Papers by Ewa Banachowicz
Physical review, Jun 1, 2000
Journal of Applied Crystallography, Apr 3, 2009
Two members of the intrinsically disordered proteins (IDP) family (OMM-64 and STM) have been stud... more Two members of the intrinsically disordered proteins (IDP) family (OMM-64 and STM) have been studied by means of small angle neutron scattering (SANS), dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS). SANS curves of the proteins in D2O buffers have been measured for a range of Na+ and Ca2+ salts concentrations. The same samples have been measured using DLS in order to estimate their apparent hydrodynamic radii (Rh) and the scattering intensity in the q = 0 limit. The size of the proteins as a function of Na+ and Ca2+ concentrations had been measured in nano-molar concentrations using FCS. Fits to the SANS data suggest a coiled structure of the proteins in solution. For the first time SANS curves of proteins embedded in calcium carbonate crystals have been measured. Also a coiled structure has been found (slope = -2). Exact values of the radius of gyration (Rg) from SANS need measurements at smaller q-values
Journal of Chemical Physics, Mar 5, 2018
The Journal of Physical Chemistry B, 2004
Plant, cell & environment, 2017
ZPR1 proteins belong to the C4-type of zinc finger coordinators known in animal cells to interact... more ZPR1 proteins belong to the C4-type of zinc finger coordinators known in animal cells to interact with other proteins and participate in cell growth and proliferation. In contrast, the current knowledge regarding plant ZPR1 proteins is very scarce. Here, we identify a novel potato nuclear factor belonging to this family and named StZPR1. StZPR1 is specifically expressed in photosynthetic organs during the light period, and the ZPR1 protein is located in the nuclear chromatin fraction. From modelling and experimental analyses, we reveal the StZPR1 ability to bind the circadian DNA cis motif 'CAACAGCATC', named CIRC and present in the promoter of the clock-controlled double B-box StBBX24 gene, the expression of which peaks in the middle of the day. We found that transgenic lines silenced for StZPR1 expression still display a 24 h period for the oscillation of StBBX24 expression but delayed by 4 h towards the night. Importantly, other BBX genes exhibit altered circadian regulat...
The Journal of chemical physics, Jan 28, 2017
In this work, we describe new experimental setups for Fluorescence Correlation Spectroscopy (FCS)... more In this work, we describe new experimental setups for Fluorescence Correlation Spectroscopy (FCS) where a long working distance objective is used. Using these setups, FCS measurements in a broad temperature range for a small sample volume of about 50 μl can be performed. The use of specially designed cells and a dry long working distance objective was essential for avoiding temperature gradients in the sample. The performance of the new setups and a traditional FCS setup with immersion objectives is compared. The FCS data in combination with the Stokes-Einstein (SE) relation were used to obtain the values of the nanoviscosity of a fluid. We show for selected molecular van der Waals supercooled liquids that despite the fact that in these systems, a characteristic length scale can be defined, the nanoviscosity obtained from FCS is in a very good agreement with the macroscopic (rheometric) viscosity of the sample in a broad temperature range. This result corroborates the applicability ...
Biochimica et biophysica acta, Jan 30, 2017
Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing.... more Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter...
Phys Chem Liq, 2006
A recently proposed statistical approach to the permittivity " of water in the high electric fiel... more A recently proposed statistical approach to the permittivity " of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 ) has been applied to water at T ¼ 293 K subjected to external pressure. Results are shown in the form of the set of isobars "(E ), which reveal abrupt falls at E $ 10 9 V m À1 .
Biopolymers, 2004
The article presents translational and rotational diffusion coefficients of 5S rRNA determined ex... more The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of D T , R , and R g predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.
Plant Science, 2016
Phosphatidylinositol transfer proteins (PITPs) include a large group of proteins implicated in th... more Phosphatidylinositol transfer proteins (PITPs) include a large group of proteins implicated in the non-vesicular traffic of phosphatidylinositol (PI) between membranes. In yeast, the structure and function of the PITP Sec14-p protein have been well characterized. In contrast, the knowledge on plant PITP proteins is very scarce. In this work, we characterized a novel type of PITP protein in barley named HvSec14p and related to the yeast Sec14-p protein. Our data reveal that HvSec14p consists of only the Sec14p-domain structurally homologous to the yeast phosphoinositide binding domain. We show that HvSec14p expression is up-regulated at both transcript and protein levels at specific stages of development during seed formation and germination, and in leaves of a drought-tolerant barley genotype under osmotic constraints. Modeling analyses of the protein three-dimensional structure revealed its capacity to dock the phosphoinositides, PtdIns(3)P, PtdIns(4)P, PtdIns(5)P and PtdIns(3,5)P2. Consistently, the recombinant HvSec14p protein is able to bind in vitro most PIP types, the highest affinity being observed with PtdIns(3,5)P2. Based on the high gene expression at specific developmental stages and in drought-tolerant barley genotypes, we propose that HvSec14p plays essential roles in the biogenesis of membranes in expanding cells and in their preservation under osmotic stress conditions.
Langmuir, 2014
Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coef... more Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13-0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS.
Physics and Chemistry of Liquids, 2006
Physics and Chemistry of Liquids, 2006
A recently proposed statistical approach to the permittivity " of water in the high electric fiel... more A recently proposed statistical approach to the permittivity " of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 ) has been applied to water at T ¼ 293 K subjected to external pressure. Results are shown in the form of the set of isobars "(E ), which reveal abrupt falls at E $ 10 9 V m À1 .
Physical Chemistry Chemical Physics, 2011
Recent measurements of lysozyme hydration water density under non-denaturing pressure show that i... more Recent measurements of lysozyme hydration water density under non-denaturing pressure show that it is higher than that of bulk water in the same conditions. High protein hydration layer density has earlier been observed at ambient conditions and ascribed to electrostriction. We calculate the pressure-induced protein mean surface charge density increment Ds. Within the hydration layer, the higher fields due to Ds lead to an additional water compression via electrostriction. The increment Ds is considered as due to a mechanoelectric effect in protein molecules. The mean value of the effective mechanoelectric coefficient d is calculated and compared with piezoelectric coefficients of amino acids and their compounds.
Journal of Molecular Liquids, 2007
The rigorous equation of state of an open system containing water in an electric field above 10 8... more The rigorous equation of state of an open system containing water in an electric field above 10 8 V m − 1 under pressure applied in the range 10 − 4 ≤ P o ≤ 0.8 GPa leads to phase diagrams with two possible kinds of phase transitions at 293 K. The first one is the discontinuous phase transition under pressure applied in the range 10 − 4 ≤ P o ≤ 0.05 GPa in the Π, σ coordinates (Π is the electrostriction pressure and σ denotes the surface charge density at an adjacent charged surface). The second one represents the continuous phase transition under pressure applied in the range 10 − 4 ≤ P o ≤ 0.8 GPa; it occurs at higher values of σ than the former one.
Journal of Molecular Liquids, 2013
Static electric permittivity of water at equilibrium saturated vapor pressures in electric field ... more Static electric permittivity of water at equilibrium saturated vapor pressures in electric field in the range 10 8 b E b 10 11 V m −1 was calculated. A quantitative measure of the dielectric saturation phenomenon was introduced. It is found that, according to the definition of this measure, well-defined first hydration shells of numerous ions investigated by X-ray and neutron scattering methods described in literature are electrically saturated, and that at various conditions. Calculations show that around some ions, including Ag + , whose hydration shells are not saturated at ambient conditions, dielectric saturation of water can be achieved by increasing temperature and pressure up to the values not far from the critical ones. This is compared with extended X-ray absorption fine structure (EXAFS) and XAFS data for Ag + and Rb + found in literature.
Journal of Computer-Aided Molecular Design, 2006
The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domai... more The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cam-bridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors-molecules possessing two phosphonic acid moieties at distal ends of the molecule.
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Papers by Ewa Banachowicz