Assignment of congested NMR spectra: carbonyl backbone enrichment via the Entner-Doudoroff pathway

In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many (13)C-(13)C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner-Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1-(13)C d-glucose ((13)C in position 1) as the sole carbon source, as well as (15)NH(4)Cl as the only nitrogen source. The 37MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D (15)N-(15)N data provided strong verification of many previous assignments of (15)N amide and (13)C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.     

The Application of Ultrasound in the Enzymatic Hydrolysis of Switchgrass

In a series of experiments, untreated and ammonium hydroxide pretreated Klenow lowland variety switchgrasses are converted to reducing sugars using low-frequency (20 kHz) ultrasound and commercially available cellulase enzyme. Results from experiments using untreated and pretreated switchgrasses with and without ultrasound are presented and discussed. In untreated switchgrass experiments, the combination of ultrasound and enzymes resulted in an increase of 7.5% in reducing sugars compared to experiments using just enzymes. In experiments using ammonium hydroxide pretreated switchgrass, the combination of ultrasound and enzymes resulted in an increase of 9.3% in reducing sugars compared to experiments using just enzymes. Experimental evidence indicates that there is a synergistic effect from the combination of ultrasound and enzymes which lowers the diffusion-limiting barrier to enzyme/substrate binding and results in an increase in reaction rate. Scanning electron microscopic images provide evidence that ultrasound-induced pitting increases substrate surface area and affects reaction rate and yield.     

Characterization of a core fragment of the rhesus monkey TRIM5α protein

Background  

Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown.     

Thermal behavior of carbon nanotubes decorated with gold nanoparticles

Three different forms of carbon, i.e., multi-walled carbon nanotubes (CNTs), single-walled CNTs, and soot, were decorated with gold nanoparticles by a new method. In this method C₁₀H₈ ⁻ ions transfer electrons to the CNTs or soot. These electrons on the carbon surface can then reduce Au³⁺ species to form supported Au nanoparticles with a narrow particle size distribution. Thermogravimetric/differential thermal analyses (TG/DTA), XRD, Raman, and TEM show that naphthalene molecules remain trapped inside the Au nanoparticles and can only be removed by treatment at ca. 300 °C. Remarkable effect of the Au nanoparticles on the oxidation of carbon by O₂ is also observed by TG/DTA, i.e., on-set oxidation temperature and activation energy (E _a). It is shown that as the Au particle size decreases from 25 to 2 nm a linear decrease of the oxidation temperature is observed. Au particles larger than 25 nm do not produce any significant effect on carbon oxidation. These results are discussed in terms of spillover catalytic effect where Au nanoparticles activate O₂ molecules to produce active oxygen species which oxidize the different carbon supports.     

A finite-volume version of Aizenman–Higuchi theorem for the 2d Ising model

In the late 1970s, in two celebrated papers, Aizenman and Higuchi independently established that all infinite-volume Gibbs measures of the two-dimensional ferromagnetic nearest-neighbor Ising model at inverse temperature ${\beta\geq 0}$ are of the form ${\alpha\mu^{+}_\beta + (1-\alpha)\mu^{-}_\beta}$ , where ${\mu^{+}_\beta}$ and ${\mu^{-}_\beta}$ are the two pure phases and ${0\leq\alpha\leq 1}$ . We present here a new approach to this result, with a number of advantages: (a) We obtain an optimal finite-volume, quantitative analogue (implying the classical claim); (b) the scheme of our proof seems more natural and provides a better picture of the underlying phenomenon; (c) this new approach might be applicable to systems for which the classical method fails.     

Probing Membrane Protein Insertion into Lipid Bilayers by Solid-State NMR

Determination of the environment surrounding a protein is often key to understanding its function and can also be used to infer the structural properties of the protein. By using proton-detected solid-state NMR, we show that reduced spin diffusion within the protein under conditions of fast magic-angle spinning, high magnetic field, and sample deuteration allows the efficient measurement of site-specific exposure to mobile water and lipids. We demonstrate this site specificity on two membrane proteins, the human voltage dependent anion channel, and the alkane transporter AlkL from Pseudomonas putida. Transfer from lipids is observed selectively in the membrane spanning region, and an average lipid-protein transfer rate of 6 s⁻¹ was determined for residues protected from exchange. Transfer within the protein, as tracked in the ¹⁵N-¹H 2D plane, was estimated from initial rates and found to be in a similar range of about 8 to 15 s⁻¹ for several resolved residues, explaining the site specificity.     

Dynamic Nuclear Polarization of 13C Nuclei in the Liquid State over a 10 Tesla Field Range

Nuclear magnetic resonance (NMR) techniques play an essential role in natural science and medicine. In spite of the tremendous utility associated with the small energies detected, the most severe limitation is the low signal‐to‐noise ratio. Dynamic nuclear polarization (DNP), a technique based on transfer of polarization from electron to nuclear spins, has emerged as a tool to enhance sensitivity of NMR. However, the approach in liquids still faces several challenges. Herein we report the observation of room‐temperature, liquid DNP ¹³C signal enhancements in organic small molecules as high as 600 at 9.4 Tesla and 800 at 1.2 Tesla. A mechanistic investigation of the ¹³C‐DNP field dependence shows that DNP efficiency is raised by proper choice of the polarizing agent (paramagnetic center) and by halogen atoms as mediators of scalar hyperfine interaction. Observation of sizable DNP of ¹³CH₂ and ¹³CH₃ groups in organic molecules at 9.4 T opens perspective for a broader application of this method.     

High-resolution solid-state NMR structure of Alanyl-Prolyl-Glycine

We present a de novo high-resolution structure of the peptide Alanyl-Prolyl-Glycine using a combination of sensitive solid-state NMR techniques that each yield precise structural constraints. High-quality ¹³C–¹³C distance constraints are extracted by fitting rotational resonance width (R²W) experiments using Multimode Multipole Floquet Theory and experimental chemical shift anisotropy (CSA) orientations. In this strategy, a structure is first calculated using DANTE-REDOR and torsion angle measurements and the resulting relative CSA orientations are used as an input parameter in the ¹³C–¹³C distance calculations. Finally, a refined structure is calculated using all the constraints. We investigate the effect of different structural constraints on structure quality, as determined by comparison to the crystal structure and also self-consistency of the calculated structures. Inclusion of all or subsets of these constraints into CNS calculations resulted in high-quality structures (0.02 Å backbone RMSD using all 11 constraints).     

Soft spin wave near nu=1: evidence for a magnetic instability in Skyrmion systems

The ground state of the two-dimensional electron gas near nu=1 is investigated by inelastic light scattering measurements carried down to very low temperatures. Away from nu=1, the ferromagnetic spin wave collapses and a new low-energy spin wave emerges below the Zeeman gap. The emergent spin wave shows soft behavior as its energy increases with temperature and reaches the Zeeman energy for temperatures above 2 K. The observed softening indicates an instability of the two-dimensional electron gas towards a magnetic order that breaks spin rotational symmetry. We discuss our findings in light of the possible existence of a Skyrme crystal.