2018 |
Meier, G; Gapinski, J; Ratajczyk, M; Lettinga, M P; Hirtz, K; Banachowicz, E; Patkowski, A Nano-viscosity of supercooled liquid measured by fluorescence correlation spectroscopy: Pressure and temperature dependence and the density scaling (Journal Article) Journal of Chemical Physics, 148 (9), 2018. @article{Meier2018, title = {Nano-viscosity of supercooled liquid measured by fluorescence correlation spectroscopy: Pressure and temperature dependence and the density scaling}, author = {G Meier and J Gapinski and M Ratajczyk and M P Lettinga and K Hirtz and E Banachowicz and A Patkowski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043241251&doi=10.1063%2f1.5011196&partnerID=40&md5=7ff21d9328490a278846753bf2963eef}, doi = {10.1063/1.5011196}, year = {2018}, date = {2018-01-01}, journal = {Journal of Chemical Physics}, volume = {148}, number = {9}, abstract = {The Stokes-Einstein relation allows us to calculate apparent viscosity experienced by tracers in complex media on the basis of measured self-diffusion coefficients. Such defined nano-viscosity values can be obtained through single particle techniques, like fluorescence correlation spectroscopy (FCS) and particle tracking (PT). In order to perform such measurements, as functions of pressure and temperature, a new sample cell was designed and is described in this work. We show that this cell in combination with a long working distance objective of the confocal microscope can be used for successful FCS, PT, and confocal imaging experiments in broad pressure (0.1-100 MPa) and temperature ranges. The temperature and pressure dependent nano-viscosity of a van der Waals liquid obtained from the translational diffusion coefficient measured in this cell by means of FCS obeys the same scaling as the rotational relaxation and macro-viscosity of the system. © 2018 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Stokes-Einstein relation allows us to calculate apparent viscosity experienced by tracers in complex media on the basis of measured self-diffusion coefficients. Such defined nano-viscosity values can be obtained through single particle techniques, like fluorescence correlation spectroscopy (FCS) and particle tracking (PT). In order to perform such measurements, as functions of pressure and temperature, a new sample cell was designed and is described in this work. We show that this cell in combination with a long working distance objective of the confocal microscope can be used for successful FCS, PT, and confocal imaging experiments in broad pressure (0.1-100 MPa) and temperature ranges. The temperature and pressure dependent nano-viscosity of a van der Waals liquid obtained from the translational diffusion coefficient measured in this cell by means of FCS obeys the same scaling as the rotational relaxation and macro-viscosity of the system. © 2018 Author(s). |
2017 |
Poznar, M; Hołubowicz, R; Wojtas, M; Gapiński, J; Banachowicz, E; Patkowski, A; Ożyhar, A; Dobryszycki, P Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64) (Journal Article) Biochimica et Biophysica Acta - Proteins and Proteomics, 1865 (11), pp. 1358-1371, 2017. @article{Poznar20171358, title = {Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)}, author = {M Poznar and R Hołubowicz and M Wojtas and J Gapiński and E Banachowicz and A Patkowski and A Ożyhar and P Dobryszycki}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028973818&doi=10.1016%2fj.bbapap.2017.08.019&partnerID=40&md5=cc06b6f7c6d7030a283109ae7be182c7}, doi = {10.1016/j.bbapap.2017.08.019}, year = {2017}, date = {2017-01-01}, journal = {Biochimica et Biophysica Acta - Proteins and Proteomics}, volume = {1865}, number = {11}, pages = {1358-1371}, abstract = {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 ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. © 2017 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. © 2017 Elsevier B.V. |
Kiełbowicz-Matuk, A; Czarnecka, J; Banachowicz, E; Rey, P; Rorat, T Solanum tuberosum ZPR1 encodes a light-regulated nuclear DNA-binding protein adjusting the circadian expression of StBBX24 to light cycle (Journal Article) Plant Cell and Environment, 40 (3), pp. 424-440, 2017. @article{Kiełbowicz-Matuk2017424, title = {Solanum tuberosum ZPR1 encodes a light-regulated nuclear DNA-binding protein adjusting the circadian expression of StBBX24 to light cycle}, author = {A Kiełbowicz-Matuk and J Czarnecka and E Banachowicz and P Rey and T Rorat}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010876891&doi=10.1111%2fpce.12875&partnerID=40&md5=86c3b8d09297181f99101409f66c5c62}, doi = {10.1111/pce.12875}, year = {2017}, date = {2017-01-01}, journal = {Plant Cell and Environment}, volume = {40}, number = {3}, pages = {424-440}, abstract = {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 regulation in these lines. Our data demonstrate that StZPR1 allows fitting of the StBBX24 circadian rhythm to the light period and provide evidence that ZPR1 is a novel clock-associated protein in plants necessary for the accurate rhythmic expression of specific circadian-regulated genes. � 2016 John Wiley & Sons Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 regulation in these lines. Our data demonstrate that StZPR1 allows fitting of the StBBX24 circadian rhythm to the light period and provide evidence that ZPR1 is a novel clock-associated protein in plants necessary for the accurate rhythmic expression of specific circadian-regulated genes. � 2016 John Wiley & Sons Ltd |
Połatyńska, A; Tomczyk, K; Pochylski, M; Meier, G; Gapinski, J; Banachowicz, E; Śliwa, T; Patkowski, A Temperature dependent FCS studies using a long working distance objective: Viscosities of supercooled liquids and particle size (Journal Article) Journal of Chemical Physics, 146 (8), 2017. @article{Połatyńska2017, title = {Temperature dependent FCS studies using a long working distance objective: Viscosities of supercooled liquids and particle size}, author = {A Połatyńska and K Tomczyk and M Pochylski and G Meier and J Gapinski and E Banachowicz and T Śliwa and A Patkowski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014534145&doi=10.1063%2f1.4977047&partnerID=40&md5=aaf1db984ce8c7f88dbbf172fe779519}, doi = {10.1063/1.4977047}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {146}, number = {8}, abstract = {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 of the SE relation to supercooled liquids at temperatures above 1.2 Tg. We also show that the temperature dependent size of thermoresponsive microgel particles can be determined by FCS using the designed cells and a long working distance objective in a broader size range without a need to use the correction procedure since the size correction is proportional to the square of the ratio of the hydrodynamic radius to the confocal volume size. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 of the SE relation to supercooled liquids at temperatures above 1.2 Tg. We also show that the temperature dependent size of thermoresponsive microgel particles can be determined by FCS using the designed cells and a long working distance objective in a broader size range without a need to use the correction procedure since the size correction is proportional to the square of the ratio of the hydrodynamic radius to the confocal volume size. © 2017 Author(s). |
2016 |
Kiełbowicz-Matuk, A; Banachowicz, E; Turska-Tarska, A; Rey, P; Rorat, T Expression and characterization of a barley phosphatidylinositol transfer protein structurally homologous to the yeast Sec14p protein (Journal Article) Plant Science, 246 , pp. 98-111, 2016. @article{Kiełbowicz-Matuk201698, title = {Expression and characterization of a barley phosphatidylinositol transfer protein structurally homologous to the yeast Sec14p protein}, author = {A Kiełbowicz-Matuk and E Banachowicz and A Turska-Tarska and P Rey and T Rorat}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959450223&doi=10.1016%2fj.plantsci.2016.02.014&partnerID=40&md5=cf0214fd03e1dd30c2b0cc6685bd1ff5}, doi = {10.1016/j.plantsci.2016.02.014}, year = {2016}, date = {2016-01-01}, journal = {Plant Science}, volume = {246}, pages = {98-111}, abstract = {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. © 2016 Elsevier Ireland Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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. © 2016 Elsevier Ireland Ltd. |
2014 |
Banachowicz, E; Patkowski, A; Meier, G; Klamecka, K; Gapiński, J Successful FCS experiment in nonstandard conditions (Journal Article) Langmuir, 30 (29), pp. 8945-8955, 2014. @article{Banachowicz20148945, title = {Successful FCS experiment in nonstandard conditions}, author = {E Banachowicz and A Patkowski and G Meier and K Klamecka and J Gapiński}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905013347&doi=10.1021%2fla5015708&partnerID=40&md5=d68b947f722e3956b07ad9dae0aa1709}, doi = {10.1021/la5015708}, year = {2014}, date = {2014-01-01}, journal = {Langmuir}, volume = {30}, number = {29}, pages = {8945-8955}, abstract = {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. © 2014 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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. © 2014 American Chemical Society. |
2013 |
Danielewicz-Ferchmin, I; Banachowicz, E M; Ferchmin, A R Journal of Molecular Liquids, 187 , pp. 157-164, 2013. @article{Danielewicz-Ferchmin2013157, title = {Dielectric saturation in water as quantitative measure of formation of well-defined hydration shells of ions at various temperatures and pressures. Vapor-liquid equilibrium case}, author = {I Danielewicz-Ferchmin and E M Banachowicz and A R Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884553188&doi=10.1016%2fj.molliq.2013.06.005&partnerID=40&md5=6fa86bd4de2209722bf0a7f6c1d07961}, doi = {10.1016/j.molliq.2013.06.005}, year = {2013}, date = {2013-01-01}, journal = {Journal of Molecular Liquids}, volume = {187}, pages = {157-164}, abstract = {Static electric permittivity Ïμ of water at equilibrium saturated vapor pressures in electric field in the range 108 < E < 1011 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. © 2013 Published by Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Static electric permittivity Ïμ of water at equilibrium saturated vapor pressures in electric field in the range 108 < E < 1011 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. © 2013 Published by Elsevier B.V. |
Banachowicz, Ewa Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza, 2013, ISBN: 9788323226246 . @book{EBbook2013, title = {Struktura i parametry fizyczne biopolimerów: badania z zastosowaniem metod rozproszeniowych i modelowania komputerowego}, author = {Ewa Banachowicz}, url = {https://www.nieprzeczytane.pl/Struktura-i-parametry-fizyczne-biopolimerow,product320280.html}, isbn = {9788323226246 }, year = {2013}, date = {2013-01-01}, publisher = {Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza}, abstract = {The structures of proteins and nucleic acids in solution are studied by the dynamic light scattering (DSL), small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) as well as Monte Carlo simulations and homology modelling. On the basis of the proteins sequences, complementarity of data from different sources, interpretation of the diffusion coefficient, form factors and structure factors forpolydisperse and interacting particles, the predictions are made of the protein volume, surface area, hydration, net electric charge and other properties.}, keywords = {}, pubstate = {published}, tppubtype = {book} } The structures of proteins and nucleic acids in solution are studied by the dynamic light scattering (DSL), small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) as well as Monte Carlo simulations and homology modelling. On the basis of the proteins sequences, complementarity of data from different sources, interpretation of the diffusion coefficient, form factors and structure factors forpolydisperse and interacting particles, the predictions are made of the protein volume, surface area, hydration, net electric charge and other properties. |
2011 |
Danielewicz-Ferchmin, I; Banachowicz, E M; Ferchmin, A R Role of electromechanical and mechanoelectric effects in protein hydration under hydrostatic pressure (Journal Article) Physical Chemistry Chemical Physics, 13 (39), pp. 17722-17728, 2011. @article{Danielewicz-Ferchmin201117722, title = {Role of electromechanical and mechanoelectric effects in protein hydration under hydrostatic pressure}, author = {I Danielewicz-Ferchmin and E M Banachowicz and A R Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80053475947&doi=10.1039%2fc1cp21819k&partnerID=40&md5=d8d13e266ad6772da0a4ea8560a7107f}, doi = {10.1039/c1cp21819k}, year = {2011}, date = {2011-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {13}, number = {39}, pages = {17722-17728}, abstract = {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 Δσ. Within the hydration layer, the higher fields due to Δσ lead to an additional water compression via electrostriction. The increment Δσ 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. This journal is © the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 Δσ. Within the hydration layer, the higher fields due to Δσ lead to an additional water compression via electrostriction. The increment Δσ 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. This journal is © the Owner Societies. |
2009 |
Banachowicz, E; Kozak, M; Patkowski, A; Meier, G; Kohlbrecher, J High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution (Journal Article) Journal of Applied Crystallography, 42 (3), pp. 461-468, 2009. @article{Banachowicz2009461, title = {High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution}, author = {E Banachowicz and M Kozak and A Patkowski and G Meier and J Kohlbrecher}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66249136855&doi=10.1107%2fS0021889809007456&partnerID=40&md5=b53f04e35829dcbb202ee22ca5cf53af}, doi = {10.1107/S0021889809007456}, year = {2009}, date = {2009-01-01}, journal = {Journal of Applied Crystallography}, volume = {42}, number = {3}, pages = {461-468}, abstract = {Small-angle neutron scattering (SANS) of solutions of glucose/xylose isomerase from Streptomyces rubiginosus was measured as a function of pressure. It is shown that the structure of the enzyme in solution as seen by SANS is practically the same as that in the crystal and does not change with pressure up to 150 MPa. This reflects the unusually high structural stability of this material, which makes it extremely interesting to use as a secondary standard for pressure-dependent SANS experiments. This lack of pressure dependence of the SANS data also indicates that any possible change in hydration of the protein induced by pressure is not visible in the SANS curves. An appropriate correction procedure must be used for the SANS data in order to account for the distortion of the intensity curve due to hard-sphere and electrostatic interactions. After this correction, the isomerase can be readily used as a secondary standard for SANS measurements. © 2009 International Union of Crystallography.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Small-angle neutron scattering (SANS) of solutions of glucose/xylose isomerase from Streptomyces rubiginosus was measured as a function of pressure. It is shown that the structure of the enzyme in solution as seen by SANS is practically the same as that in the crystal and does not change with pressure up to 150 MPa. This reflects the unusually high structural stability of this material, which makes it extremely interesting to use as a secondary standard for pressure-dependent SANS experiments. This lack of pressure dependence of the SANS data also indicates that any possible change in hydration of the protein induced by pressure is not visible in the SANS curves. An appropriate correction procedure must be used for the SANS data in order to account for the distortion of the intensity curve due to hard-sphere and electrostatic interactions. After this correction, the isomerase can be readily used as a secondary standard for SANS measurements. © 2009 International Union of Crystallography. |
2007 |
Danielewicz-Ferchmin, I; Banachowicz, E; Ferchmin, A R Water phases under high electric field and pressure applied simultaneously (Journal Article) Journal of Molecular Liquids, 135 (1-3), pp. 75-85, 2007. @article{Danielewicz-Ferchmin200775, title = {Water phases under high electric field and pressure applied simultaneously}, author = {I Danielewicz-Ferchmin and E Banachowicz and A R Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34247592340&doi=10.1016%2fj.molliq.2006.10.006&partnerID=40&md5=06972fa5929a6c4e6e715216c0861269}, doi = {10.1016/j.molliq.2006.10.006}, year = {2007}, date = {2007-01-01}, journal = {Journal of Molecular Liquids}, volume = {135}, number = {1-3}, pages = {75-85}, abstract = {The rigorous equation of state of an open system containing water in an electric field above 108 V m- 1 under pressure applied in the range 10- 4 ≤ Po ≤ 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 ≤ Po ≤ 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 ≤ Po ≤ 0.8 GPa; it occurs at higher values of σ than the former one. © 2007.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The rigorous equation of state of an open system containing water in an electric field above 108 V m- 1 under pressure applied in the range 10- 4 ≤ Po ≤ 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 ≤ Po ≤ 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 ≤ Po ≤ 0.8 GPa; it occurs at higher values of σ than the former one. © 2007. |
2006 |
Danielewicz-Ferchmin, I; Banachowicz, E M; Ferchmin, A R Properties of hydration shells of protein molecules at their pressure- and temperature-induced native-denatured transition (Journal Article) ChemPhysChem, 7 (10), pp. 2126-2133, 2006. @article{Danielewicz-Ferchmin20062126, title = {Properties of hydration shells of protein molecules at their pressure- and temperature-induced native-denatured transition}, author = {I Danielewicz-Ferchmin and E M Banachowicz and A R Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750235245&doi=10.1002%2fcphc.200600289&partnerID=40&md5=4cd9ddda337a0103c0610e1aa3911108}, doi = {10.1002/cphc.200600289}, year = {2006}, date = {2006-01-01}, journal = {ChemPhysChem}, volume = {7}, number = {10}, pages = {2126-2133}, abstract = {Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures Pt and temperatures Tt, with the points (Pt,Tt) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density a are investigated with the help of the equation of state of water in an open system. The local values of σ rather close to each other (σD ∼ 0.3 C m-2) are found for six different experimental lines of the N-D transition found in the literature, The values σD correspond to the crossings of the total pressure (Pt+Π) vs σ isotherms at different T t (Π-electrostriction pressure). The pressures Pt and temperatures Tt appear to be related with some selected sites at the surfaces of the protein molecules. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures Pt and temperatures Tt, with the points (Pt,Tt) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density a are investigated with the help of the equation of state of water in an open system. The local values of σ rather close to each other (σD ∼ 0.3 C m-2) are found for six different experimental lines of the N-D transition found in the literature, The values σD correspond to the crossings of the total pressure (Pt+Π) vs σ isotherms at different T t (Π-electrostriction pressure). The pressures Pt and temperatures Tt appear to be related with some selected sites at the surfaces of the protein molecules. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA. |
Hoffmann, M; Eitner, K; Grotthuss, Von M; Rychlewski, L; Banachowicz, E; Grabarkiewicz, T; Szkoda, T; Kolinski, A Journal of Computer-Aided Molecular Design, 20 (5), pp. 305-319, 2006. @article{Hoffmann2006305, title = {Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors}, author = {M Hoffmann and K Eitner and M Von Grotthuss and L Rychlewski and E Banachowicz and T Grabarkiewicz and T Szkoda and A Kolinski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-39049182995&doi=10.1007%2fs10822-006-9057-z&partnerID=40&md5=9b4af75acd4a909263b2aadc971ead74}, doi = {10.1007/s10822-006-9057-z}, year = {2006}, date = {2006-01-01}, journal = {Journal of Computer-Aided Molecular Design}, volume = {20}, number = {5}, pages = {305-319}, abstract = {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 Cambridge 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. © Springer Science+Business Media B.V. 2006.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 Cambridge 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. © Springer Science+Business Media B.V. 2006. |
Banachowicz, E Light scattering studies of proteins under compression (Journal Article) Biochimica et Biophysica Acta - Proteins and Proteomics, 1764 (3), pp. 405-413, 2006. @article{Banachowicz2006405, title = {Light scattering studies of proteins under compression}, author = {E Banachowicz}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33645986479&doi=10.1016%2fj.bbapap.2006.01.014&partnerID=40&md5=d37ac678ba7ef94881d31d0d00a13e1c}, doi = {10.1016/j.bbapap.2006.01.014}, year = {2006}, date = {2006-01-01}, journal = {Biochimica et Biophysica Acta - Proteins and Proteomics}, volume = {1764}, number = {3}, pages = {405-413}, abstract = {The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed. © 2006 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed. © 2006 Elsevier B.V. All rights reserved. |
Banachowicz, E; Danielewicz-Ferchmin, I Static permittivity of water in electric field higher than 108 Vm-1 and pressure varying from 0.1 to 600 MPa at room temperature (Journal Article) Physics and Chemistry of Liquids, 44 (1), pp. 95-105, 2006. @article{Banachowicz200695, title = {Static permittivity of water in electric field higher than 108 Vm-1 and pressure varying from 0.1 to 600 MPa at room temperature}, author = {E Banachowicz and I Danielewicz-Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-30544433709&doi=10.1080%2f00319100500338912&partnerID=40&md5=898672b3148209737419ebb208ab7882}, doi = {10.1080/00319100500338912}, year = {2006}, date = {2006-01-01}, journal = {Physics and Chemistry of Liquids}, volume = {44}, number = {1}, pages = {95-105}, abstract = {A recently proposed statistical approach to the permittivity ε of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 (2004)) has been applied to water at T = 293 K subjected to external pressure. Results are shown in the form of the set of isobars ε(E), which reveal abrupt falls at E ∼ 109 V m-1. © 2006 Taylor & Francis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A recently proposed statistical approach to the permittivity ε of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 (2004)) has been applied to water at T = 293 K subjected to external pressure. Results are shown in the form of the set of isobars ε(E), which reveal abrupt falls at E ∼ 109 V m-1. © 2006 Taylor & Francis. |
2004 |
Jurga-Nowak, H; Banachowicz, E; Dobek, A; Patkowski, A Supramolecular guanosine 5′-monophosphate structures in solution. Light scattering study (Journal Article) Journal of Physical Chemistry B, 108 (8), pp. 2744-2750, 2004. @article{Jurga-Nowak20042744, title = {Supramolecular guanosine 5′-monophosphate structures in solution. Light scattering study}, author = {H Jurga-Nowak and E Banachowicz and A Dobek and A Patkowski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-1542365439&partnerID=40&md5=a00f33b925ab0526b2780e4a577f6855}, year = {2004}, date = {2004-01-01}, journal = {Journal of Physical Chemistry B}, volume = {108}, number = {8}, pages = {2744-2750}, abstract = {During the past decade, from the vast evidence it became clear that DNA oligomers rich in guanine stretches can form in solution highly ordered forms called G-quadruplexes and G-wires. G-quadruplexes are present in many sites of the human genome, can inhibit telomerase, and can be used as drug delivery supramolecules. G-wires and related structures seem to be an excellent material of biological origin for nanostructures. Therefore, in this paper we have studied the structures formed by specific association of guanosine 5′-monophosphate (GMP) nucleotide molecules in water solutions by photon correlation spectroscopy and depolarized Rayleigh light scattering. One relaxation process with distinct amplitude was observed, as a function of temperature and sample concentration. It was attributed to the translational diffusion coefficient of the stacks of G-quartets in a range of high concentration and to the stacks of GMP monomer associates for low concentration (less than 40 mg/mL). From the measurements the hydrodynamic radius of GMP molecule has been estimated as rH ≃ 5.4 Å. The bead modeling of the hydrodynamic parameters allowed us to distinguish the wide spectrum of structures formed in solution: from single GMP nucleotides to stacks of multiassociates of G-quartets of GMP.}, keywords = {}, pubstate = {published}, tppubtype = {article} } During the past decade, from the vast evidence it became clear that DNA oligomers rich in guanine stretches can form in solution highly ordered forms called G-quadruplexes and G-wires. G-quadruplexes are present in many sites of the human genome, can inhibit telomerase, and can be used as drug delivery supramolecules. G-wires and related structures seem to be an excellent material of biological origin for nanostructures. Therefore, in this paper we have studied the structures formed by specific association of guanosine 5′-monophosphate (GMP) nucleotide molecules in water solutions by photon correlation spectroscopy and depolarized Rayleigh light scattering. One relaxation process with distinct amplitude was observed, as a function of temperature and sample concentration. It was attributed to the translational diffusion coefficient of the stacks of G-quartets in a range of high concentration and to the stacks of GMP monomer associates for low concentration (less than 40 mg/mL). From the measurements the hydrodynamic radius of GMP molecule has been estimated as rH ≃ 5.4 Å. The bead modeling of the hydrodynamic parameters allowed us to distinguish the wide spectrum of structures formed in solution: from single GMP nucleotides to stacks of multiassociates of G-quartets of GMP. |
Skibinska, L; Banachowicz, E; Gapiński, J; Patkowski, A; Barciszewski, J Structural Similarity of E. coli 5S rRNA in Solution and within the Ribosome (Journal Article) Biopolymers, 73 (3), pp. 316-325, 2004. @article{Skibinska2004316, title = {Structural Similarity of E. coli 5S rRNA in Solution and within the Ribosome}, author = {L Skibinska and E Banachowicz and J Gapiński and A Patkowski and J Barciszewski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-1242269420&doi=10.1002%2fbip.10598&partnerID=40&md5=42f5529eb7f8d4d0fec97356be388b30}, doi = {10.1002/bip.10598}, year = {2004}, date = {2004-01-01}, journal = {Biopolymers}, volume = {73}, number = {3}, pages = {316-325}, abstract = {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 DT, τ R, and Rg 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. © 2004 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } 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 DT, τ R, and Rg 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. © 2004 Wiley Periodicals, Inc. |
2003 |
Danielewicz-Ferchmin, I; Banachowicz, E; Ferchmin, A R Protein hydration and the huge electrostriction (Journal Article) Biophysical Chemistry, 106 (2), pp. 147-153, 2003. @article{Danielewicz-Ferchmin2003147, title = {Protein hydration and the huge electrostriction}, author = {I Danielewicz-Ferchmin and E Banachowicz and A R Ferchmin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0141527424&doi=10.1016%2fS0301-4622%2803%2900188-1&partnerID=40&md5=cef8028b25e51dbc05ddbcf3750b1fb0}, doi = {10.1016/S0301-4622(03)00188-1}, year = {2003}, date = {2003-01-01}, journal = {Biophysical Chemistry}, volume = {106}, number = {2}, pages = {147-153}, abstract = {Recent experiments indicated the existence of hydration shells about biomolecules with densities markedly higher than that of bulk water. The compression is due to the pull of the dipoles of H2O molecules, necessary to achieve the thermodynamic equilibrium, from bulk water into the high field (approx. 109 V/m) region at the surface of the protein molecule. The electric field values at the surfaces of the biomolecules are calculated on the basis of the known densities. The reverse calculation of the limiting density values on the basis of known electric field distributions is performed, too. The results compare favourably with experiment. © 2003 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent experiments indicated the existence of hydration shells about biomolecules with densities markedly higher than that of bulk water. The compression is due to the pull of the dipoles of H2O molecules, necessary to achieve the thermodynamic equilibrium, from bulk water into the high field (approx. 109 V/m) region at the surface of the protein molecule. The electric field values at the surfaces of the biomolecules are calculated on the basis of the known densities. The reverse calculation of the limiting density values on the basis of known electric field distributions is performed, too. The results compare favourably with experiment. © 2003 Elsevier B.V. All rights reserved. |
2002 |
Kaszyńska, K; Banachowicz, E; Ślósarek, G; Morawiec, A; Gawrońska, I; Barciszewski, J Dynamic light scattering and NMR studies of napin (Journal Article) Journal of Solution Chemistry, 31 (12), pp. 987-993, 2002. @article{Kaszyńska2002987, title = {Dynamic light scattering and NMR studies of napin}, author = {K Kaszyńska and E Banachowicz and G Ślósarek and A Morawiec and I Gawrońska and J Barciszewski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0141832127&doi=10.1023%2fA%3a1021877526536&partnerID=40&md5=171405e81bf297573d596326e474abf5}, doi = {10.1023/A:1021877526536}, year = {2002}, date = {2002-01-01}, journal = {Journal of Solution Chemistry}, volume = {31}, number = {12}, pages = {987-993}, abstract = {We analyze the structure of napin (BngNAP1), a storage protein (m.w. 14.5 kDa) from Brassica napus. On the basis of the results of 1H NMR spectroscopy and dynamic light scattering (DLS) studies, the overall shape and secondary structure of the molecule are estimated.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We analyze the structure of napin (BngNAP1), a storage protein (m.w. 14.5 kDa) from Brassica napus. On the basis of the results of 1H NMR spectroscopy and dynamic light scattering (DLS) studies, the overall shape and secondary structure of the molecule are estimated. |
2000 |
Patkowski, A; Thurn-Albrecht, Th.; Banachowicz, E; Steffen, W; Bösecke, P; Narayanan, T; Fischer, E W Long-range density fluctuations in orthoterphenyl as studied by means of ultrasmall-angle X-ray scattering (Journal Article) Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 61 (6 B), pp. 6909-6913, 2000. @article{Patkowski20006909, title = {Long-range density fluctuations in orthoterphenyl as studied by means of ultrasmall-angle X-ray scattering}, author = {A Patkowski and Th. Thurn-Albrecht and E Banachowicz and W Steffen and P Bösecke and T Narayanan and E W Fischer}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034206458&doi=10.1103%2fPhysRevE.61.6909&partnerID=40&md5=3aa40958d52cc80b6d71b4cb80871e07}, doi = {10.1103/PhysRevE.61.6909}, year = {2000}, date = {2000-01-01}, journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, volume = {61}, number = {6 B}, pages = {6909-6913}, abstract = {The structure factor of a fragile glass-forming liquid, orthoterphenyl (OTP), was measured in a previously inaccessible q range between the conventional light scattering (LS) and small-angle x-ray scattering (SAXS) ranges using the low-angle beamline at the European Synchrotron Radiation Facility (ESRF). Measurement results indicate that the long-range density fluctuation in glass-forming liquids can be observed both in the isotropic component of scattered light and in the USAXS, provided the proper q range is covered.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure factor of a fragile glass-forming liquid, orthoterphenyl (OTP), was measured in a previously inaccessible q range between the conventional light scattering (LS) and small-angle x-ray scattering (SAXS) ranges using the low-angle beamline at the European Synchrotron Radiation Facility (ESRF). Measurement results indicate that the long-range density fluctuation in glass-forming liquids can be observed both in the isotropic component of scattered light and in the USAXS, provided the proper q range is covered. |
Banachowicz, E; Gapiński, J; Patkowski, A Solution structure of biopolymers: A new method of constructing a bead model (Journal Article) Biophysical Journal, 78 (1), pp. 70-78, 2000. @article{Banachowicz200070, title = {Solution structure of biopolymers: A new method of constructing a bead model}, author = {E Banachowicz and J Gapiński and A Patkowski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034112766&doi=10.1016%2fS0006-3495%2800%2976573-8&partnerID=40&md5=de9caf0c9593b1a40a2a184fc8f4c0fa}, doi = {10.1016/S0006-3495(00)76573-8}, year = {2000}, date = {2000-01-01}, journal = {Biophysical Journal}, volume = {78}, number = {1}, pages = {70-78}, abstract = {We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius σ = 5.0 Å was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (τ(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and τ(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger σ = 5.7 Å. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of σ = 4.5 Å for amino acids. The lack of experimental data on τ(R) for proteins restricted the tests to the translational diffusion properties.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius σ = 5.0 Å was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (τ(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and τ(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger σ = 5.7 Å. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of σ = 4.5 Å for amino acids. The lack of experimental data on τ(R) for proteins restricted the tests to the translational diffusion properties. |