independent external medium-related and internal protein-related ordering of the spin-bearing probe. Griesinger et al. developed a method for treating RDCs in proteins. The global ordering is given in the standard manner by a rank 2 tensor specified in a known molecular frame, MF. The local ordering is described by the spherical harmonic ensemble averages, ⟨Y2m(θ, φ)⟩, m = 0, ±1, ±2, also given in MF. From these quantities, a method we call mf-RDC derives the squared generalized order parameter (Srdc2), the amplitude (direction) of the anisotropic disorder, η (Φ′), and an approximation, (N–H)eff, to the average probe orientation, i.e., to the local director. (N–H)eff is determined through a frame transformation where ⟨Y20⟩ is maximized. Φ′ is associated with a subsequent frame transformation where ⟨Y22 + Y2–2⟩ is maximized. The mf-RDC method was applied previously to N–H and C–Cmethyl sites in ubiquitin. In this study, we convert the respective ⟨Y...

Corrigendum: Atomic model of the type III secretion system needle

Abstract: Nature 486, 276–279 (2012); 10.1038/nature11079 In this Letter, we omitted to cite ref. 1, which presents a cryo-electron-microscopic map of the Shigella flexneri needle at a resolution of 7 A, significantly higher than for previous maps. Our Salmonella typhimurium needle model (2.1-A backbone) fitsvery well into this high-resolution cryo-electron-microscopic map, and observed differences regarding the location of the amino terminus will be discussed in a future publication.

Guiding protein-ligand docking with different experimental NMR-data

Abstract: Today’s scoring functions are one of the main reasons that state-of-the-art protein-ligand dockings fail in about 20 % to 40 % of the targets due to the sometimes severe approximations they make. However these approximations are necessary for performance reasons. One possibility to overcome these problems is the inclusion of additional, preferably experimental information in the docking process. Especially ligand-based NMR experiments that are far less demanding than the solution of the whole complex structure are helpful. Here we present the inclusion of three different types of NMR-data into the ChemPLP [1] scoring function of our docking tool PLANTS [2]. First, STD and intraligand trNOE spectra were used to obtain distant constraints between ligand and protein atoms. This approach proved beneficial for the docking of larger peptide ligands i. e. the epitope of MUC-1 glycoprotein to the SM3 antibody [3]. In the second part the usefulness of INPHARMA data [4,5] is shown by combinig a score, evaluating the agreement between simulated and measured INPHARMA spectra, with the PLANTS ChemPLP scoring function. First results from rescoring after local optimization of the poses and full docking experiments are shown.

TOCSY in ROESY and ROESY in TOCSY

Abstract: The sections in this article are 1 Introduction 2 Theory 3 Separation of Hartmann–Hahn Transfer and Cross Relaxation 4 Acknowledgements

Fascinated by NMR since 30 years.

Abstract: The biographical instances that guided Christian Griesinger toward NMR were early interest in chemistry (enhanced by participation in two chemistry olympiads) and physics, NMR relying on both basic sciences, and contact with NMR during undergraduate studies. History of scientific contributions covered are correlation experiments, three-dimensional NMR, sensitivity enhancement, cross-correlated relaxation, protein dynamics, structural biology, and finally neurodegeneration. Keywords: liquid state NMR methodology; 3D NMR; sensitivity enhancement; structural biology; protein dynamics; neurodegeneration; cross-correlated relaxation