Dmytro Soloviov

European Molecular Biology Laboratory | EMBL · EMBL Hamburg

Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elucidation of such mechanisms is a challenge. It requires true-atomic-resolution structures of all key proton-conducting states. Here we presen...

Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different p...

An effect of receptor‐binding domain (RBD) of SARS‐CoV‐2 S‐protein on structural parameters of model lipid membranes presented by dimyristoylphosphatidylcholine (DMPC) systems with cholesterol and melatonin impurities is studied by small angle neutron scattering (SANS). It is shown that an increase in melatonin concentration in the lipid membrane l...

We have studied by means of small angle neutron scattering and diffraction, and molecular dynamics simulations the effect of lipid membrane fluidity on the amyloid-beta peptide interactions with the membrane. These interactions have been discovered previously to trigger the reorganization of model membranes between unilamellar vesicles and planar m...

We 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 pho...

The influence of the surface modification on the magnetism of 4–14 nm sized core and core/shell gallium ferrites obtained by different preparation methods (Massart’s and thermal decomposition from acetylacetonates) was studied. The physical properties of GaxFe3-xO4 were investigated in a wide range of Ga admixtures 0 ≤ x ≤ 1.5. Ga ions location at...

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 “b...

The Aquivion®‐type perfluorinated proton conducting membranes were studied subjected to a specially developed technique of uniaxial orientational stretching. Membranes were prepared from copolymer produced by aqueous‐emulsion copolymerization and by pressing the melt copolymer precursor or by casting a solution of copolymer in sulfonyl alkaline for...

Absorption of light quanta by microbial rhodopsins (or more generally by retinal proteins) leads to conversion of the light energy to the generation of transmembrane anion or cation gradients, optically gated channels, or signal states in photoreception. All these processes are accompanied by series of reaction steps with half-times ranging from fe...

The amyloid-beta peptide (Aβ) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of tempera...

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...

The amyloid-beta peptide (Aβ) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of tempera...

Diamond nanoparticles have significant prospects for technological applications, so their manufacture and subsequent disaggregation are a challenging task. In this paper, the porous structure of aggregates in detonation nanodiamond powders has been analyzed using small-angle neutron scattering. The influence of high pressure allowed the contributio...

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 fro...

We have studied the impact of cholesterol and/or melatonin on the static and dynamical properties of bilayers made of DPPC or DOPC utilizing neutron scattering techniques, Raman spectroscopy and molecular dynamics simulations. While differing in the amplitude of the effect due to cholesterol or melatonin when comparing their interactions with the t...

Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structur...

Introduction. Today, the Joint Institute for Nuclear Research (JINR) is a kind of scientific and technical framework for Ukrainian nuclear researchers who are directly involved in conducting the cutting-edge nuclear physics experiments. Problem Statement. An important aspect of international cooperation for the Ukrainian researchers in the field of...

This work provides the first characteristics of the rhodopsin SpaR from Sphingomonas paucimobilis, aerobic bacteria associated with opportunistic infections. The sequence analysis of SpaR has shown that this protein has unusual DTS motif which has never reported in rhodopsins from Proteobacteria. We report that SpaR operates as an outward proton pu...

New data on gallium ferrite particles are reported. The results of studies of Fe3O4/GaxFe3-xO4 and GaxFe3 xO4/Fe3O4 (x = 0.2, 0.4, 0.6 and 0.8) nanoparticles by X-ray and neutron diffraction, small angle neutron scattering, transmission electron microscopy, magnetization measurements, and Mössbauer spectroscopy. The cubic core–shell ferrites struct...

The photocycle of the membrane protein bacteriorhodopsin in Dipalmitoyl phosphatidylcholine(DPPC)/Cholesterol membranes with various cholesterol concentrations has been studied using the time-resolved spectroscopy method. The temperature dependences of the rate constants of bacteriorhodopsin transitions between transient states are shown to satisfy...

Introduction. Today, the Joint Institute for Nuclear Research (JINR) is a kind of scientific and technical framework for Ukrainian nuclear researchers who are directly involved in conducting the cutting-edge nuclear physics experiments. Problem Statement. An important aspect of international cooperation for the Ukrainian researchers in the field of...

In biological membranes lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. As a result, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, w...

Significance Although it is believed that the raft formation in a cell membrane is governed by a selective interaction of different lipids and proteins, mechanisms driving and regulating the lateral membrane heterogeneity remain poorly understood. Here, using multicomponent lipid mixtures and inelastic X-ray scattering, we provide a spatial–tempora...

Phytoplankton is the base of the marine food chain, oxygen, carbon cycle playing a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses regulating the dynamics of phytoplankton comprise genes of rhodopsins of two distinct families. We present a function-structure characterization of two homologous proteins representatives of fami...

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 Diff...

The work presents the results of studying the structure of binary liquid nanocarbon systems obtained by mixing hydrosol of detonation nanodiamond and aqueous dispersions of single layer graphene oxide flakes. We studied size and space distribution of nanocarbon clusters formed upon interaction of the components in aqueous media by mutually compleme...

The stability in time is a critical feature of magnetic nanoparticles in aqueous suspensions, straightly related to the usability in various biomedical fields. This study was focused on the granularity features of cobalt ferrite nanoparticles, dispersed in water by using as stabilizer shell either citrate ions or oleate ones, since fine granulation...

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 centra...

During the last decade, stimuli-responsible polymers based on poly(N-isopropylacrylamide) having conformational transition in the range of physiological temperature have been discussed as novel drug delivery nanosystems. A star-like copolymer with a dextran core and grafted poly(N-isopropylacrylamide) arms (D-g-PNIPAM) was synthesized, characterize...

During the last decade, stimuli-responsible polymers based on poly(N-isopropylacrylamide) having conformational transition in the range of physiological temperature have been discussed as novel drug delivery nanosystems. A star-like copolymer with a dextran core and grafted poly(N-isopropylacrylamide) arms (D-g-PNIPAM) was synthesized, characterize...

This paper reports our progress toward developing the best methods to prepare Ga-doped magnetite nanoparticles. Results of X-ray powder diffraction, small angle neutron scattering and the Mössbauer spectroscopy measurements of core-shell Ga0.2Fe2.8O4/ Fe3O4 and Fe3O4/Ga0.2Fe2.8O4 nanoparticles are presented. They all were found to crystallize in th...

In recent years, responsive polymer-based structures have been studied extensively due to their unique ability to alter their physical properties upon exposure to external stimuli. Despite this, the nanoscale Q-resolved dynamic properties of these materials have barely been explored, which is limiting the development and applications of these mater...

Structural aspects of powders containing magnetic nanoparticles Fe3O4/CoFe2O4 with the anticipated “core-shell” structure are considered by means of comparative analysis with individual particles of Fe3O4, CoFe2O4 in accordance of data obtained from X-ray powder diffraction and small-angle scattering of X-ray (synchrotron) radiation and neutrons. I...

Recent inelastic X-ray scattering (IXS) experiments on mesogens have revealed entirely new capabilities with regards to their nanoscale phonon-assisted heat management. Mesogens such as nematic liquid crystals (LCs) are appealing systems for study because their structure and morphology can easily be tuned. We report on Q-resolved ultra-high-resolut...

The method of small angle scattering (SAS) is widely used in the field of biophysical research of proteins in aqueous solutions. Obtaining low-resolution structure of proteins is still a highly valuable method despite the advances in high-resolution methods such as X-ray diffraction, cryo-EM etc. SAS offers the unique possibility to obtain structur...

Preliminary small-angle neutron scattering investigations on aqueous suspensions of several cobalt doped ferrites (CoxFe3-xO4, x=0; 0.5; 1) nanoparticles prepared by chemical co-precipitation method, are reported. The measurements were accomplished at the YuMO instrument in function at the IBR-2 reactor. Results of intermediary data treatment are p...

Using a multidetector system on the YuMO spectrometer allows shortening the time of measurements. The quantitative comparison of the measurement time using one and two-detector mode is done. The time range for experiments was from several minutes up to 12 hours. It was shown that two-detector system shortens more than twice the time of the measurem...

ABSTRACTWe have succeeded in synthesizing orthorhombic Ga(1?x)Fe(1+x)O3 (?0.05?≤ x?≤ 0.5), hexagonal GayFe(2?y)O3 (0 ≤ y ≤1.8) and cubic Ga(1+z)Fe(2?z)O4 (?0.1≤ z ≤0.8) nanograins of gallium ferrites using conventional precursors and an organic environment of Pechini scenario under atmospheric-pressure conditions (SG method). Phase composition and...

The antitumor activity of pristine C60 fullerene aqueous solution (C60FAS) compared to 5-fluorouracil (5-FU) and pyrrole derivative 1-(4-Cl-benzyl)-3-Cl-4-(CF3-fenylamino)-1H-pyrrol-2.5-dione (MI-1) cytostatic drugs was investigated and analyzed in detail using the model of colorectal cancer induced by 1.2-dimethylhydrazine (DMH) in rats. The numbe...

The work is a review of neutronographic investigations of supramolecular structures on upgraded small-angle spectrometer YuMO. Here, key parameters of small-angle spectrometers are considered. It is shown that two-detector system is the basis of YuMO upgrade. It allows to widen the dynamic q-range twice. In result, the available q-range is widened...

The management of the radioactive waste assume the conditioning in a cement matrix as an embedding, stable, disposal material. Cement matrix is the first and most important engineering barrier against the migration in the environment of the radionuclides contained in the waste packages. Knowing how the microstructure develops is therefore desirable...

Small angle neutron scattering (SANS) experiment on CoFe2O4/lauric acid/sodium dodecyl sulphate/H2O ferrofluid was performed at the time-of-flight YuMO spectrometer. Concentration effects on the structure variation of the investigated ferrofluid are presented. Using the zero concentration approximation, the structure factors of samples with differe...

The changes of the SAS program have been made as an attempt to adapt it to a two-detector system for the YuMO spectrometer. It is shown that applying weight algorithm technique for the raw data averaging procedure allows one to avoid a "sewing" problem resulting from using different detectors in rather wide q-range. The operating scheme and the bac...

The structure of phycobiliproteins of the cyanobacterium Acaryochloris marina was investigated in buffer solution at physiological temperatures, i.e. under the same conditions applied in spectroscopic experiments, using small angle neutron scattering. The scattering data of intact phycobiliproteins in buffer solution containing phosphate can be wel...

This Article was originally published with an incorrect publication date. This paper was due to be published on 26 May 2016 together with other content on a similar topic, but due to an error was published earlier on the 12 May 2016. The publication date in both the PDF and HTML versions of the paper has been updated to reflect this.

The passive transport of molecules through a cell membrane relies on thermal motions of the lipids. However, the nature of transmembrane transport and the precise mechanism remain elusive and call for a comprehensive study of phonon excitations. Here we report a high resolution inelastic X-ray scattering study of the in-plane phonon excitations in...

The present work demonstrates a validation of small-angle X-ray scattering (SAXS) combining with ultra violet and visible (UV-vis) spectroscopy and quasi-elastic light scattering (QELS) analysis for characterization of silver sols synthesized in polymer matrices. Polymer matrix internal structure and polymer chemical nature actually controlled the...

The micellization in mixed aqueous systems based on a nonionic surfactant, heptaethylene glycol monotetradecyl ether (C14E7), and an anionic surfactant, cesium dodecyl sulfate, has been investigated by small-angle neutron scattering. Preliminary data on the behavior of the C14E7 aqueous solutions (with three concentrations, 0.17, 0.5, and 1%) mixed...

Small-angle neutron scattering has been applied to study the structure peculiarities of perfluorinated proton conducting polymer samples containing sulfonic groups of the Aquivion® type in dry and moistened conditions, which differ from Nafion® type membranes by the length of the side chains with sulfonic acid groups. The fine structure of the memb...

The results of small angle scattering investigation of protein apoferritin are presented. In particular, the results of approximation to zero value of concentration are calculated. The procedure of approximating at zero concentration of apoferritin in this work is considered. The sizes and shapes, including those determined by indirect Fourier t...

The results of small angle scattering investigation of protein apoferritin are presented. In particular, the results of approximation to zero value of concentration are calculated. The procedure of approximating at zero concentration of apoferritin in this work is considered. The sizes and shapes, including those determined by indirect Fourier tran...

Preliminary microstructural results on a new CoFe2O4/lauric acid/DDS -Na/H2O ferrofluid by means of small angle neutron scattering (SANS), transmission electron microscopy (TEM) and selected area electron diffraction (SAED) are presented. The ferrofluid was prepared by coprecipitation of Fe(OH)3 and Co(OH)2, ferritisation of hydroxide mixture in 1M...

Multilamellar structures formed in DPPC/water/glycerol and DPPC/water/oxyethylated glycerol systems are studied by small-angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) methods. The effects of glycerol, oxyethylated glycerol, and other membranotropic agents (MTAs) on the lamellar repeat distance 𝐷 are compared in gel, ripp...

Multibilayer structures of hydrated phospholipids, often considered as model biological membranes, are, from the physical viewpoint, lyotropic liquid crystalline systems undergoing temperature-induced mesomorphic phase transitions. Effects of silver nitrate and urocanic acid on lyotropic phase states of hydrated L-a-dipalmitoylphosphatidylcholine (...

This paper describes the study of lipid DPPC, carried out on setup for simultaneous investigations by P–V–T and SANS methods. The data allowed us to calculate in area per lipid molecule changes during the lipid phase transition from ripple phase to liquid-crystalline phase.

Transparent oxyfluoride silicate precursor glasses and glass ceramics with the novel composition (1) SiO 3+ /Yb 3+ ions were synthesized. X-ray diffraction analysis (XRD) and Er 3+ absorption spectra revealed precipitation of PbF 2 nanocrystals dispersed in the glassy matrix. Under 980 nm laser excitation, intense green, red and near IR bands of up...