Backbone-only restraints for fast determination of the protein fold: the role of paramagnetism-based restraints. Cytochrome b562 as an example

CH(alpha) residual dipolar couplings (Deltardc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH(alpha) Deltardc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Deltardc's, which are largely isooriented within alpha helices. The whole structure is now significantly refined with the chemical shift index and CH(alpha) Deltardc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Deltardc's.     

A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.     

Toward a Raman/FORS discrimination between Art Nouveau and contemporary stained glasses from CdSxSe1 − x nanoparticles signatures

CdS_xSe_{1 − x} quantum dots received considerable attention in academic studies and as cut‐off filters and indirect‐gap semiconductors. These later compounds have also been used for artistic purposes to produce colored glass since the 1920s thanks to their bright colors. Because non‐invasive conditions are now mandatory when considering objects belonging to the cultural heritage, the use of Raman and fiber optics reflectance spectroscopy has been identified as potential ones to obtain information about the nanostructure of six samples of historical glass produced between the late 1920s and modern days. The average elemental composition of the nanocrystals has been deduced processing both optical and vibrational data, and the result arising has been compared taking into account the several factors affecting the experimental results. The diffusion of zinc inside the nanocrystals has also been questioned by the shift caused on the CdS‐ and CdSe‐like phonon band wavenumber and on the absorption edge wavelength. An investigation of the size distribution and crystallinity of CdS_xSe_{1 − x} nanoparticles has been also performed considering those parameters that are mainly influenced by the disorder of the system, such as the extent of the Urbach tail and the Raman bandwidth. Thanks to the results obtained, discrimination between the more recent glass and the older Art Nouveau ones has been verified, leading to the identification of a useful analytical protocol for conservation purposes. Copyright © 2015 John Wiley & Sons, Ltd.     

Hippocampal activity during the transverse patterning task declines with cognitive competence but not with age

Background  

The hippocampus is a brain region that is particularly affected by age-related morphological changes. It is generally assumed that a loss in hippocampal volume results in functional deficits that contribute to age-related cognitive decline. In a combined cross-sectional behavioural and magnetoencephalography (MEG) study we investigated whether hippocampal-associated neural current flow during a transverse patterning task - which requires learning relational associations between stimuli - correlates with age and whether it is modulated by cognitive competence.     

Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein

The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.     

Reverse lexicographic and lexicographic shifting

A short new proof of the fact that all shifted complexes are fixed by reverse lexicographic shifting is given. A notion of lexicographic shifting, Δ_lex—an operation that transforms a monomial ideal of S = K[x_i: i ∈ ℕ] that is finitely generated in each degree into a squarefree strongly stable ideal—is defined and studied. It is proved that (in contrast to the reverse lexicographic case) a squarefree strongly stable ideal I ⊂ S is fixed by lexicographic shifting if and only if I is a universal squarefree lexsegment ideal (abbreviated USLI) of S. Moreover, in the case when I is finitely generated and is not a USLI, it is verified that all the ideals in the sequence } are distinct. The limit ideal is well defined and is a USLI that depends only on a certain analog of the Hilbert function of I. Research partially supported by NSF grants DMS 0070571 and DMS 0100141.     

Development of an Accurate Mass Retention Time Database for Untargeted Metabolomic Analysis and Its Application to Plasma and Urine Pediatric Samples

Liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is currently the method of choice for untargeted metabolomic analysis. The availability of established protocols to achieve a high confidence identification of metabolites is crucial. The aim of this work is to describe the workflow that we have applied to build an Accurate Mass Retention Time (AMRT) database using a commercial metabolite library of standards. LC-HRMS analysis was carried out using a Vanquish Horizon UHPLC system coupled to a Q-Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Milan, Italy). The fragmentation spectra, obtained with 12 collision energies, were acquired for each metabolite, in both polarities, through flow injection analysis. Several chromatographic conditions were tested to obtain a protocol that yielded stable retention times. The adopted chromatographic protocol included a gradient separation using a reversed phase (Waters Acquity BEH C18) and a HILIC (Waters Acquity BEH Amide) column. An AMRT database of 518 compounds was obtained and tested on real plasma and urine samples analyzed in data-dependent acquisition mode. Our AMRT library allowed a level 1 identification, according to the Metabolomics Standards Initiative, of 132 and 124 metabolites in human pediatric plasma and urine samples, respectively. This library represents a starting point for future metabolomic studies in pediatric settings.