Mapping of spectral density functions using heteronuclear NMR relaxation measurements

A method is proposed for direct mapping of spectral density functions of the rotational motions of H-X bond vectors, such as 1H---15N, by measuring a set of NMR relaxation parameters. The well known and frequently measured relaxation parameters T1 and T2 probe the spectral density function J([omega]) at five frequencies: 0, [omega]N, [omega]H, [omega]H - [omega]N, and [omega]H + [omega]N. In this study, the longitudinal relaxation time T1(Nz), the transverse relaxation times of in-phase coherence, T2(Nx,y), and of antiphase coherence, T2(2HzNx,y), the relaxation time of longitudinal two-spin order, T1(2HzNz), and the heteronuclear cross-relaxation rate [sigma]HN are measured for the heteronucleus N. These five relaxation parameters sample the spectral density function J([omega]) at the same five points where each measurement samples a subset of these frequencies with different weights. The five measurements permit an analytical calculation of J([omega]) at these five frequencies. Since longitudinal proton relaxation plays a role in these relaxation parameters, a sixth measurement is necessary to determine this relaxation time. The theory and experimental techniques for measuring these relaxation parameters are discussed. Preliminary results of these techniques as applied to the 15N-enriched protein eglin c are described. The proposed approach has the advantage that it does not rely on any a priori model assumptions about the shape of J([omega]); i.e., measurement of J([omega]) and interpretation can be separated.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30338/1/0000740.pd

Improved accuracy of heteronuclear transverse relaxation time measurements in macromolecules. elimination of antiphase contributions

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29618/1/0000707.pd

2D heteronuclear NMR measurements of spin-lattice relaxation times in the rotating frame of X nuclei in heteronuclear HX spin systems

Theoretical and experimental aspects of T1p are discussed for a heteronuclear HX two-spin system (T1pX) where only the X nucleus is spin-locked. An expression for T1pX in terms of spectral density functions and the effective magnetic field parameters is developed. It shows that T1pX offers potentially different information about the spectral densities than either T1X, T2X, or the steady-state NOEx. We present a 2D heteronuclear NMR pulse sequence for measuring site-specific T1pX's in biomolecules. The sequence is based on a double-INEPT transfer and applies a spin lock to the heteronuclei for variable delays. If a weak on-resonance spin lock is used, and if the spectral density functions are assumed to be Lorentzians, then T1pX, is theoretically indistinguishable from T2x. We conclude with an application of the pulse sequence to the uniformly 15N-enriched protein eglin c. The T1pX data reflect the differential mobility in the molecule.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29540/1/0000628.pd

Unusual heavy-mass nearly ferromagnetic state with a surprisingly large Wilson ratio in the double layered ruthenates (Sr1−x_{1-x}Cax_{x})3_{3}Ru2_{2}O7_{7}

We report an unusual nearly ferromagnetic, heavy-mass state with a surprisingly large Wilson ratio $R_{\textrm{w}}$ (e.g., $R_{\textrm{w}}\sim$ 700 for $x =$ 0.2) in double layered ruthenates (Sr$_{1-x}$Ca$_{x}$)$_{3}$Ru$_{2}$O$_{7}$ with 0.08 $< x <$ 0.4. This state does not evolve into a long-range ferromagnetically ordered state despite considerably strong ferromagnetic correlations, but freezes into a cluster-spin-glass at low temperatures. In addition, evidence of non-Fermi liquid behavior is observed as the spin freezing temperature of the cluster-spin-glass approaches zero near $x \approx$ 0.1. We discuss the origin of this unique magnetic state from the Fermi surface information probed by Hall effect measurements.Comment: 4 pages, 4 figures; to be published in Physical Review B Rapid Communication; solve the problem with Fig.

Stability of Transonic Shock Solutions for One-Dimensional Euler-Poisson Equations

In this paper, both structural and dynamical stabilities of steady transonic shock solutions for one-dimensional Euler-Poission system are investigated. First, a steady transonic shock solution with supersonic backgroumd charge is shown to be structurally stable with respect to small perturbations of the background charge, provided that the electric field is positive at the shock location. Second, any steady transonic shock solution with the supersonic background charge is proved to be dynamically and exponentially stable with respect to small perturbation of the initial data, provided the electric field is not too negative at the shock location. The proof of the first stability result relies on a monotonicity argument for the shock position and the downstream density, and a stability analysis for subsonic and supersonic solutions. The dynamical stability of the steady transonic shock for the Euler-Poisson equations can be transformed to the global well-posedness of a free boundary problem for a quasilinear second order equation with nonlinear boundary conditions. The analysis for the associated linearized problem plays an essential role

Measure representation and multifractal analysis of complete genomes

This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is to discuss the multifractal property of the measure representation and the classification of bacteria. From the measure representations and the values of the $D_{q}$ spectra and related $C_{q}$ curves, it is concluded that these complete genomes are not random sequences. In fact, spectral analyses performed indicate that these measure representations considered as time series, exhibit strong long-range correlation. For substrings with length K=8, the $D_{q}$ spectra of all organisms studied are multifractal-like and sufficiently smooth for the $C_{q}$ curves to be meaningful. The $C_{q}$ curves of all bacteria resemble a classical phase transition at a critical point. But the 'analogous' phase transitions of chromosomes of non-bacteria organisms are different. Apart from Chromosome 1 of {\it C. elegans}, they exhibit the shape of double-peaked specific heat function.Comment: 12 pages with 9 figures and 1 tabl

An initial event in insect innate immune response: structural and biological studies of interactions between β-1,3-glucan and the N-terminal domain of β-1,3-glucan recognition protein

In response to invading microorganisms, insect β-1,3-glucan recognition protein (βGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the NMR solution structure of the N-terminal domain of βGRP (N-βGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-βGRP with laminarihexaose, a glucose hexamer containing β-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~ 6 kDa) containing β-1,3 and β-1,6 links that activates the proPO pathway, to N-βGRP results in the loss of NMR cross-peaks from the backbone 15N-1H groups of the protein, suggesting the formation of a large complex. Analytical ultra centrifugation (AUC) studies of formation of N-βGRP:laminarin complex show that ligand-binding induces sel-fassociation of the protein:carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~ 102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to sub-micromolar concentrations. The structural model thus derived from the present studies for N-βGRP:laminarin complex in solution differs from the one in which a single N-βGRP molecule has been proposed to bind to a triple helical form of laminarin on the basis of an X-ray crystallographic structure of N-βGRP:laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements carried out with the designed mutants of N-βGRP indicate that electrostatic interactions involving Asp45, Arg54, and Asp68 between the ligand-bound protein molecules contribute in part to the stability of N-βGRP:laminarin macro complex and that a decreased stability is accompanied by a reduced activation of the proPO pathway. Increased β-1,6 branching in laminarin also results in destabilization of the macro complex. These novel findings suggest that ligand-induced self-association of βGRP:β-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the initial signal of pathogen recognition for the activation of the proPO pathway

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multisystem microbiome comparisons

Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought