Point Information Gain and Multidimensional Data Analysis

We generalize the Point information gain (PIG) and derived quantities, i.e. Point information entropy (PIE) and Point information entropy density (PIED), for the case of R\'enyi entropy and simulate the behavior of PIG for typical distributions. We also use these methods for the analysis of multidimensional datasets. We demonstrate the main properties of PIE/PIED spectra for the real data on the example of several images, and discuss possible further utilization in other fields of data processing.Comment: 16 pages, 6 figure

Synthesis and Characterization of Complex Nanostructured Thin Films Based on Titanium for Industrial Applications

Titanium-based composites—titanium and silver (TiAg) and titanium and carbon (TiC)—were synthesized by the Thermionic Vacuum Arc (TVA) method on substrates especially for gear wheels and camshaft coating as mechanical components of irrigation pumps. The films were characterized by surface morphology, microstructure, and roughness through X-ray Diffraction (XRD), Atomic Force Microscopy (AFM), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Small-Angle Neutron Scattering (SANS). The silver (Ag) films crystallized into a cubic system with lattice a = 4.0833 Å at room temperature, indexed as cubic Ag group Fm3m. The crystallites were oriented in the [111] direction, and mean grain size was <D>111 = 265 Å. The TiC structure revealed a predominant cubic TiC phase, with a = 0.4098 as a lattice parameter determined by Cohen’s method. Average roughness (Ra) was 8 nm for the as-grown 170 nm thick TiAg film, and 1.8 nm for the as-grown 120 nm thick TiC film. Characteristic SANS contribution was detected from the TiAg layer deposited on a substrate of high-quality stainless steel with 0.45% carbon (OLC45) in the range of 0.015 Å−1 ≤ Q ≤ 0.4 Å−1, revealing the presence of sharp surfaces and an averaged triaxial ellipsoidal core-shell object

Stages of OCP–FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration

International audienceWe used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTEO is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCPO. In contrast, the pink form OCP-ΔNTEP, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTEP can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCPR. The dimeric structure of OCP-ΔNTEP is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP–FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP

Functional lipid pairs as building blocks of phase-separated membranes

Biological membranes exhibit a great deal of compositional and phase heterogeneity due to hundreds of chemically distinct components. As a result, phase separation processes in cell membranes are extremely difficult to study, especially at the molecular level. It is currently believed that the lateral membrane heterogeneity and the formation of domains, or rafts, are driven by lipid–lipid and lipid–protein interactions. Nevertheless, the underlying mechanisms regulating membrane heterogeneity remain poorly understood. In the present work, we combine inelastic X-ray scattering with molecular dynamics simulations to provide direct evidence for the existence of strongly coupled transient lipid pairs. These lipid pairs manifest themselves experimentally through optical vibrational (a.k.a. phononic) modes observed in binary (1,2-dipalmitoyl-sn-glycero-3-phosphocholine [DPPC]–cholesterol) and ternary (DPPC–1,2-dioleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-glycero-3-phosphocholine [DOPC/POPC]–cholesterol) systems. The existence of a phononic gap in these vibrational modes is a direct result of the finite size of patches formed by these lipid pairs. The observation of lipid pairs provides a spatial (subnanometer) and temporal (subnanosecond) window into the lipid–lipid interactions in complex mixtures of saturated/unsaturated lipids and cholesterol. Our findings represent a step toward understanding the lateral organization and dynamics of membrane domains using a well-validated probe with a high spatial and temporal resolution

Structural and Thermomagnetic Properties of Gallium Nanoferrites and Their Influence on Cells In Vitro

Magnetite and gallium substituted cuboferrites with a composition of GaxFe3−xO4 (0 ≤ x ≤ 1.4) were fabricated by thermal decomposition from acetylacetonate salts. The effect of Ga3+ cation substitution on the structural and thermomagnetic behavior of 4–12 nm sized core-shell particles was explored by X-ray and neutron diffraction, small angle neutron scattering, transmission electron microscopy, Mössbauer spectroscopy, and calorimetric measurements. Superparamagnetic (SPM) behavior and thermal capacity against increasing gallium concentration in nanoferrites were revealed. The highest heat capacity typical for [email protected] and Ga0.6Fe2.4O4@Fe3O4 is accompanied by a slight stimulation of fibroblast culture growth and inhibition of HeLa cell growth. The observed effect is concentration dependent in the range of 0.01–0.1 mg/mL and particles of Ga0.6Fe2.4O4@Fe3O4 design have a greater effect on cells. Observed magnetic heat properties, as well as interactions with tumor and healthy cells, provide a basis for further biomedical research to use the proposed nanoparticle systems in cancer thermotherapy (magnetic hyperthermia)

Composite Films of HDPE with SiO2 and ZrO2 Nanoparticles: The Structure and Interfacial Effects

Herein, we investigated the influence of two types of nanoparticle fillers, i.e., amorphous SiO2 and crystalline ZrO2, on the structural properties of their nanocomposites with high-density polyethylene (HDPE). The composite films were prepared by melt-blending with a filler content that varied from 1% to 20% v/v. The composites were characterized by small- and wide-angle x-ray scattering (SAXS and WAXS), small-angle neutron scattering (SANS), Raman spectroscopy, differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). For both fillers, the nanoaggregates were evenly distributed in the polymer matrix and their initial state in the powders determined their surface roughness and fractal character. In the case of the nano-ZrO2 filler, the lamellar thickness and crystallinity degree remain unchanged over a broad range of filler concentrations. SANS and SEM investigation showed poor interfacial adhesion and the presence of voids in the interfacial region. Temperature-programmed SANS investigations showed that at elevated temperatures, these voids become filled due to the flipping motions of polymer chains. The effect was accompanied by a partial aggregation of the filler. For nano-SiO2 filler, the lamellar thickness and the degree of crystallinity increased with increasing the filler loading. SAXS measurements show that the ordering of the lamellae is disrupted even at a filler content of only a few percent. SEM images confirmed good interfacial adhesion and integrity of the SiO2/HDPE composite. This markedly different impact of both fillers on the composite structure is discussed in terms of nanoparticle surface properties and their affinity to the HDPE matrix

Mechanisms of membrane protein crystallization in ‘bicelles’

Despite remarkable progress, mainly due to the development of LCP and ‘bicelle’ crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the “bicelle” crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of “bicelle” MP crystallization and will support rational design of crystallization

Structure-based insights into evolution of rhodopsins

Rhodopsins, most of which are proton pumps generating transmembrane electrochemical proton gradients, span all three domains of life, are abundant in the biosphere, and could play a crucial role in the early evolution of life on earth. Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins, rhodopsins from unicellular eukaryotes have not been well characterized. To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach, we performed a structural and functional analysis of the light-driven proton pump LR (Mac) from the pathogenic fungus Leptosphaeria maculans. The first high-resolution structure of fungi rhodopsin and its functional properties reveal the striking similarity of its membrane part to archaeal but not to bacterial rhodopsins. We show that an unusually long N-terminal region stabilizes the protein through direct interaction with its extracellular loop (ECL2). We compare to our knowledge all available structures and sequences of outward light-driven proton pumps and show that eukaryotic and archaeal proton pumps, most likely, share a common ancestor

Unique structure and function of viral rhodopsins

Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists