71 results on '"Strancar, J."'
Search Results
2. P02-05 Validating In finite prediction of time-evolved inflammation triggered by particulate matter
- Author
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Urbancic, I., Sebastijanovic, A., Koklic, T., Stoeger, T., Vogel, U., and Strancar, J.
- Published
- 2024
- Full Text
- View/download PDF
3. P01-44 Particulate matter constituents trigger the formation of extracellular amyloid β and Tau-containing plaques and neurite shortening in vitro
- Author
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Sebastijanovic, A., Camassa, L.M.A., Malmborg, V., Kralj, S., Pagels, J., Vogel, U., Zienolddiny-Narui, S., Urbancic, I., Koklic, T., and Strancar, J.
- Published
- 2024
- Full Text
- View/download PDF
4. P01-27 Possible environmental factors influencing microtubule disruption and binucleation as determined by an in vitro cell coculture system and high throughput screening
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Koklic, T., Urbančič, I., Vogel, U., and Štrancar, J.
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- 2024
- Full Text
- View/download PDF
5. New correlative microscopy approaches for toxicology studies of nanomaterials
- Author
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(0000-0001-8584-3274) Podlipec, R., Kriselj, A., Pirker, L., (0000-0001-7192-716X) Hlawacek, G., Kelemen, M., Strancar, J., (0000-0001-8584-3274) Podlipec, R., Kriselj, A., Pirker, L., (0000-0001-7192-716X) Hlawacek, G., Kelemen, M., and Strancar, J.
- Abstract
A comprehensive understanding of the mechanisms leading to chronic inflammation of tissues after exposure to different types of nanomaterials is greatly lacking. In the case of lung tissue, repeating events of exposure to metal-oxide or carbon nanomaterials can eventually lead to persistent inflammation and further cardiovascular diseases [1,2]. A similar outcome can occur in periprosthetic tissues suffering severe inflammation from the constant influx of metal wear debris from nearby implant materials [3]. To better understand these adverse outcomes, one needs to dig into the initial events that are formed on a molecular, nanoscale, thus requiring an advanced combination of microscopy techniques. Lately, more and more studies in live science are tackled by correlative microscopy (CM) which implements an optimal combination of complementary and advanced techniques on the same sample to be able to reveal new phenomena. In our recent studies related to both lung and periprosthetic tissue inflammation, we show the new workflow of advanced microscopies and spectroscopies from which we have gained new structural as well as functional insights (Figure 1) [4,5]. With the combination of super-resolution optical microscopy (STED), hyperspectral and fluorescence lifetime imaging (sp-FLIM), Helium Ion Microscopy (HIM), Scanning electron microscopy (SEM-EDS), and Proton Induced X-ray Emission (PIXE) we reveal/present the new mechanisms and impact of nanomaterial interaction with lung epithelium and periprosthetic tissue, which leads to better knowledge and causal relations of the nanotoxicity on such small scales. References: 1. X. Li, L. Jin, H. Kan, Nature 2019, 570, 437-439. 2. E. Underwood, Science 2017, 355, 342–345. 3. S.B. Goodman, J. Gallo, E. Gibon, M. Takagi, Expert Rev Med Devices 2020, 17, 41–56. 4. H. Kokot, et. al, Advanced Materials, 2020, 32, 2003913-1-15. 5. R. Podlipec, et. al, Materials, 2021, 14, 3048.
- Published
- 2022
6. Spatially resolved temperature distribution in a rare-earth-doped transparent glass-ceramic
- Author
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Sedmak, I., (0000-0001-8584-3274) Podlipec, R., Urbancic, I., Strancar, J., Mortier, M., Golobic, I., Sedmak, I., (0000-0001-8584-3274) Podlipec, R., Urbancic, I., Strancar, J., Mortier, M., and Golobic, I.
- Abstract
Knowing the temperature distribution within the conducting walls of various multilayer-type materials is crucial for a better understanding of heat-transfer processes. This applies to many engineering fields, good examples being photovoltaics and microelectronics. In this work, we present a novel fluorescence technique that makes possible the non-invasive imaging of local temperature distributions within a transparent, temperature-sensitive, co-doped Er:GPF1Yb0.5Er glass-ceramic with micrometer spatial resolution. The thermal imaging was performed with a high-resolution, fluorescence microscopy system, measuring different focal planes along the z-axis. This ultimately enabled a precise axial reconstruction of the temperature distribution across a 500-µm-thick glass-ceramic sample. The experimental measurements showed excellent agreement with computer-modeled heat simulations and suggest that the technique could be adopted for the spatial analyses of local thermal processes within optically transparent materials. For instance, the technique could be used to measure the temperature distribution of intermediate, transparent layers of novel ultra-high-efficiency solar cells at the micron and sub-micron levels.
- Published
- 2022
7. The properties of bioactive TiO2 coatings on Ti-based implants
- Author
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Drnovšek, N., Rade, K., Milačič, R., Štrancar, J., and Novak, S.
- Published
- 2012
- Full Text
- View/download PDF
8. New correlative microscopy approaches for toxicology studies of nanomaterials
- Author
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Podlipec, R., Kriselj, A., Pirker, L., Hlawacek, G., Kelemen, M., and Strancar, J.
- Abstract
A comprehensive understanding of the mechanisms leading to chronic inflammation of tissues after exposure to different types of nanomaterials is greatly lacking. In the case of lung tissue, repeating events of exposure to metal-oxide or carbon nanomaterials can eventually lead to persistent inflammation and further cardiovascular diseases [1,2]. A similar outcome can occur in periprosthetic tissues suffering severe inflammation from the constant influx of metal wear debris from nearby implant materials [3]. To better understand these adverse outcomes, one needs to dig into the initial events that are formed on a molecular, nanoscale, thus requiring an advanced combination of microscopy techniques. Lately, more and more studies in live science are tackled by correlative microscopy (CM) which implements an optimal combination of complementary and advanced techniques on the same sample to be able to reveal new phenomena. In our recent studies related to both lung and periprosthetic tissue inflammation, we show the new workflow of advanced microscopies and spectroscopies from which we have gained new structural as well as functional insights (Figure 1) [4,5]. With the combination of super-resolution optical microscopy (STED), hyperspectral and fluorescence lifetime imaging (sp-FLIM), Helium Ion Microscopy (HIM), Scanning electron microscopy (SEM-EDS), and Proton Induced X-ray Emission (PIXE) we reveal/present the new mechanisms and impact of nanomaterial interaction with lung epithelium and periprosthetic tissue, which leads to better knowledge and causal relations of the nanotoxicity on such small scales. References: 1. X. Li, L. Jin, H. Kan, Nature 2019, 570, 437-439. 2. E. Underwood, Science 2017, 355, 342–345. 3. S.B. Goodman, J. Gallo, E. Gibon, M. Takagi, Expert Rev Med Devices 2020, 17, 41–56. 4. H. Kokot, et. al, Advanced Materials, 2020, 32, 2003913-1-15. 5. R. Podlipec, et. al, Materials, 2021, 14, 3048.
- Published
- 2022
9. Correlative light and Helium Ion Microscopy to identify lung response to metal oxide and carbon nanomaterials done on model lung epithelium
- Author
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Podlipec, R., Kriselj, A., Vogel Mikus, K., Klingner, N., Hlawacek, G., and Strancar, J.
- Abstract
Comprehensive understanding of molecular events governing lung epithelium response to inhaled nanoparticles is still lacking. These repeating events in lungs could eventually lead to persistent inflammation and further cardiovascular diseases [1,2]. To better understand how it all start on a molecular, nanoscale level one urgently needs an appropriate model system and an advanced imaging technique(s) capable of unravelling key information on a nanoscale. Many studies addressing such complex biological problems have been lately tackled by correlative microscopy (CM) approach using an optimal combination of complementary and advanced techniques [3]. Our approach was thus to apply live cell epithelium model imaging using an advanced high-resolution fluorescence microscopy followed by helium ion microscopy (HIM) to visualize structures and morphology further down at nano-scale. One of the HIM advantages to other high-resolution, high-vacuum imaging techniques is large depth of focus, sub-nm resolution, nm surface sensitivity, and especially no need for sample coating that changes the nanostructure morphology on the surface. To gather any further structure-function information of the investigated biological system using such diametrical techniques, an appropriate sample preparation needed to be developed. Once done, we could study sub-micron to nanometer changes that govern model lung epithelium interaction with various nanoparticles. Exposure of metal oxide (TiO2) nanotubes has revealed active passivation of nanomaterial-biological matter composites on the cell surface with lipo-proteins present, identified both with optical and ion beam technique (Figure, below). Findings of CM studies have contributed to better understand chronic inflammation prediction in lung diseases [4]. On the other hand, exposed carbon nanoparticles have shown completely different cell response and will be discussed. 1. Li, X., Jin, L. & Kan, H. Air pollution: a global problem needs local fixes. Nature 570, 437–439 (2019). 2. Underwood, E. The polluted brain. Science 355, 342–345 (2017). 3. Ando, T. The 2018 correlative microscopy techniques roadmap, J. Phys. D: Appl. Phys. 51, (2018). 4. Kokot, H., et. al, Prediction of Chronic Inflammation for Inhaled Particles: the Impact of Material Cycling and Quarantining in the Lung Epithelium, Advanced Materials 32, 2003913 (2020)
- Published
- 2021
10. Correlative light and Helium Ion Microscopy to identify lung response to metal oxide and carbon nanomaterials done on model lung epithelium
- Author
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(0000-0001-8584-3274) Podlipec, R., Kriselj, A., Vogel Mikus, K., (0000-0001-9539-5874) Klingner, N., (0000-0001-7192-716X) Hlawacek, G., Strancar, J., (0000-0001-8584-3274) Podlipec, R., Kriselj, A., Vogel Mikus, K., (0000-0001-9539-5874) Klingner, N., (0000-0001-7192-716X) Hlawacek, G., and Strancar, J.
- Abstract
Comprehensive understanding of molecular events governing lung epithelium response to inhaled nanoparticles is still lacking. These repeating events in lungs could eventually lead to persistent inflammation and further cardiovascular diseases [1,2]. To better understand how it all start on a molecular, nanoscale level one urgently needs an appropriate model system and an advanced imaging technique(s) capable of unravelling key information on a nanoscale. Many studies addressing such complex biological problems have been lately tackled by correlative microscopy (CM) approach using an optimal combination of complementary and advanced techniques [3]. Our approach was thus to apply live cell epithelium model imaging using an advanced high-resolution fluorescence microscopy followed by helium ion microscopy (HIM) to visualize structures and morphology further down at nano-scale. One of the HIM advantages to other high-resolution, high-vacuum imaging techniques is large depth of focus, sub-nm resolution, nm surface sensitivity, and especially no need for sample coating that changes the nanostructure morphology on the surface. To gather any further structure-function information of the investigated biological system using such diametrical techniques, an appropriate sample preparation needed to be developed. Once done, we could study sub-micron to nanometer changes that govern model lung epithelium interaction with various nanoparticles. Exposure of metal oxide (TiO2) nanotubes has revealed active passivation of nanomaterial-biological matter composites on the cell surface with lipo-proteins present, identified both with optical and ion beam technique (Figure, below). Findings of CM studies have contributed to better understand chronic inflammation prediction in lung diseases [4]. On the other hand, exposed carbon nanoparticles have shown completely different cell response and will be discussed. 1. Li, X., Jin, L. & Kan, H. Air pollution: a global problem needs local fixes.
- Published
- 2021
11. Helium Ion Microscopy to address relevant questions in the impact of nanomaterials on lung epithelium – correlative microscopy approach
- Author
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Podlipec, R., Krišelj, A., Pirker, L., Klingner, N., Hlawacek, G., Strancar, J., and Borany, J.
- Abstract
Helium Ion Microscopy (HIM) has not been thoroughly exploited for biological studies addressing relevant questions that range from the cellular to the subcellular level. One of the benefits of HIM compared to other high-resolution imaging techniques is definitely the large depth of focus, sub-nm resolution, nm surface sensitivity, and especially that no sample coating is needed that can change the nanostructure morphology on the surface. The prerequisite to getting the most from the technique is thus the appropriate sample preparation. Besides, to get the most from understanding the addressed biological question, a successful correlative microscopy approach is necessary. This is best shown in our recently published study (H Kokot, Advanced Materials, 2020), where we have addressed one of the most critical issues in toxicology, that is the poor understanding of chronic inflammation initiation in lung tissue caused by inhaled nanoparticles, with the correlative microscopy approach using advanced multimodal optical microscopy and HIM. HIM nicely revealed the TiO2 nanotube organization and passivation on the cell surface and confirmed lipid and protein binding to the TiO2 surface (Figure below), identified as well by in silico simulations. In brief, HIM is an extremely powerful technique for the surface, and in the case of porous samples also in-depth morphology characterization on an nm scale. In combination with complementary imaging techniques and proper sample preparation, many relevant biological questions can be addressed and solved. Still, there are many limitations and challenges in cell preparation and imaging using helium ions, such as imaging of internal structures, definitely pursuing discussions and new developments in the future.
- Published
- 2020
12. Characterization of blood coagulation dynamics and oxygenation in ex‐vivo retinal vessels by fluorescence hyperspectral imaging
- Author
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Podlipec, R., Arsov, Z., Koklic, T., and Strancar, J.
- Subjects
biomedical optics and biophotonics ,fluorescence hyperspectral imaging ,optical tweezers ,comparative animal models ,hemoglobin oxygenation ,diagnostics ,Blood coagulation - Abstract
Blood coagulation mechanisms forming a blood clot and preventing hemorrhage have been extensively studied in the last decades. Knowing the mechanisms behind becomes very important particularly in the case of blood vessel diseases. Real‐time and accurate diagnostics accompanied by the therapy are particularly needed for example in diseases related to retinal vasculature. In our study, we employ for the first time fluorescence hyperspectral imaging (fHSI) combined with the spectral analysis algorithm concept to assess physical as well as functional information of blood coagulation in real‐time. By laser‐induced local disruption of retinal vessels to mimic blood leaking and subsequent coagulation and a proper fitting algorithm, we were able to reveal and quantify the extent of local blood coagulation through direct identification of the change of oxyhemoglobin concentration within few minutes. We confirmed and illuminated the spatio‐temporal evolution of the essential role of erythrocytes in the coagulation cascade as the suppliers of oxygenated hemoglobin. By additional optical tweezers force manipulation, we showed immediate aggregation of erythrocytes at the coagulation site. The presented fluorescence‐based imaging concept could become a valuable tool in various blood coagulation diagnostics as well as theranostic systems if coupled with the laser therapy.
- Published
- 2020
13. Correlative microscopy of lung epithelial in vitro model exposed to nanoparticles by using super-resolution optical and advanced ion/electron based techniques
- Author
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Podlipec, R., Klingner, N., Heller, R., Majaron, H., Pelicon, P., Strancar, J., and Borany, J.
- Subjects
optical microscopy ,lung epithelium ,Correlative microscopy ,helium ion microscopy ,in-vitro model ,TiO2 nanoparticles - Abstract
Clear understanding of molecular events followed by lung epithelial cells/tissue response to inhaled nanoparticles is still lacking. As these interaction events in lungs eventually lead to diseases and potentially persistent inflammation [1,2], one urgently needs new and relevant investigation methods which could provide new insights into the key mechanisms of interaction. In our latest research we have thus focused on this toxicology problem first by developing an appropriate in vitro lung epithelial model and second by developing and implementing relevant advanced correlative imaging techniques capable of gathering more insight of interaction properties on scales well below optical resolution limit. In order to understand the mechanisms of molecular initiative events we have first performed live cell imaging using STED super-resolution microscopy by which few tens to hundred nm resolution was achieved locally. As the technique is incapable of providing resolution further down to nm and lacks the visualization of non-labeled surrounding structures and morphology, we thus introduced suitable complementary correlative microscopy techniques with high surface contrast, SEM and Helium Ion Microscopy (HIM). Main focus, besides sample and sample holder preparation for these high vacuum techniques, was dedicated to HIM measurements which in general are capable of providing better resolution and sensitivity compared to SEM [3]. From this ongoing study we briefly present the first interesting results of correlative microscopy combining optical, electron and ion based techniques on the epithelial cells exposed to TiO2 nanoparticles from micro to nano scale. References: 1. Li, X., Jin, L. & Kan, H. Air pollution: a global problem needs local fixes. Nature 570, 437–439 (2019). 2. Underwood, E. The polluted brain. Science 355, 342–345 (2017). 3. Hlawacek, G. et Al. Helium Ion Microscopy. J. Vac. Sci. Technol. 32, (2014)
- Published
- 2019
14. Correlative microscopy of lung epithelial in vitro model exposed to nanoparticles by using super-resolution optical and advanced ion/electron based techniques
- Author
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(0000-0001-8584-3274) Podlipec, R., (0000-0001-9539-5874) Klingner, N., Heller, R., Majaron, H., Pelicon, P., Strancar, J., Borany, J., (0000-0001-8584-3274) Podlipec, R., (0000-0001-9539-5874) Klingner, N., Heller, R., Majaron, H., Pelicon, P., Strancar, J., and Borany, J.
- Abstract
Clear understanding of molecular events followed by lung epithelial cells/tissue response to inhaled nanoparticles is still lacking. As these interaction events in lungs eventually lead to diseases and potentially persistent inflammation [1,2], one urgently needs new and relevant investigation methods which could provide new insights into the key mechanisms of interaction. In our latest research we have thus focused on this toxicology problem first by developing an appropriate in vitro lung epithelial model and second by developing and implementing relevant advanced correlative imaging techniques capable of gathering more insight of interaction properties on scales well below optical resolution limit. In order to understand the mechanisms of molecular initiative events we have first performed live cell imaging using STED super-resolution microscopy by which few tens to hundred nm resolution was achieved locally. As the technique is incapable of providing resolution further down to nm and lacks the visualization of non-labeled surrounding structures and morphology, we thus introduced suitable complementary correlative microscopy techniques with high surface contrast, SEM and Helium Ion Microscopy (HIM). Main focus, besides sample and sample holder preparation for these high vacuum techniques, was dedicated to HIM measurements which in general are capable of providing better resolution and sensitivity compared to SEM [3]. From this ongoing study we briefly present the first interesting results of correlative microscopy combining optical, electron and ion based techniques on the epithelial cells exposed to TiO2 nanoparticles from micro to nano scale. References: 1. Li, X., Jin, L. & Kan, H. Air pollution: a global problem needs local fixes. Nature 570, 437–439 (2019). 2. Underwood, E. The polluted brain. Science 355, 342–345 (2017). 3. Hlawacek, G. et Al. Helium Ion Microscopy. J. Vac. Sci. Technol. 32, (2014)
- Published
- 2019
15. Correlative microscopy of relevant ex-vivo and in-vitro biological systems by multimodal optical and high resolution ion/electron based techniques
- Author
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Podlipec, R., Klingner, N., Heller, R., Kriselj, A., Pelicon, P., Strancar, J., Borany, J., Podlipec, R., Klingner, N., Heller, R., Kriselj, A., Pelicon, P., Strancar, J., and Borany, J.
- Abstract
Correlative microscopy combining light and electron microscopy (CLEM) has become one of the important and unmissable tools in various investigations of complex biological systems revealing high-resolution structural and highly-specific functional information [1]. In the last years more combinations of other advanced techniques have been developed, such as combining optical microscopy with atomic force spectroscopy/microscopy (AFM) or with magnetic resonance imaging, etc [2] whereas in our study multimodal optical microscopy has been correlated with ion and electron based techniques such as is helium ion microscopy (HIM) [3]. The purpose for using combination of the complementary techniques was to elucidate or better interpret specific biological problems which could not be explained just by one technique lacking of whether resolution, sensitivity of specificity. We focused on toxicology related scientific questions of how inhaled nanoparticles interact with lung epithelial cells/tissue once get into direct contact and why interactions can eventually lead to diseases and potentially persistent inflammation [4,5]. In order to better understand the interaction on nanometer scales we first developed proper lung in-vitro model which was followed by proper sample preparation for efficient correlative microscopy using multimodal optical microscopy and high resolution HIM microscopy. By latter we managed to image single metal oxide nanoparticles on cell surfaces interacting with cell membranes, while functional information of the same events was prior measured with confocal and super-resolution optical microscopy. Besides, we implemented described correlative microscopies also for scientific problem related to rejection of hip implants where material debris is found everywhere in the surrounding periprosthetic tissue with lack of knowledge what happens on a molecular scale. The latest findings of both ongoing studies will be presented. References: 1. P. de Boer, JP Hoogenbo
- Published
- 2019
16. Fast and Accurate Characterization of Biological Membranes by EPR Spectral Simulations of Nitroxides
- Author
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Štrancar, J, Šentjurc, M, and Schara, M
- Published
- 2000
- Full Text
- View/download PDF
17. The nature of chlorine-inhibition of photocatalytic degradation of dichloroacetic acid in a TiO2-based microreactor
- Author
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Krivec, M., Dillert, Ralf, Bahnemann, Detlef W., Mehle, A., Strancar, J., Drazic, G., Krivec, M., Dillert, Ralf, Bahnemann, Detlef W., Mehle, A., Strancar, J., and Drazic, G.
- Abstract
Photocatalytic degradation of dichloroacetic acid (DCA) was studied in a continuous-flow set-up using a titanium microreactor with an immobilized double-layered TiO2 nanoparticle/nanotube film. Chloride ions, formed during the degradation process, negatively affect the photocatalytic efficiency and at a certain concentration (approximately 0.5 mM) completely stop the reaction in the microreactor. Two proposed mechanisms of inhibition with chloride ions, competitive adsorption and photogenerated-hole scavenging, have been proposed and investigated by adsorption isotherms and electron paramagnetic resonance (EPR) measurements. The results show that chloride ions block the DCA adsorption sites on the titania surface and reduce the amount of adsorbed DCA molecules. The scavenging effect of chloride ions during photocatalysis through the formation of chlorine radicals was not detected.
- Published
- 2014
18. Analysis of side chain rotational restrictions of membrane-embedded
- Author
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Strancar, J., Kavalenka, A.A., Ziherl, P., Stopar, D., and Hemminga, M.A.
- Subjects
Biofysica ,alpha-helix ,paramagnetic-resonance spectra ,EPS-3 ,fret ,Biophysics ,dynamics ,simulation ,major coat protein ,biosystem complexity - Abstract
Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296¿1305]
- Published
- 2009
19. Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy
- Author
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Strancar, J., Kavalenka, A., Ziherl, P., Stopar, D., and Hemminga, M. A.
- Subjects
ТЕХНИЧЕСКИЕ И ПРИКЛАДНЫЕ НАУКИ. ОТРАСЛИ ЭКОНОМИКИ::Электроника. Радиотехника [ЭБ БГУ] - Abstract
Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296–1305].
- Published
- 2009
20. Anterior lens epithelial cells attachment to the basal lamina
- Author
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ANDJELIC, S, primary, DRASLAR, K, additional, HVALA, A, additional, LOPIC, N, additional, STRANCAR, J, additional, and HAWLINA, M, additional
- Published
- 2014
- Full Text
- View/download PDF
21. Modeling membrane protein structure through site-directed ESR spectroscopy
- Author
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van Amerongen, Herbert, Hemminga, Marcus, Strancar, J., Kavalenka, A.A., van Amerongen, Herbert, Hemminga, Marcus, Strancar, J., and Kavalenka, A.A.
- Abstract
Site-directed spin labeling (SDSL) electron spin resonance (ESR) spectroscopy is a relatively new biophysical tool for obtaining structural information about proteins. This thesis presents a novel approach, based on powerful spectral analysis techniques (multicomponent spectral simulations and evolutionary optimizations of ESR spectra) and modeling of the protein structure by calculating the restrictions of the conformational space of the attached spin label. First, the feasibility of the ESR spectral analysis was enhanced by speeding-up the spectrum optimization and by automation of the analysis routines to enable the handling of large sets of spectroscopic data (e.g., for the joint analysis of SDSL-ESR spectra from multiple sites of a spin-labeled protein). According to the testing examples a speed-up factor of 5-7 was achieved. Secondly, SDSL-ESR was used to study the topology of the long N-terminal domain of the photosynthetic light-harvesting complex CP29. Wild-type protein containing a single cysteine at position 108 and nine single cysteine mutants were produced, allowing to label different parts of the domain with a nitroxide spin label. In all cases the apoproteins were either solubilized in detergent, or they were reconstituted with their native pigments in vitro. The spin label ESR spectra were analyzed in terms of a multi-component spectral simulation approach. These results permit to trace the structural organization of the long Nterminal domain of CP29 leading to a structural model for its N-terminal domain. Thirdly, we proposed a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. The proposed structural model takes into account the restricting effect of the protein backbone, amino acid side chains an
- Published
- 2009
22. Site-directed spin labeling study of the light-harvesting complex CP29
- Author
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Kavalenka, A.A., Spruijt, R.B., Wolfs, C.J.A.M., Strancar, J., Croce, R., Hemminga, M.A., van Amerongen, H., Kavalenka, A.A., Spruijt, R.B., Wolfs, C.J.A.M., Strancar, J., Croce, R., Hemminga, M.A., and van Amerongen, H.
- Abstract
The topology of the long N-terminal domain (100 amino-acid residues) of the photosynthetic Lhc CP29 was studied using electron spin resonance. Wild-type protein containing a single cysteine at position 108 and nine single-cysteine mutants were produced, allowing to label different parts of the domain with a nitroxide spin label. In all cases, the apoproteins were either solubilized in detergent or they were reconstituted with their native pigments (holoproteins) in vitro. The spin-label electron spin resonance spectra were analyzed in terms of a multicomponent spectral simulation approach, based on hybrid evolutionary optimization and solution condensation. These results permit to trace the structural organization of the long N-terminal domain of CP29. Amino-acid residues 97 and 108 are located in the transmembrane pigment-containing protein body of the protein. Positions 65, 81, and 90 are located in a flexible loop that is proposed to extend out of the protein from the stromal surface. This loop also contains a phosphorylation site at Thr81, suggesting that the flexibility of this loop might play a role in the regulatory mechanisms of the light-harvesting process. Positions 4, 33, 40, and 56 are found to be located in a relatively rigid environment, close to the transmembrane protein body. On the other hand, position 15 is located in a flexible region, relatively far away from the transmembrane domain
- Published
- 2009
23. Motional restrictions of membrane proteins: a site-directed spin labeling study
- Author
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Stopar, D., Strancar, J., Spruijt, R.B., Hemminga, M.A., Stopar, D., Strancar, J., Spruijt, R.B., and Hemminga, M.A.
- Abstract
Site-directed mutagenesis was used to produce 27 single cysteine mutants of bacteriophage M13 major coat protein spanning the whole primary sequence of the protein. Single-cysteine mutants were labeled with nitroxide spin labels and incorporated into phospholipid bilayers with increasing acyl chain length. The SDSL is combined with ESR and CD spectroscopy. CD spectroscopy provided information about the overall protein conformation in different mismatching lipids. The spin label ESR spectra were analyzed in terms of a new spectral simulation approach based on hybrid evolutionary optimization and solution condensation. This method gives the residue-level free rotational space (i.e., the effective space within which the spin label can wobble) and the diffusion constant of the spin label attached to the protein. The results suggest that the coat protein has a large structural flexibility, which facilitates a stable protein-to-membrane association in lipid bilayers with various degrees of hydrophobic mismatch.
- Published
- 2006
24. Determination of Partition Coefficient of Spin Probe between Different Lipid Membrane Phases
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Arsov, Z. and Strancar, J.
- Abstract
Model lipid membranes made from binary mixtures of dimyristoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DMPC/DPPC) and dimyristoylphosphatidylcholine/cholesterol (DMPC/Chol) exhibit coexistence of diverse lipid phases at appropriate temperature and composition. Since lipids in different phases show different structural and motional properties, it is expected that the corresponding spin probe electron paramagnetic resonance (EPR) spectra will be superposition of several spectral components. From comparison of proportions of spectral components of the EPR spectrum with the fractions of the corresponding lipid phases obtained from known phase diagrams the partition coefficient of spin probe methyl ester of 5-doxyl palmitate between different lipid phases was determined. The results indicate that the used spin probe partitions approximately equally between different phases.
- Published
- 2005
25. Speeding Up a Genetic Algorithm for EPR-Based Spin Label Characterization of Biosystem Complexity
- Author
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Kavalenka, A. A., Filipic, B., Hemminga, M. A., and Strancar, J.
- Abstract
Complexity of biological systems is one of the toughest problems for any experimental technique. Complex biochemical composition and a variety of biophysical interactions governing the evolution of a state of a biological system imply that the experimental response of the system would be superimposed of many different responses. To obtain a reliable characterization of such a system based on spin-label Electron Paramagnetic Resonance (EPR) spectroscopy, multiple Hybrid Evolutionary Optimization (HEO) combined with spectral simulation can be applied. Implemented as the GHOST algorithm this approach is capable of handling the huge solution space and provides an insight into the quasicontinuous distribution of parameters that describe the biophysical properties of an experimental system. However, the analysis procedure requires several hundreds of runs of the evolutionary optimization routine making this algorithm extremely computationally demanding. As only the best parameter sets from each run are assumed to contribute into the final solution, this algorithm appears far from being optimized. The goal of this study is to modify the optimization routine in a way that 20−40 runs would be enough to obtain qualitatively the same characterization. However, to keep the solution diversity throughout the HEO run, fitness sharing and newly developed shaking mechanisms are applied and tested on various test EPR spectra. In addition, other evolutionary optimization parameters such as population size and probability of genetic operators were also varied to tune the algorithm. According to the testing examples a speed-up factor of 5−7 was achieved.
- Published
- 2005
26. Exploring the Local Conformational Space of a Membrane Protein by Site-Directed Spin Labeling
- Author
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Stopar, D., Strancar, J., Spruijt, R. B., and Hemminga, M. A.
- Abstract
Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function−structure relationship of membrane proteins.
- Published
- 2005
27. Spin Label EPR-Based Characterization of Biosystem Complexity
- Author
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Strancar, J., Koklic, T., Arsov, Z., Filipic, B., Stopar, D., and Hemminga, M. A.
- Abstract
Following the widely spread EPR spin-label applications for biosystem characterization, a novel approach is proposed for EPR-based characterization of biosystem complexity. Hereto a computational method based on a hybrid evolutionary optimization (HEO) is introduced. The enormous volume of information obtained from multiple HEO runs is reduced with a novel so-called GHOST condensation method for automatic detection of the degree of system complexity through the construction of two-dimensional solution distributions. The GHOST method shows the ability of automatic quantitative characterization of groups of solutions, e.g. the determination of average spectral parameters and group contributions. The application of the GHOST condensation algorithm is demonstrated on four synthetic examples of different complexity and applied to two physiologically relevant examples − the determination of domains in biomembranes (lateral heterogeneity) and the study of the low-resolution structure of membrane proteins.
- Published
- 2005
28. An elevated rate of whole-genome duplications in cancers from Black patients.
- Author
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Brown LM, Hagenson RA, Koklič T, Urbančič I, Qiao L, Strancar J, and Sheltzer JM
- Subjects
- Female, Humans, Male, Middle Aged, DNA Copy Number Variations, Mutation, United States epidemiology, White, Black or African American genetics, Genome, Human, Neoplasms genetics, Neoplasms ethnology, Neoplasms mortality
- Abstract
In the United States, Black individuals have higher rates of cancer mortality than any other racial group. Here, we examine chromosome copy number changes in cancers from more than 1800 self-reported Black patients. We find that tumors from self-reported Black patients are significantly more likely to exhibit whole-genome duplications (WGDs), a genomic event that enhances metastasis and aggressive disease, compared to tumors from self-reported white patients. This increase in WGD frequency is observed across multiple cancer types, including breast, endometrial, and lung cancer, and is associated with shorter patient survival. We further demonstrate that combustion byproducts are capable of inducing WGDs in cell culture, and cancers from self-reported Black patients exhibit mutational signatures consistent with exposure to these carcinogens. In total, these findings identify a type of genomic alteration that is associated with environmental exposures and that may influence racial disparities in cancer outcomes., (© 2024. The Author(s).)
- Published
- 2024
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29. Anterior lens epithelial cells attachment to the basal lamina.
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Andjelic S, Drašlar K, Hvala A, Lopic N, Strancar J, and Hawlina M
- Subjects
- Anterior Capsule of the Lens metabolism, Basement Membrane metabolism, Capsulorhexis, Cataract Extraction, Epithelial Cells metabolism, Humans, Microscopy, Confocal, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Anterior Capsule of the Lens ultrastructure, Basement Membrane ultrastructure, Cell Adhesion physiology, Epithelial Cells ultrastructure
- Abstract
Purpose: To study the structure of the anterior lens epithelial cells (aLECs) and the contacts of the aLECs with the basal lamina (BL) in order to understand their role in the lens epithelium's function., Methods: The aLCs (BL and associated aLECs) were obtained from routine uneventful cataract surgery, prepared for and studied by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and confocal microscopy., Results: SEM shows that the basal surface of the aLECs (~10-15 μm) is with aLECs foldings (~1-3 μm) and extensions (~0.5-3 μm) attached to the BL. Confocal microscopy images of the basal sections of the aLECs after membrane staining also suggest that the basal part of aLECs has foldings (~1-3 μm). TEM shows in the aLECs basal parts, towards BL, the structures that look like entanglement (~1-4 μm). In cases where there is a swelling of the cytoplasm and offset of the aLECs from the BL, individual extensions (~0.5-2 μm) that extend to the BL are visible by TEM., Conclusions: We provide detail evidence about the structural organization of the aLECs, in particular about their basal side which is in contact with the BL. This is supported by the complementary use of three techniques, SEM, TEM and confocal microscopy, each of them showing the same morphological features, the extensions and the entanglements of the aLECs cytoplasmic membrane at the border with the BL. The basal surface of the aLECs is increased. It suggests the functional importance of the contact between aLECs and BL., (© 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.)
- Published
- 2016
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30. Protein Corona Prevents TiO2 Phototoxicity.
- Author
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Garvas M, Testen A, Umek P, Gloter A, Koklic T, and Strancar J
- Subjects
- Animals, Blood Proteins metabolism, Cattle, Cell Line, Cell Survival drug effects, Humans, Nanoparticles metabolism, Nanoparticles ultrastructure, Photochemical Processes, Reactive Oxygen Species metabolism, Titanium metabolism, Ultraviolet Rays, Nanoparticles toxicity, Protein Corona metabolism, Titanium toxicity
- Abstract
Background & Aim: TiO2 nanoparticles have generally low toxicity in the in vitro systems although some toxicity is expected to originate in the TiO2-associated photo-generated radical production, which can however be modulated by the radical trapping ability of the serum proteins. To explore the role of serum proteins in the phototoxicity of the TiO2 nanoparticles we measure viability of the exposed cells depending on the nanoparticle and serum protein concentrations., Methods & Results: Fluorescence and spin trapping EPR spectroscopy reveal that the ratio between the nanoparticle and protein concentrations determines the amount of the nanoparticles' surface which is not covered by the serum proteins and is proportional to the amount of photo-induced radicals. Phototoxicity thus becomes substantial only at the protein concentration being too low to completely coat the nanotubes' surface., Conclusion: These results imply that TiO2 nanoparticles should be applied with ligands such as proteins when phototoxic effects are not desired - for example in cosmetics industry. On the other hand, the nanoparticles should be used in serum free medium or any other ligand free medium, when phototoxic effects are desired - as for efficient photodynamic cancer therapy.
- Published
- 2015
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31. Molecular mobility of scaffolds' biopolymers influences cell growth.
- Author
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Podlipec R, Gorgieva S, Jurašin D, Urbančič I, Kokol V, and Strancar J
- Subjects
- Animals, Biocompatible Materials pharmacology, Biopolymers pharmacology, Cell Line, Elasticity, Gelatin chemistry, Gelatin pharmacology, Mice, Biocompatible Materials chemistry, Biopolymers chemistry, Cell Proliferation drug effects, Tissue Scaffolds chemistry
- Abstract
Understanding biocompatibility of materials and scaffolds is one of the main challenges in the field of tissue engineering and regeneration. The complex nature of cell-biomaterial interaction requires extensive preclinical functionality testing by studying specific cell responses to different biomaterial properties, from morphology and mechanics to surface characteristics at the molecular level. Despite constant improvements, a more general picture of biocompatibility is still lacking and tailormade scaffolds are not yet available. The scope of our study was thus the investigation of the correlation of fibroblast cell growth on different gelatin scaffolds with their morphological, mechanical as well as surface molecular properties. The latter were thoroughly investigated via polymer molecular mobility studied by site-directed spin labeling and electron paramagnetic resonance spectroscopy (EPR) for the first time. Anisotropy of the rotational motion of the gelatin side chain mobility was identified as the most correlated quantity with cell growth in the first days after adhesion, while weaker correlations were found with scaffold viscoelasticity and no correlations with scaffold morphology. Namely, the scaffolds with highly mobile or unrestricted polymers identified with the cell growth being five times less efficient (N(cells) = 60 ± 25 mm(-2)) as compared to cell growth on the scaffolds with considerable part of polymers with the restricted rotational motion (N(cells) = 290 ± 25 mm(-2)). This suggests that molecular mobility of scaffold components could play an important role in cell response to medical devices, reflecting a new aspect of the biocompatibility concept.
- Published
- 2014
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32. Bleaching-corrected fluorescence microspectroscopy with nanometer peak position resolution.
- Author
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Urbančič I, Arsov Z, Ljubetič A, Biglino D, and Strancar J
- Subjects
- Algorithms, Artifacts, Fluorescent Dyes chemistry, Spectrometry, Fluorescence methods
- Abstract
Fluorescence microspectroscopy (FMS) with environmentally sensitive dyes provides information about local molecular surroundings at microscopic spatial resolution. Until recently, only probes exhibiting large spectral shifts due to local changes have been used. For filter-based experimental systems, where signal at different wavelengths is acquired sequentially, photostability has been required in addition. Herein, we systematically analyzed our spectral fitting models and bleaching correction algorithms which mitigate both limitations. We showed that careful analysis of data acquired by stochastic wavelength sampling enables nanometer spectral peak position resolution even for highly photosensitive fluorophores. To demonstrate how small spectral shifts and changes in bleaching rates can be exploited, we analyzed vesicles in different lipid phases. Our findings suggest that a wide range of dyes, commonly used in bulk spectrofluorimetry but largely avoided in microspectroscopy due to the above-mentioned restrictions, can be efficiently applied also in FMS.
- Published
- 2013
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33. Coexistence of probe conformations in lipid phases-a polarized fluorescence microspectroscopy study.
- Author
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Urbančič I, Ljubetič A, Arsov Z, and Strancar J
- Subjects
- Membrane Microdomains chemistry, Fluorescence Polarization methods, Fluorescent Dyes chemistry, Molecular Conformation, Phospholipids chemistry
- Abstract
Several well-established fluorescence methods depend on environment-sensitive probes that report about molecular properties of their local environment. For reliable interpretation of experiments, careful characterization of probes' behavior is required. In this study, bleaching-corrected polarized fluorescence microspectroscopy with nanometer spectral peak position resolution was applied to characterize conformations of two alkyl chain-labeled 7-nitro-2-1,3-benzoxadiazol-4-yl phospholipids in three model membranes, representing the three main lipid phases. The combination of polarized and spectral detection revealed two main probe conformations with their preferential fluorophore dipole orientations roughly parallel and perpendicular to membrane normal. Their peak positions were separated by 2-6 nm because of different local polarities and depended on lipid environment. The relative populations of conformations, estimated by a numerical model, indicated a specific sensitivity of the two probes to molecular packing with cholesterol. The coexistence of probe conformations could be further exploited to investigate membrane organization below microscopy spatial resolution, such as lipid rafts. With the addition of polarized excitation or detection to any environment-sensitive fluorescence imaging technique, the conformational analysis can be directly applied to explore local membrane complexity., (Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2013
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34. Influence of cancerostatic perifosine on membrane fluidity of liposomes and different cell lines as measured by electron paramagnetic resonance.
- Author
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Podlipec R, Koklic T, Strancar J, Mravljak J, and Sentjurc M
- Subjects
- Animals, Drug Resistance, Neoplasm, Fibroblasts drug effects, Humans, Metallothionein 3, Mice, Phosphorylcholine pharmacology, Spin Labels, Tumor Cells, Cultured, Antineoplastic Agents pharmacology, Cell Membrane drug effects, Electron Spin Resonance Spectroscopy, Liposomes, Membrane Fluidity drug effects, Phosphorylcholine analogs & derivatives
- Abstract
Aim: To test whether membrane fluidity and its changes are important for the sensitivity of cells to the action of perifosine (OPP), a new anticancer drug targeting cell membrane and not DNA., Method: Influence of OPP on the membrane structure of OPP-resistant MCF7, and OPP-sensitive MT3 breast cancer cell lines, as well as of mouse fibroblasts (L929) cell lines, and model cells (liposomes) was investigated by electron paramagnetic resonance, using spin labeled derivative of OPP (P5) and 5-doxylpalmitoyl methylester (MeFASL(10,3)) as spin probes., Results: OPP increased membrane fluidity of all cell lines at concentrations higher than 50 μM (on the level of P≤0.05, t test). In cells, the differences were observed only by P5 and not by MeFASL(10,3). Average order parameter Seff decreased for about 12% in MCF7 and L929 and only for 8% in OPP-sensitive MT3 cells, showing that there was no correlation between membrane fluidity changes and sensitivity of cells to OPP. The only correlation we found was between OPP sensitivity and the cell growth rate. In liposomes, both spin probes were sensitive to the action of OPP. Seff decreased with increasing concentration of OPP. For MeFASL(10,3) a significant decrease was observed at 4 mol% OPP, while for P5 it was observed at 8 mol%., Conclusion: Influence of OPP on plasma membrane fluidity of breast cancer cells is not the determining factor in the sensitivity of cells to OPP.
- Published
- 2012
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35. EPR investigation of clomipramine interaction with phosphatidylcholine membranes in presence and absence of cholesterol.
- Author
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Yonar D, Paktaş DD, Horasan N, Strancar J, Sentjurc M, and Sünnetçioğlu MM
- Subjects
- Antidepressive Agents, Tricyclic chemistry, Computer Simulation, Molecular Structure, Cholesterol chemistry, Clomipramine chemistry, Electron Spin Resonance Spectroscopy methods, Lipid Bilayers chemistry, Liposomes chemistry, Phosphatidylcholines chemistry
- Abstract
The effects of tricylic antidepressant clomipramine (CLO) on the membrane properties of saturated dimyristoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine as well as on unsaturated egg yolk phosphatidylcholine liposomes were investigated by the electron paramagnetic resonance spin-labeling technique, in combination with the simulation of the spectra, taking into account that the membrane is heterogeneous and composed of the regions with different fluidity characteristics. Different spin labels, monitoring membrane properties in the upper and inner parts of the membrane, were used. In general, two spectral components, having different motional characteristics, were detected in all liposomes investigated. In liposomes with saturated chains, CLO decreased the phase-transition temperature, disordered the membrane, and increased polarity in the upper part of the membrane. However, less impact was observed in liposomes with unsaturated chains. In dipalmitoyl phosphatidylcholine liposomes, it also induced molecular rearrangements near the pretransition temperature. The presence of 30 mol% cholesterol increased the fluidizing effect of CLO and modified the lateral diffusion of nitroxide in the inner part of the membrane. A unique anomalous increase in diffusion of nitroxide, dependent on CLO concentration, was detected in the temperature region where the phosphatidylcholine membrane without cholesterol experiences the phase transitions. Since the changes in the central part of the membrane were even more pronounced than in the upper part of the membrane, it could be concluded that CLO incorporates into the membrane with its hydrophobic ring parallel to the phospholipid chains.
- Published
- 2011
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36. Fluorescence microspectroscopy as a tool to study mechanism of nanoparticles delivery into living cancer cells.
- Author
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Arsov Z, Urbančič I, Garvas M, Biglino D, Ljubetič A, Koklič T, and Strancar J
- Abstract
Lack of better understanding of nanoparticles targeted delivery into cancer cells calls for advanced optical microscopy methodologies. Here we present a development of fluorescence microspectroscopy (spectral imaging) based on a white light spinning disk confocal microscope with emission wavelength selection by a liquid crystal tunable filter. Spectral contrasting of images was used to localize polymer nanoparticles and cell membranes labeled with fluorophores that have substantially overlapping spectra. In addition, fluorescence microspectroscopy enabled spatially-resolved detection of small but significant effects of local molecular environment on the properties of environment-sensitive fluorescent probe. The observed spectral shift suggests that the delivery of suitably composed cancerostatic alkylphospholipid nanoparticles into living cancer cells might rely on the fusion with plasma cell membrane.
- Published
- 2011
- Full Text
- View/download PDF
37. Fluorescence and ESR spectroscopy studies on the interaction of isoflavone genistein with biological and model membranes.
- Author
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Kużdżał M, Wesołowska O, Strancar J, and Michalak K
- Subjects
- Animals, Cattle, Electron Spin Resonance Spectroscopy, Models, Molecular, Spectrometry, Fluorescence, 1,2-Dipalmitoylphosphatidylcholine chemistry, Dimyristoylphosphatidylcholine chemistry, Erythrocyte Membrane chemistry, Genistein chemistry, Membranes, Artificial
- Abstract
Genistein (5,7,4'-trihydroxyisoflavone) the common soy beans isoflavone has attracted scientific interest due to its antioxidant, estrogenic, antiangiogenic and aniticancer activities. The aim of the present study was to investigate the interaction of genistein with biological (erythrocyte) and model membranes (dimyristoyl- and dipalmitoylphosphatidylcholine). Using Laurdan and Prodan as fluorescent probes, we demonstrated phase behavior and membrane fluidity changes induced by genistein. ESR spectroscopy revealed alterations caused by genistein in membrane domains structure and mobility of spin probes with free radicals located at different depths of membrane. The method of ESR spectra decomposition and computer simulation of the recorded spectra were used in order to visualize domain coexistence by GHOST condensation method. Fluorescence and ESR spectroscopy experiments performed at different temperatures enabled us to observe the effect of isoflavone on phospholipid bilayers in either gel or liquid crystalline phase. It was concluded that genistein preferentially intercalated into lipid headgroup region, to some extent into polar-apolar interface and only in minimal degree into hydrophobic core of the membrane. According to our best knowledge this is the first study on modification of domain structure of membranes by genistein., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2011
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38. Strong correlations in highly electron-doped Zn(II)-DNA complexes.
- Author
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Omerzu A, Anzelak B, Turel I, Strancar J, Potocnik A, Arcon D, Arcon I, Mihailović D, and Matsui H
- Subjects
- Animals, Cattle, Electron Spin Resonance Spectroscopy, Temperature, DNA chemistry, Electrons, Organometallic Compounds chemistry, Zinc chemistry
- Abstract
We present spectroscopic measurements on the first example of a chemically electron-doped metal-DNA complex. We show that a doping level as high as the stoichiometric limit of one electron per base pair can be achieved. The doped unpaired electrons occupy lowest unoccupied molecular orbital levels of the nucleobases as detected with electron spin resonance and x-ray absorption near edge structure measurements. Delocalization and strong correlations between the unpaired electrons are evident from a temperature-independent spin susceptibility and a microwave conductivity above 100 K.
- Published
- 2010
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39. Conformational analysis of the partially disordered measles virus N(TAIL)-XD complex by SDSL EPR spectroscopy.
- Author
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Kavalenka A, Urbancic I, Belle V, Rouger S, Costanzo S, Kure S, Fournel A, Longhi S, Guigliarelli B, and Strancar J
- Subjects
- Computer Simulation, Protein Conformation, Crystallography methods, Electron Spin Resonance Spectroscopy methods, Measles virus chemistry, Models, Chemical, Models, Molecular, Nucleoproteins chemistry, Nucleoproteins ultrastructure
- Abstract
To characterize the structure of dynamic protein systems, such as partly disordered protein complexes, we propose a novel approach that relies on a combination of site-directed spin-labeled electron paramagnetic resonance spectroscopy and modeling of local rotation conformational spaces. We applied this approach to the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) both free and in complex with the X domain (XD, aa 459-507) of the viral phosphoprotein. By comparing measured and modeled temperature-dependent restrictions of the side-chain conformational spaces of 12 SL cysteine-substituted N(TAIL) variants, we showed that the 490-500 region of N(TAIL) is prestructured in the absence of the partner, and were able to quantitatively estimate, for the first time to our knowledge, the extent of the alpha-helical sampling of the free form. In addition, we showed that the 505-525 region of N(TAIL) conserves a significant degree of freedom even in the bound form. The latter two findings provide a mechanistic explanation for the reported rather high affinity of the N(TAIL)-XD binding reaction. Due to the nanosecond timescale of X-band EPR spectroscopy, we were also able to monitor the disordering in the 488-525 region of N(TAIL), in particular the unfolding of the alpha-helical region when the temperature was increased from 281 K to 310 K., (Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2010
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- View/download PDF
40. SDSL-ESR-based protein structure characterization.
- Author
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Strancar J, Kavalenka A, Urbancic I, Ljubetic A, and Hemminga MA
- Subjects
- Binding Sites, Humans, Models, Molecular, Protein Conformation, Proteins metabolism, Electron Spin Resonance Spectroscopy methods, Proteins chemistry, Spin Labels
- Abstract
As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.
- Published
- 2010
- Full Text
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41. Interaction of the chemopreventive agent resveratrol and its metabolite, piceatannol, with model membranes.
- Author
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Wesołowska O, Kuzdzał M, Strancar J, and Michalak K
- Subjects
- Calorimetry, Differential Scanning, Electron Spin Resonance Spectroscopy, Liposomes chemistry, Membranes, Artificial, Resveratrol, Spectrometry, Fluorescence, Stilbenes pharmacology, Thermodynamics, Stilbenes chemistry
- Abstract
Resveratrol and piceatannol are plant-derived polyphenols possessing extremely wide range of biological activities such as cancer chemopreventive, cardio- and neuroprotective, antioxidant, anti-inflammatory, anticancer and lifespan extending properties. Despite great interest in these stilbenes, their interactions with lipid bilayers have not been extensively studied. In the present work, the interaction of both resveratrol and piceatannol with model membranes composed of phosphatidylcholine (DMPC and DPPC) was investigated by means of fluorescence spectroscopy, differential scanning calorimetry (DSC) and electron spin resonance spectroscopy (ESR). Generalized polarization of two fluorescent probes Laurdan and Prodan measured in pure lipid and lipid:stilbene mixtures revealed that resveratrol and piceatannol changed bilayer properties in both gel-like and liquid crystalline phase and interacted with lipid headgroup region of the membrane. These findings were corroborated by DSC experiments in which the stilbene-induced decrease of lipid melting temperature and transition cooperativity were recorded. Resveratrol and piceatannol restricted also the ESR-measured mobility of spin probes GluSIN18, 5DSA and 16DSA with nitroxide group localized at different depths. Since the most pronounced effect was exerted on the spin probe located near membrane surface, we concluded that also ESR results pointed to the preferential interaction of resveratrol and piceatannol with headgroup region of lipid bilayer.
- Published
- 2009
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42. Site-directed spin-labeling study of the light-harvesting complex CP29.
- Author
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Kavalenka AA, Spruijt RB, Wolfs CJ, Strancar J, Croce R, Hemminga MA, and van Amerongen H
- Subjects
- Apoproteins genetics, Apoproteins metabolism, Arabidopsis, Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Carotenoids metabolism, Computer Simulation, Electron Spin Resonance Spectroscopy, Escherichia coli, Light-Harvesting Protein Complexes genetics, Models, Biological, Mutagenesis, Site-Directed, Mutation, Photosystem II Protein Complex genetics, Spinacia oleracea, Light-Harvesting Protein Complexes chemistry, Light-Harvesting Protein Complexes metabolism, Photosystem II Protein Complex chemistry, Photosystem II Protein Complex metabolism, Protein Conformation
- Abstract
The topology of the long N-terminal domain (approximately 100 amino-acid residues) of the photosynthetic Lhc CP29 was studied using electron spin resonance. Wild-type protein containing a single cysteine at position 108 and nine single-cysteine mutants were produced, allowing to label different parts of the domain with a nitroxide spin label. In all cases, the apoproteins were either solubilized in detergent or they were reconstituted with their native pigments (holoproteins) in vitro. The spin-label electron spin resonance spectra were analyzed in terms of a multicomponent spectral simulation approach, based on hybrid evolutionary optimization and solution condensation. These results permit to trace the structural organization of the long N-terminal domain of CP29. Amino-acid residues 97 and 108 are located in the transmembrane pigment-containing protein body of the protein. Positions 65, 81, and 90 are located in a flexible loop that is proposed to extend out of the protein from the stromal surface. This loop also contains a phosphorylation site at Thr81, suggesting that the flexibility of this loop might play a role in the regulatory mechanisms of the light-harvesting process. Positions 4, 33, 40, and 56 are found to be located in a relatively rigid environment, close to the transmembrane protein body. On the other hand, position 15 is located in a flexible region, relatively far away from the transmembrane domain.
- Published
- 2009
- Full Text
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43. Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy.
- Author
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Strancar J, Kavalenka A, Ziherl P, Stopar D, and Hemminga MA
- Subjects
- Capsid Proteins chemistry, Lipids chemistry, Models, Molecular, Protein Conformation, Electron Spin Resonance Spectroscopy methods, Membrane Proteins chemistry, Spin Labels
- Abstract
Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296-1305].
- Published
- 2009
- Full Text
- View/download PDF
44. Mapping alpha-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy.
- Author
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Belle V, Rouger S, Costanzo S, Liquière E, Strancar J, Guigliarelli B, Fournel A, and Longhi S
- Subjects
- Amino Acid Substitution, Circular Dichroism, Crystallography, X-Ray, Cysteine genetics, Electron Spin Resonance Spectroscopy, Electrophoresis, Polyacrylamide Gel, Mutant Proteins chemistry, Mutant Proteins isolation & purification, Mutant Proteins metabolism, Nucleocapsid Proteins, Protein Structure, Secondary, Protein Structure, Tertiary, Sucrose, Temperature, Trifluoroethanol chemistry, Nucleoproteins chemistry, Nucleoproteins metabolism, Protein Folding, Spin Labels, Viral Proteins chemistry, Viral Proteins metabolism
- Abstract
Using site-directed spin-labeling EPR spectroscopy, we mapped the region of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)) that undergoes induced folding. In addition to four spin-labeled N(TAIL) variants (S407C, S488C, L496C, and V517C) (Morin et al. (2006), J Phys Chem 110: 20596-20608), 10 new single-site cysteine variants were designed, purified from E. coli, and spin-labeled. These 14 spin-labeled variants enabled us to map in detail the gain of rigidity of N(TAIL) in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol or the C-terminal domain X (XD) of the viral phosphoprotein. Different regions of N(TAIL) were shown to contribute to a different extent to the binding to XD, while the mobility of the spin labels grafted at positions 407 and 460 was unaffected upon addition of XD; that of the spin labels grafted within the 488-502 and the 505-522 regions was severely and moderately reduced, respectively. Furthermore, EPR experiments in the presence of 30% sucrose allowed us to precisely map to residues 488-502, the N(TAIL) region undergoing alpha-helical folding. The mobility of the 488-502 region was found to be restrained even in the absence of the partner, a behavior that could be accounted for by the existence of a transiently populated folded state. Finally, we show that the restrained motion of the 505-522 region upon binding to XD is due to the alpha-helical transition occurring within the 488-502 region and not to a direct interaction with XD.
- Published
- 2008
- Full Text
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45. Rigidification of neutral lipid bilayers in the presence of salts.
- Author
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Pabst G, Hodzic A, Strancar J, Danner S, Rappolt M, and Laggner P
- Subjects
- Computer Simulation, Elasticity, Hydrogen-Ion Concentration, Molecular Conformation, Osmolar Concentration, Permeability, Phase Transition, Lipid Bilayers chemistry, Membrane Fluidity, Models, Chemical, Models, Molecular, Salts chemistry
- Abstract
We studied the influence of sodium and calcium chloride on the global and local membrane properties of fluid palmitoyl-oleoyl phosphatidylcholine bilayers, applying synchrotron small-angle x-ray diffraction, spin-labeling electron paramagnetic resonance spectroscopy, and differential scanning calorimetry, as well as simultaneous density and acoustic measurements. The salt concentration was varied over a wide range from 0 to 5 M. We found that NaCl leads to a continuous swelling of the bilayers, whereas the behavior of the bilayer separation dW in the presence of CaCl2 is more complex, showing an initial large dW value, which decreased upon further addition of salt and finally increased again in the high concentration regime. This can be understood by a change of balance between electrostatic and van der Waals interactions. We were further able to show that both salts lead to a significant increase of order within the lipid bilayer, leading to a decrease of bilayer elasticity and shift of main phase transition temperature. This effect is more pronounced for Ca2+, and occurs mainly in the high salt-concentration regime. Thus, we were able to reconcile previous controversies between molecular dynamics simulations and x-ray diffraction experiments regarding the effect of salts on neutral lipid bilayers.
- Published
- 2007
- Full Text
- View/download PDF
46. Motional restrictions of membrane proteins: a site-directed spin labeling study.
- Author
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Stopar D, Strancar J, Spruijt RB, and Hemminga MA
- Subjects
- Amino Acid Substitution, Circular Dichroism methods, Computer Simulation, Electron Spin Resonance Spectroscopy methods, Motion, Mutagenesis, Site-Directed, Protein Conformation, Spin Labels, Structure-Activity Relationship, Capsid Proteins chemistry, Capsid Proteins ultrastructure, Models, Chemical, Models, Molecular
- Abstract
Site-directed mutagenesis was used to produce 27 single cysteine mutants of bacteriophage M13 major coat protein spanning the whole primary sequence of the protein. Single-cysteine mutants were labeled with nitroxide spin labels and incorporated into phospholipid bilayers with increasing acyl chain length. The SDSL is combined with ESR and CD spectroscopy. CD spectroscopy provided information about the overall protein conformation in different mismatching lipids. The spin label ESR spectra were analyzed in terms of a new spectral simulation approach based on hybrid evolutionary optimization and solution condensation. This method gives the residue-level free rotational space (i.e., the effective space within which the spin label can wobble) and the diffusion constant of the spin label attached to the protein. The results suggest that the coat protein has a large structural flexibility, which facilitates a stable protein-to-membrane association in lipid bilayers with various degrees of hydrophobic mismatch.
- Published
- 2006
- Full Text
- View/download PDF
47. Effects of lipid composition on the membrane activity and lipid phase behaviour of Vibrio sp. DSM14379 cells grown at various NaCl concentrations.
- Author
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Danevcic T, Rilfors L, Strancar J, Lindblom G, and Stopar D
- Subjects
- Biophysical Phenomena, Biophysics, Cell Membrane metabolism, Chromatography, Gas, Chromatography, Thin Layer, Dose-Response Relationship, Drug, Electron Spin Resonance Spectroscopy, Lysophospholipids chemistry, Magnetic Resonance Spectroscopy, Phosphatidylethanolamines chemistry, Spin Labels, Triacetoneamine-N-Oxyl, Lipids chemistry, Sodium Chloride pharmacology, Vibrio metabolism
- Abstract
The membrane lipid composition of living cells generally adjusts to the prevailing environmental and physiological conditions. In this study, membrane activity and lipid composition of the Gram-negative bacterium Vibrio sp. DSM14379, grown aerobically in a peptone-yeast extract medium supplemented with 0.5, 1.76, 3, 5 or 10% (w/v) NaCl, was determined. The ability of the membrane to reduce a spin label was studied by EPR spectroscopy under different salt concentrations in cell suspensions labeled with TEMPON. For lipid composition studies, cells were harvested in a late exponential phase and lipids were extracted with chloroform-methanol-water, 1:2:0.8 (v/v). The lipid polar head group and acyl chain compositions were determined by thin-layer and gas-liquid chromatographies. (31)P-NMR spectroscopy was used to study the phase behaviour of the cell lipid extracts with 20 wt.% water contents in a temperature range from -10 to 50 degrees C. The results indicate that the ability of the membrane to reduce the spin label was highest at optimal salt concentrations. The composition of both polar head groups and acyl chains changed markedly with increasing salinity. The fractions of 16:0, 16:1 and 18:0 acyl chains increased while the fraction of 18:1 acyl chains decreased with increasing salinity. The phosphatidylethanolamine fraction correlated inversely with the lysophosphatidylethanolamine fraction, with phosphatidylethanolamine exhibiting a minimum, and lysophosphatidylethanolamine a maximum, at the optimum growth rate. The fraction of lysophosphatidylethanolamine was surprisingly high in the lipid extracts. This lipid can form normal micellar and hexagonal phases and it was found that all lipid extracts form a mixture of lamellar and normal isotropic liquid crystalline phases. This is an anomalous behaviour since the nonlamellar phases formed by total lipid extracts are generally of the reversed type.
- Published
- 2005
- Full Text
- View/download PDF
48. The membrane lateral domain approach in the studies of lipid-protein interaction of GPI-anchored bovine erythrocyte acetylcholinesterase.
- Author
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Arsov Z, Schara M, Zorko M, and Strancar J
- Subjects
- Animals, Cattle, Computer Simulation, Enzyme Activation, Membrane Microdomains chemistry, Protein Binding, Protein Conformation, Acetylcholinesterase chemistry, Electron Spin Resonance Spectroscopy methods, Erythrocyte Membrane chemistry, Glycosylphosphatidylinositols chemistry, Lipid Bilayers chemistry, Membrane Fluidity, Models, Chemical
- Abstract
A novel membrane lateral domain approach was used to test whether the activity of the membrane-bound enzyme acetylcholinesterase (AChE) depends on the local properties (e.g. local lipid ordering) of bovine erythrocyte-ghost membrane. This issue has an additional aspect of interest due to an alternative mode of insertion of AChE molecules into the membrane by the glycosylphosphatidylinositol (GPI) anchor. In our experiments the lateral domain membrane structure was influenced by temperature and by the addition of n-butanol, and was quantitatively characterized using the method of EPR spectrum decomposition. The activity of AChE was determined by a colorimetric assay in the same samples. The results show that the membrane stabilizes the conformation of the membrane-bound AChE compared to the isolated AChE. In addition, a correlation was observed between the temperature dependence of order parameter of the most-ordered domain type and the activity of AChE. Therefore, our findings support the idea that the function of GPI proteins can be modulated by the lipid bilayer. Based on the assumption that the overall activity of AChE depends on the order parameters of particular domain types as well as their proportions, two models for AChE activity were introduced. In the first, a random distribution of enzyme molecules was proposed, and in the second, localization of enzyme molecules in a single (cholesterol-rich) domain type was assumed. Better agreement between measured and calculated activity values speaks in favor of the second model.
- Published
- 2004
- Full Text
- View/download PDF
49. Phospholipid mesophases at solid interfaces: in-situ X-ray diffraction and spin-label studies.
- Author
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Rappolt M, Amenitsch H, Strancar J, Teixeira CV, Kriechbaum M, Pabst G, Majerowicz M, and Laggner P
- Subjects
- Cell Membrane chemistry, Electron Spin Resonance Spectroscopy instrumentation, Electron Spin Resonance Spectroscopy methods, Mathematics, Membrane Fusion, Models, Theoretical, Surface Properties, X-Ray Diffraction, Lipid Bilayers chemistry, Phospholipids chemistry, Spin Labels
- Abstract
In this work, we report on recent investigations, both on the global and on the local molecular architecture of supported phospholipid model membranes. A brief theoretical introduction explains how global structural information on supramolecular lipid ensembles can be retrieved from surface X-ray diffraction measurements as well as how spin-label electron paramagnetic resonance spectroscopy (EPR) provides complementary information on the local environment of probe molecules. The combination of especially designed X-ray cells with the technique of small- and wide-angle X-ray surface scattering makes it possible to explore various fields of lipid research and its applications. Examples for different physico-chemical conditions are presented: (i) in situ chemistry under excess of water conditions demonstrating how solid-supported lipid films sense salinity, (ii) the 3D electron density reconstruction of a vesicle-fusion intermediate under controlled humidity, and (iii) complementary temperature and pressure effects on oriented phospholipid samples. Further, special attention has been given to the influence of different film preparation techniques with respect to quality and the defect structure manifestation. To resolve the proportions and local properties of defects in a hydrated lipid-deposited surface, spin-label EPR was applied. The results from 9.6 GHz EPR as well as from 1.2 GHz EPR suggest the alignment to be in the range between 30% and 80%. In addition, slow time-dependent EPR measurements point to nano-structural rearrangements due to water flow and reduction of alignment quality.
- Published
- 2004
- Full Text
- View/download PDF
50. Soft picture of lateral heterogeneity in biomembranes.
- Author
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Strancar J, Koklic T, and Arsov Z
- Subjects
- Animals, Horses, Macromolecular Substances, Molecular Conformation, Neutrophils chemistry, Neutrophils ultrastructure, Pulmonary Disease, Chronic Obstructive blood, Pulmonary Disease, Chronic Obstructive pathology, 1,2-Dipalmitoylphosphatidylcholine chemistry, Algorithms, Cell Membrane chemistry, Cell Membrane ultrastructure, Electron Spin Resonance Spectroscopy methods, Liposomes chemistry, Membrane Microdomains chemistry, Membrane Microdomains ultrastructure
- Abstract
Standard methods of characterization of electron paramagnetic resonance (EPR) spectra of spin-labeled biomembranes limit the resolution of lateral heterogeneity to only two or three domain types. This disables examination of the structure-function relationship in complex membranes, which might be composed of a larger number of different domain types. To enable exploration of this kind, a new approach based on analysis of EPR spectra with multi-run, hybrid evolutionary optimization is proposed here. From the multiple runs a quasi-continuous distribution of membrane spectral parameters (order parameter, proportion of spectral component, polarity correction factor, rotational correlation time and broadening constant) can be constructed and presented by a new presentation technique CODE (colored distribution of E PR spectral parameters). Through this the concept of a "soft" picture of membrane heterogeneity is introduced, in contrast to the standard "discrete" domain picture. The "soft" characterization method, established on synthetic spectra, was used to examine the lateral heterogeneity of liposome membranes as well as of membranes of neutrophils from healthy and asthmatic horses. In liposome membranes the determined number of domain types was the same as already established by standard procedures of EPR spectra line-shape interpretation. In membranes of neutrophils a quasi-continuous distribution of membrane domain properties was detected by the new method.
- Published
- 2003
- Full Text
- View/download PDF
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