1H detection and dynamic nuclear polarization-enhanced NMR of Aß1-42 fibrils.

Several publications describing high-resolution structures of amyloid-ß (Aß) and other fibrils have demonstrated that magic-angle spinning (MAS) NMR spectroscopy is an ideal tool for studying amyloids at atomic resolution. Nonetheless, MAS NMR suffers from low sensitivity, requiring relatively large amounts of samples and extensive signal acquisition periods, which in turn limits the questions that can be addressed by atomic-level spectroscopic studies. Here, we show that these drawbacks are removed by utilizing two relatively recent additions to the repertoire of MAS NMR experiments-namely, 1H detection and dynamic nuclear polarization (DNP). We show resolved and sensitive two-dimensional (2D) and three-dimensional (3D) correlations obtained on 13C,15N-enriched, and fully protonated samples of M0Aß1-42 fibrils by high-field 1H-detected NMR at 23.4 T and 18.8 T, and 13C-detected DNP MAS NMR at 18.8 T. These spectra enable nearly complete resonance assignment of the core of M0Aß1-42 (K16-A42) using submilligram sample quantities, as well as the detection of numerous unambiguous internuclear proximities defining both the structure of the core and the arrangement of the different monomers. An estimate of the sensitivity of the two approaches indicates that the DNP experiments are currently ∼6.5 times more sensitive than 1H detection. These results suggest that 1H detection and DNP may be the spectroscopic approaches of choice for future studies of Aß and other amyloid systems.

An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum.

Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.

1H-detected characterization of carbon-carbon networks in highly flexible protonated biomolecules using MAS NMR.

In the last three decades, the scope of solid-state NMR has expanded to exploring complex biomolecules, from large protein assemblies to intact cells at atomic-level resolution. This diversity in macromolecules frequently features highly flexible components whose insoluble environment precludes the use of solution NMR to study their structure and interactions. While High-resolution Magic-Angle Spinning (HR-MAS) probes offer the capacity for gradient-based 1H-detected spectroscopy in solids, such probes are not commonly used for routine MAS NMR experiments. As a result, most exploration of the flexible regime entails either 13C-detected experiments, the use of partially perdeuterated systems, or ultra-fast MAS. Here we explore proton-detected pulse schemes probing through-bond 13C-13C networks to study mobile protein sidechains as well as polysaccharides in a broadband manner. We demonstrate the use of such schemes to study a mixture of microtubule-associated protein (MAP) tau and human microtubules (MTs), and the cell wall of the fungus Schizophyllum commune using 2D and 3D spectroscopy, to show its viability for obtaining unambiguous correlations using standard fast-spinning MAS probes at high and ultra-high magnetic fields.

Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1 H-Detected Solid-State NMR Spectroscopy.

Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field 1 H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.

Pf1 bacteriophage hydration by magic angle spinning solid-state NMR.

High resolution two- and three-dimensional heteronuclear correlation spectroscopy ((1)H-(13)C, (1)H-(15)N, and (1)H-(13)C-(13)C HETCOR) has provided a detailed characterization of the internal and external hydration water of the Pf1 virion. This long and slender virion (2000 nm × 7 nm) contains highly stretched DNA within a capsid of small protein subunits, each only 46 amino acid residues. HETCOR cross-peaks have been unambiguously assigned to 25 amino acids, including most external residues 1-21 as well as residues 39-40 and 43-46 deep inside the virion. In addition, the deoxyribose rings of the DNA near the virion axis are in contact with water. The sets of cross-peaks to the DNA and to all 25 amino acid residues were from the same hydration water (1)H resonance; some of the assigned residues do not have exchangeable side-chain protons. A mapping of the contacts onto structural models indicates the presence of water "tunnels" through a highly hydrophobic region of the capsid. The present results significantly extend and modify results from a lower resolution study, and yield a comprehensive hydration surface map of Pf1. In addition, the internal water could be distinguished from external hydration water by means of paramagnetic relaxation enhancement. The internal water population may serve as a conveniently localized magnetization reservoir for structural studies.

A structural and dynamic visualization of the interaction between MAP7 and microtubules.

Microtubules (MTs) are key components of the eukaryotic cytoskeleton and are essential for intracellular organization, organelle trafficking and mitosis. MT tasks depend on binding and interactions with MT-associated proteins (MAPs). MT-associated protein 7 (MAP7) has the unusual ability of both MT binding and activating kinesin-1-mediated cargo transport along MTs. Additionally, the protein is reported to stabilize MTs with its 112 amino-acid long MT-binding domain (MTBD). Here we investigate the structural basis of the interaction of MAP7 MTBD with the MT lattice. Using a combination of solid and solution-state nuclear magnetic resonance (NMR) spectroscopy with electron microscopy, fluorescence anisotropy and isothermal titration calorimetry, we shed light on the binding mode of MAP7 to MTs at an atomic level. Our results show that a combination of interactions between MAP7 and MT lattice extending beyond a single tubulin dimer and including tubulin C-terminal tails contribute to formation of the MAP7-MT complex.

High aspect ratio diamond nanosecond laser machining.

Laser processing of diamond has become an important technique for fabricating next generation microelectronic and quantum devices. However, the realization of low taper, high aspect ratio structures in diamond remains a challenge. We demonstrate the effects of pulse energy, pulse number and irradiation profile on the achievable aspect ratio with 532 nm nanosecond laser machining. Strong and gentle ablation regimes were observed using percussion hole drilling of type Ib HPHT diamond. Under percussion hole drilling a maximum aspect ratio of 22:1 was achieved with 10,000 pulses. To reach aspect ratios on average 40:1 and up to 66:1, rotary assisted drilling was employed using > 2 M pulse accumulations. We additionally demonstrate methods of obtaining 0.1° taper angles via ramped pulse energy machining in 10:1 aspect ratio tubes. Finally, effects of laser induced damage are studied using confocal Raman spectroscopy with observation of up to 36% increase in tensile strain following strong laser irradiation. However, we report that upon application of 600 °C heat treatment, induced strain is reduced by up to ~ 50% with considerable homogenization of observed strain. Supplementary Information: The online version contains supplementary material available at 10.1007/s00339-023-06755-2.

The complex structure of Fomes fomentarius represents an architectural design for high-performance ultralightweight materials.

High strength, hardness, and fracture toughness are mechanical properties that are not commonly associated with the fleshy body of a fungus. Here, we show with detailed structural, chemical, and mechanical characterization that Fomes fomentarius is an exception, and its architectural design is a source of inspiration for an emerging class of ultralightweight high-performance materials. Our findings reveal that F. fomentarius is a functionally graded material with three distinct layers that undergo multiscale hierarchical self-assembly. Mycelium is the primary component in all layers. However, in each layer, mycelium exhibits a very distinct microstructure with unique preferential orientation, aspect ratio, density, and branch length. We also show that an extracellular matrix acts as a reinforcing adhesive that differs in each layer in terms of quantity, polymeric content, and interconnectivity. These findings demonstrate how the synergistic interplay of the aforementioned features results in distinct mechanical properties for each layer.

Diamond rotors.

The resolution of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra remains bounded by the spinning frequency, which is limited by the material strength of MAS rotors. Since diamond is capable of withstanding 1.5-2.5x greater MAS frequencies, compared to state-of-the art zirconia, we fabricated rotors from single crystal diamond. When combined with bearings optimized for spinning with helium gas, diamond rotors could achieve the highest MAS frequencies to date. Furthermore, the excellent microwave transmission properties and thermal conductivity of diamond could improve sensitivity enhancements in dynamic nuclear polarization (DNP) experiments. The fabrication protocol we report involves novel laser micromachining and produced rotors that presently spin at ωr/2π = 111.000 ±â€¯0.004 kHz, with stable spinning up to 124 kHz, using N2 gas as the driving fluid. We present the first proton-detected 13C/15N MAS spectra recorded using diamond rotors, a critical step towards studying currently inaccessible ex-vivo protein samples with MAS NMR. Previously, the high aspect ratio of MAS rotors (∼10:1) precluded fabrication of MAS rotors from diamond.

Biradical Polarizing Agents at High Fields.

The sensitivity enhancements available from dynamic nuclear polarization (DNP) are rapidly reshaping the research landscape and expanding the field of nuclear magnetic resonance (NMR) spectroscopy as a tool for solving complex chemical and structural problems. The past decade has seen considerable advances in this burgeoning method, while efforts to further improve its capabilities continue along many avenues. In this report, we examine the influence of static magnetic field strength and temperature on the reported 1H DNP enhancements from three conventional organic biradicals: TOTAPOL, AMUPol, and SPIROPOL. In contrast to the conventional wisdom, our findings show that at liquid nitrogen temperatures and 700 MHz/460.5 GHz, these three bisnitroxides all provide similar 1H DNP enhancements, ε ≈ 60. Furthermore, we investigate the influence of temperature, microwave power, magnetic field strength, and protein sample deuteration on the NMR experimental results.

Adsorption and surface complexation study of L-DOPA on Rutile (α-TiO2) in NaCl solutions.

Dihydroxyphenylalanine (DOPA) and similar molecules are of considerable interest in studies of bioadhesion to minerals, solar cells involving titanium dioxide, and biomedical imaging. However, the extent and mechanisms of DOPA adsorption on oxides in salt solutions are unknown. We report measurements of DOPA adsorption on well-characterized rutile (α-TiO2) particles over a range of pH, ionic strength, and surface coverage as well as a surface complexation model analysis establishing the stoichiometry, model surface speciation, and thermodynamic equilibrium constants, which permits predictions in more complex systems. DOPA forms two surface species on rutile, the proportions of which vary strongly with pH but weakly with ionic strength and surface loading. At pH < 4.5 a species involving four attachment points ("lying down") is important, whereas at pH > 4.5 a species involving only two attachment points via the phenolic oxygens ("standing up") predominates. Based on evidence of strong attachment of DOPA to titanium dioxide from single molecule AFM (Lee, H. et al., Proc. Natl. Acad. Sci.2006, 103, 12999-12003) and studies of catechol adsorption, one or more of the DOPA attachments for each species is inner-sphere, the others are likely to be H-bonds.