Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations

In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.

Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy

Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.

Comparison of the 3D structures of mouse and human α-synuclein fibrils by solid-state NMR and STEM

Intra-neuronal aggregation of α-synuclein into fibrils is the molecular basis for α-synucleinopathies, such as Parkinson's disease. The atomic structure of human α-synuclein (hAS) fibrils was recently determined by Tuttle et al. using solid-state NMR (ssNMR). The previous study found that hAS fibrils are composed of a single protofilament. Here, we have investigated the structure of mouse α-synuclein (mAS) fibrils by STEM and isotope-dilution ssNMR experiments. We found that in contrast to hAS, mAS fibrils consist of two or even three protofilaments which are connected by rather weak interactions in between them. Although the number of protofilaments appears to be different between hAS and mAS, we found that they have a remarkably similar secondary structure and protofilament 3D structure as judged by secondary chemical shifts and intra-molecular distance restraints. We conclude that the two mutant sites between hAS and mAS (positions 53 and 87) in the fibril core region are crucial for determining the quaternary structure of α-synuclein fibrils.

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.

High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles

The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22 %, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility.

Automatic ¹H-NMR Screening of Fatty Acid Composition in Edible Oils

In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC). To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual) was determined by ¹H-NMR spectroscopy according to this protocol.

Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

Strategies for solid-state NMR investigations of supramolecular assemblies with large subunit sizes

Solid-state NMR is a versatile tool to study structure and dynamics of insoluble and non-crystalline biopolymers. Supramolecular protein assemblies are formed by self-association of multiple copies of single small-sized proteins. Because of their high degree of local order, solid-state NMR spectra of such systems exhibit an unusually high level of resolution, rendering them an ideal target for solid-state NMR investigations. Recently, our group has solved the structure of one particular supramolecular assembly, the type-iii-secretion-system needle. The needle subunit comprises around 80 residues. Many interesting supramolecular assemblies with unknown structure have subunits larger in size, which requires development of tailored solid-state NMR strategies to address their structures. In this "Perspective" article, we provide a view on different approaches to enhance sensitivity and resolution in biological solid-state NMR with a focus on the possible application to supramolecular assemblies with large subunit sizes.

Experimental boundaries of the quantum rotor induced polarization (QRIP) in liquid state NMR

The Haupt-effect is a rather seldom used hyperpolarization method. It is based on the interdependence between nuclear spin states and rotational states of nearly free rotating methyl groups having C3 symmetry. A sudden change in temperature from 4.2 K to room temperature by fast dissolution yields considerably enhanced (13)C and (1)H resonance signals. This phenomenon is now termed quantum rotor induced polarization. More than 40 substances have been studied by this approach in order to identify them as polarizable by the 'Haupt-effect in the liquid state'. Influencing factors have been analyzed systematically. It could be concluded that substances having a high tunneling frequency, which is due to a small and narrow potential barrier, are most likely to feature quantum rotor induced polarization-enhanced signals.

Transfer of the Haupt-hyperpolarization to neighbor spins

The NMR hyperpolarization observed for freely rotating methyl groups by exerting a temperature jump from 4.2 K to 298 K can be transferred to spins which have a spin, spin coupling with the carbon of the methyl group. First, a spin echo sequence readjusts the primary up/down signals to an in-phase multiplet. This in-phase magnetization is then decoupled and transferred by a simple COSY step using one scan. The polarization factors at the neighbor spins are about 50 by comparing their signal-to-noise ratio with the signal strength after full relaxation.

[Multiple metachronous metastases of renal cell carcinoma in the pancreas. Case report and review of the literature]

Isolated pancreatic metastases from renal-cell carcinomas (RCC) are extremely rare. Only 96 cases of clinically diagnosed renal-cell carcinoma metastatic to the pancreas have been reported in the world literature, and 70 of the patients (including ours) underwent a definitive surgical resection. In many cases the time between the nephrectomy and diagnosis of metachronous metastases is reported to exceed 10 years. Therefore, the initial diagnosis may be overlooked when there is a prolonged disease-free interval. When it does occur simultaneously or metachronously, aggressive surgical resection, when possible, seems to be the most effective treatment for this metastatic lesion. Surgical resection can provide long-term survival in selected cases. We present the case of a 69-year-old woman in whom two pancreatic metastases were treated by a left-sided subtotal pancreatectomy with splenectomy, 12 years after radical nephrectomy for a RCC. The patient simultaneously presented with both a mass in the body of the pancreas and a right-sided colon cancer. Thus, the diagnosis of pancreatic metastasis of colon cancer was suspected initially. Both tumors were radically resected, and histological examination revealed two pancreatic metastases from the previous RCC. In the world literature this report represents the eighth case of multiple pancreatic metastases due to RCC. It illustrates a rare indication of pancreatic resection because of pancreatic metastasis. The need for prolonged follow-up of patients is emphasized. The few reports on surgically treated pancreatic metastases from RCC are reviewed after the presentation of this case.

[Experiences, ideas, confusions with education for social und milieu therapy in a school and advanced training of therapeutic personel in Bethel (author's transl)]

The author, agent of advanced training, reports--on the background of ten years organisationel development in a large psychiatric institution (Bethel)--his experiences under the special view of training therapists of all kind, mainly nonacademic personel. This all is done in many different and interdependent courses, a small department of a school within. The problems, in his view, are that education for all professions in Germany don't prepare really--in the sense of giving personal and pragmatic competence--for psychiatric work with the sick or handicapped and other professionels. So advanced training courses must help during people work in the institution. The author is confused but sure, that the best training evidently can't enable people in the central point--beeing encouraged to stay beside and with the sick people, if there is not growing a community of helpers together and with the patients. So education, studies and training are very important. But it seems that it doesn't work without sharing personal existance together, personel and sick.