Alexander Demchenko - Academia.edu (original) (raw)

Papers by Alexander Demchenko

Research paper thumbnail of Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing <i>in vitro</i> and <i>in vivo</i> Microscopic Dynamics of Viscosity Free from Polarity Interference

Social Science Research Network, 2019

Research paper thumbnail of Double-exponential kinetics of binding and redistribution of the fluorescent dyes in cell membranes witness for the existence of lipid microdomains

Biochemical and Biophysical Research Communications, 2019

New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means ... more New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means of membrane-binding fluorescent dyes is proposed. The kinetics of dye incorporation into the membrane or its lateral diffusion inside the membrane is measured and decomposed into exponential components by means of the Maximum Entropy Method. Two distinct exponential components are obtained consistently in all cases for several fluorescent dyes, two different cell lines and in different types of experiments including spectroscopy, flow cytometry and fluorescence recovery after photobleaching. These components are attributed to the liquid-ordered and disordered phases in the plasma membrane of studied cells in their dynamic equilibrium.

Research paper thumbnail of Insight into the mechanism of the photoluminescence of carbon nanoparticles derived from cryogenic studies

Nanoscale, 2018

The origin of the fluorescence of carbon dots is the formation of self-trapped excitons in H-aggr... more The origin of the fluorescence of carbon dots is the formation of self-trapped excitons in H-aggregate-like structures.

Research paper thumbnail of Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing <i>In Vitro</i> and <i>In Vivo</i> Microscopic Dynamics of Viscosity Free from Polarity Interference

ACS Chemical Biology, Jun 16, 2020

We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the dis... more We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the distribution of microscopic dynamics within living cells and tissues by using the newly developed principle of fluorescence response. The bentto-planar motion in the excited state of incorporated fluorescence probes leads to elongation of the π-delocalization, resulting in microviscosity-dependent but polarity-insensitive interplay between well-separated blue and red bands in emission spectra. This allows constructing the exceptionally contrasted images of cellular dynamics. Moreover, the application of probes with increased affinity towards biological membranes allowed detecting the differences in dynamics between plasma membrane and intracellular membrane structures. Such λ-ratiometric microviscosity imaging was extended for mapping the living tissues and observing their inflammation-dependent changes. ASSOCIATED CONTENT Supporting Information The Supporting Information is available free of charge at Supporting information contains additional synthesis procedures, MD simulations, fluorescence spectra, images, and cell viability tests AUTHOR INFORMATION

Research paper thumbnail of Visualization and detection of live and apoptotic cells with fluorescent carbon nanoparticles

Journal of Nanobiotechnology, Nov 21, 2015

Apoptosis is a genetically encoded cell death program that involves different processes occurring... more Apoptosis is a genetically encoded cell death program that involves different processes occurring on molecular and sub-cellular levels. Here we report on its new features-the increased accumulation of fluorescent carbon nanoparticles (CDots) in cells and their changed distribution within cell interior, which can witness on altered mechanisms of their translocation through the membrane. The comparative studies of living (intact) and apoptotic cells were provided with two cell lines (HeLa, Vero) using two types of fluorescent nanoparticles ("violet" and "blue" CDots). In all studied cases the images of living and apoptotic cells were different; the apoptotic cells incorporated larger number of CDots resulting in their much brighter images. These nanoparticles are distributed in cell cytoplasm, however, when the cells are fixed and treated with detergent, their nucleus is also labeled. Flow cytometry allows distinguishing the sub-populations of living and apoptotic cells in their cultures and suggests a very cheap and easy way to characterize them.

Research paper thumbnail of Michael Kasha: From Photochemistry and Flowers to Spectroscopy and Music

Angewandte Chemie, Oct 30, 2014

Research paper thumbnail of Michael Kasha: von Photochemie und Blumen bis Spektroskopie und Musik

Angewandte Chemie, Oct 30, 2014

Michael Kasha (Abbildung 1) war ein brillanter Wissenschaftler mit einzigartigen Erfolgen auf ein... more Michael Kasha (Abbildung 1) war ein brillanter Wissenschaftler mit einzigartigen Erfolgen auf einer Reihe von Gebieten und eine herausragende Persçnlichkeit, wobei ihm sein neugieriges Interesse an den grundlegenden Gesetzen der Natur erlaubte, durch gewissenhafte Experimente und theoretische Methoden gewonnenes Wissen zu neuen Erkenntnissen zu verbinden. Kasha, der am 12. Juni 2013 im Alter von 92 Jahren gestorben ist, verband als Universalgenie [1] Chemie und Physik mit Musik, Photographie, der Farbe von Taglilien und Astrochemie. Er war einer der Begründer der modernen Photophysik und Photochemie sowie der Molekülspektroskopie in kondensierten Phasen. Kasha begann seine wissenschaftliche Laufbahn in den 1940er Jahren bei Gilbert N. Lewis und entwickelte damals ein grundlegendes Gesetz, das Fluoreszenz und Phosphoreszenz durch Intersystem Crossing verband. [2] Lewis und Kasha folgerten, dass bei allen von ihnen beobachteten Molekülen der phosphoreszierende Zustand ein Triplettzustand war, unabhängig davon, ob dieses Molekül einfach oder komplex, organisch oder anorganisch war. Auch kann die Kasha-Regel, die beschreibt, dass jeder strahlende elektronische Zustand einer gegebenen Multiplizität der tiefstliegende elektronisch angeregte Zustand dieser Multiplizität ist, [3] in jedem Lehrbuch der physikalischen Chemie oder der Molekülspektroskopie gefunden werden. Außerdem zeigte Kasha, dass die Wechselwirkung mit schweren Atomen bei organischen Molekülen Absorption durch Singulett-Triplett-Übergänge sowie Phosphoreszenz ermçglichen kann-der externe Schweratomeffekt oder auch Kasha-Effekt. [4] Kasha war derjenige, der die quantenmechanischen Theorien der Excitonen und des Energietransfers durch Induktionsresonanz verband. [5] Er entdeckte, dass Singulett-Sauerstoff durch chemische Reaktionen erzeugt werden kann, und untersuchte die Chemilumineszenz molekularen Sauerstoffs, [6] die sich bei späteren Untersuchungen als bedeutend für die Biologie herausstellte. Daneben klärte er die Rolle der Antennenpigmente in der Photosynthese. [7] Er war ein Pionier bei der Untersuchung von Systemen mit Protonentransfer im angeregten Zustand, egal ob intramolekular, mit doppeltem Protonentransfer oder durch das Lçsungsmittel vermittelt, [8] und er entwickelte das Vierstufendiagramm für diese Prozesse und bewies ihre Verbindung zu elektronischen Ladungstransfers. Mit jeder einzelnen dieser Vielzahl an Entdeckungen hätte er sich einen Platz in der Wissenschaftsgeschichte verdient. In diesem Essay mçchten wir persçnliche Erinnerungen nutzen, um zum biographischen Material beizutragen [9] und folgende Frage zu beantworten: Wer war dieser Mann, der so viele herausragende Beiträge leistete?

Research paper thumbnail of Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels

Frontiers in Chemistry, 2020

Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quanti... more Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).

Research paper thumbnail of Dual emissive analogue of deoxyuridine as a sensitive hydration-reporting probe for discriminating mismatched from matched DNA and DNA/DNA from DNA/RNA duplexes

Journal of Materials Chemistry C, 2016

Herein, we report the incorporation in DNA of a tailored dual emissive probe with exquisite sensi... more Herein, we report the incorporation in DNA of a tailored dual emissive probe with exquisite sensitivity to hydration.

Research paper thumbnail of Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues

RSC Advances, 2015

We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration... more We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.

Research paper thumbnail of Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers

The Scientific World Journal, 2013

A remarkable flexibility is observed in biological membranes, which allows them to form the struc... more A remarkable flexibility is observed in biological membranes, which allows them to form the structures of different curvatures. We addressed the question of intrinsic ability of phospholipid membranes to form highly curved structures and the role of cholesterol in this process. The distribution of cholesterol in the highly curved asymmetric DOPC/DOPS lipid bilayer was investigated by the coarse-grained molecular dynamics simulations in the membrane patches with large aspect ratio. It is shown that cholesterol induces uneven membrane curvature promoting the formation of extended flattened regions of the membrane interleaved by sharp bends. It is shown that the affinity of cholesterol to anionic DOPS or neutral DOPC lipids is curvature dependent. The cholesterol prefers DOPS to DOPC in either planar or highly curved parts of the membrane. In contrast, in the narrow interval of moderate membrane curvatures this preference is inverted. Our data suggest that there is a complex self-consistent interplay between the membrane curvature and cholesterol distribution in the asymmetric lipid bilayers. The suggested new function of cholesterol may have a biological relevance.

Research paper thumbnail of Clustering Monte Carlo simulations of the hierarchical protein folding on a simple lattice model

Biopolymers and Cell, 2004

A role of specific collective motions and clustering behavior In protein folding was investigated... more A role of specific collective motions and clustering behavior In protein folding was investigated using simple 2D lattice models. Two model peptides, which have the sequences of hierarchical and non-hierarchical design, were studied comparatively. Simulations were performed using three methods: Metropolis Monte Carlo with the local move set, Metropolis Monte Carlo with unspeclflc rigid rotations, and the Clustering Monte Carlo (CMC) algorithm that has been recently described by the authors. The latter was developed with particular aim to provide a realistic description of cluster dynamics. We present convincing evidence that the folding pathways and kinetics of hierarchically folding sequence are not adequately described in conventional MC simulations. In this case the account for cluster dynamics provided by CMC algorithm reveals important features of folding of hierarchically organized sequences. Our data suggest that the methods, which enable specific cluster motions, should be used for realistic description of hierarchical folding.

Research paper thumbnail of Apoptosis and eryptosis: Striking differences on biomembrane level

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2018

The cell plasma membrane plays an essential role in programmed cell death of nucleated cells (apo... more The cell plasma membrane plays an essential role in programmed cell death of nucleated cells (apoptosis) and erythrocytes (eryptosis), and its changes due to loss of transmembrane asymmetry are quite similar. However, nucleated cells possess the network of intracellular membranes, which are missing in erythrocytes. Providing comparative studies with series of molecular probes, we observe dramatic differences in membrane lipid order in the course of apoptosis and eryptosis. In contrast to nucleated cells, in which a significant drop of the lipid order in the plasma membrane is observed, the erythrocyte membrane retains the relatively high level of the lipid order. Observation in nucleated cells of significant differences between inner and plasma membranes and detection of apoptotic bodies with different organization suggest that the decrease in the lipid order of their plasma membrane could be at least partially explained by the phospholipid and/or cholesterol exchange between membranes. Such features are absent in erythrocytes.

Research paper thumbnail of MOESM1 of Visualization and detection of live and apoptotic cells with fluorescent carbon nanoparticles

Additional file 1. Fluorometry and flow cytometry measurements.

Research paper thumbnail of Characterization of Alpha-Synuclein Early Aggregates by Atomic Force Microscopy

Biophysical Journal, 2010

such amyloid fibrils in vitro. However, it exhibits poor sensitivity and reproducibility, require... more such amyloid fibrils in vitro. However, it exhibits poor sensitivity and reproducibility, requires sampling, and is insensitive to the early stages of aggregation. We introduced a new sensor molecule for the continuous monitoring of AS aggregation, denoted AS-140HC, consisting of the AS mutant (A140C, C-terminus) labeled with the 3-hydroxychromone dye MFC [1]. MFC exhibits two fluorescence bands (N* and T*) arising from Excited State Intramolecular Proton Transfer (ESIPT) [2]. The intensity ratio of (I T* /I N*) reflects the microenvironment of the probe. Addition of AS-140HC in the range of 0.5-5% to wild type AS allows the monitoring of aggregation via the strong increase of I T* /I N* (panel A), which occurs at a much earlier stage of aggregation than the ThT response (panel B). See also refs [3-6].

Research paper thumbnail of New Fluorescent Probe for Continuous Monitoring of Alpha-Synuclein Aggregation

Biophysical Journal, 2010

Research paper thumbnail of En Route to White-Light Generation Utilizing Nanocomposites Composed of Ultrasmall CdSe Nanodots and Excited-State Intramolecular Proton Transfer Dyes

ACS Applied Materials & Interfaces, 2011

Research paper thumbnail of Excited-state intramolecular proton-transfer reaction demonstrating anti-Kasha behavior

Research paper thumbnail of Fluorescent Few-Atom Clusters of Silver Formed in Organic Solvents on Polymeric Supports

Few-atom silver clusters are fluorophores with a set of attractive properties including sub-nanom... more Few-atom silver clusters are fluorophores with a set of attractive properties including sub-nanometer size, high quantum yield and large Stokes shift. Sharing high photostability with semiconductor quantum dots but being of much smaller size, lacking blinking and with expected lack of toxicity, they are especially attractive for biological imaging, down to single molecules. No less promising are their applications in chemical sensing and biosensing as well as for molecular optic and electronic devices on a single molecular level. We demonstrate that it is not a unique property of water that can provide the formation and stability of silver clusters. They can be produced on photoreduction in different organic solvents using the same polymeric template. Unique photophysical properties of these clusters share both similarities and differences to that of organic dyes.

Research paper thumbnail of Excited-state intramolecular proton-transfer reaction demonstrating anti-Kasha behavior

We report unusual photophysical properties observed on two newly designed 3-hydroxychromone deriv... more We report unusual photophysical properties observed on two newly designed 3-hydroxychromone derivatives exhibiting the excited-state intramolecular proton transfer (ESIPT) reaction. The efficiency of ESIPT reaction is greatly enhanced upon excitation with high energy quanta to Sn (n > 1) levels in lowpolarity solvents. Based on detailed analyses of excitation and emission spectra as well as time-resolved emission kinetics we derive that conditions, in which this phenomenon contradicting Kasha's rule is observed, are quite different from that for observation of anti-Kasha emission.

Research paper thumbnail of Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing <i>in vitro</i> and <i>in vivo</i> Microscopic Dynamics of Viscosity Free from Polarity Interference

Social Science Research Network, 2019

Research paper thumbnail of Double-exponential kinetics of binding and redistribution of the fluorescent dyes in cell membranes witness for the existence of lipid microdomains

Biochemical and Biophysical Research Communications, 2019

New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means ... more New technique of detecting lateral heterogeneity of the plasma membrane of living cells by means of membrane-binding fluorescent dyes is proposed. The kinetics of dye incorporation into the membrane or its lateral diffusion inside the membrane is measured and decomposed into exponential components by means of the Maximum Entropy Method. Two distinct exponential components are obtained consistently in all cases for several fluorescent dyes, two different cell lines and in different types of experiments including spectroscopy, flow cytometry and fluorescence recovery after photobleaching. These components are attributed to the liquid-ordered and disordered phases in the plasma membrane of studied cells in their dynamic equilibrium.

Research paper thumbnail of Insight into the mechanism of the photoluminescence of carbon nanoparticles derived from cryogenic studies

Nanoscale, 2018

The origin of the fluorescence of carbon dots is the formation of self-trapped excitons in H-aggr... more The origin of the fluorescence of carbon dots is the formation of self-trapped excitons in H-aggregate-like structures.

Research paper thumbnail of Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing <i>In Vitro</i> and <i>In Vivo</i> Microscopic Dynamics of Viscosity Free from Polarity Interference

ACS Chemical Biology, Jun 16, 2020

We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the dis... more We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the distribution of microscopic dynamics within living cells and tissues by using the newly developed principle of fluorescence response. The bentto-planar motion in the excited state of incorporated fluorescence probes leads to elongation of the π-delocalization, resulting in microviscosity-dependent but polarity-insensitive interplay between well-separated blue and red bands in emission spectra. This allows constructing the exceptionally contrasted images of cellular dynamics. Moreover, the application of probes with increased affinity towards biological membranes allowed detecting the differences in dynamics between plasma membrane and intracellular membrane structures. Such λ-ratiometric microviscosity imaging was extended for mapping the living tissues and observing their inflammation-dependent changes. ASSOCIATED CONTENT Supporting Information The Supporting Information is available free of charge at Supporting information contains additional synthesis procedures, MD simulations, fluorescence spectra, images, and cell viability tests AUTHOR INFORMATION

Research paper thumbnail of Visualization and detection of live and apoptotic cells with fluorescent carbon nanoparticles

Journal of Nanobiotechnology, Nov 21, 2015

Apoptosis is a genetically encoded cell death program that involves different processes occurring... more Apoptosis is a genetically encoded cell death program that involves different processes occurring on molecular and sub-cellular levels. Here we report on its new features-the increased accumulation of fluorescent carbon nanoparticles (CDots) in cells and their changed distribution within cell interior, which can witness on altered mechanisms of their translocation through the membrane. The comparative studies of living (intact) and apoptotic cells were provided with two cell lines (HeLa, Vero) using two types of fluorescent nanoparticles ("violet" and "blue" CDots). In all studied cases the images of living and apoptotic cells were different; the apoptotic cells incorporated larger number of CDots resulting in their much brighter images. These nanoparticles are distributed in cell cytoplasm, however, when the cells are fixed and treated with detergent, their nucleus is also labeled. Flow cytometry allows distinguishing the sub-populations of living and apoptotic cells in their cultures and suggests a very cheap and easy way to characterize them.

Research paper thumbnail of Michael Kasha: From Photochemistry and Flowers to Spectroscopy and Music

Angewandte Chemie, Oct 30, 2014

Research paper thumbnail of Michael Kasha: von Photochemie und Blumen bis Spektroskopie und Musik

Angewandte Chemie, Oct 30, 2014

Michael Kasha (Abbildung 1) war ein brillanter Wissenschaftler mit einzigartigen Erfolgen auf ein... more Michael Kasha (Abbildung 1) war ein brillanter Wissenschaftler mit einzigartigen Erfolgen auf einer Reihe von Gebieten und eine herausragende Persçnlichkeit, wobei ihm sein neugieriges Interesse an den grundlegenden Gesetzen der Natur erlaubte, durch gewissenhafte Experimente und theoretische Methoden gewonnenes Wissen zu neuen Erkenntnissen zu verbinden. Kasha, der am 12. Juni 2013 im Alter von 92 Jahren gestorben ist, verband als Universalgenie [1] Chemie und Physik mit Musik, Photographie, der Farbe von Taglilien und Astrochemie. Er war einer der Begründer der modernen Photophysik und Photochemie sowie der Molekülspektroskopie in kondensierten Phasen. Kasha begann seine wissenschaftliche Laufbahn in den 1940er Jahren bei Gilbert N. Lewis und entwickelte damals ein grundlegendes Gesetz, das Fluoreszenz und Phosphoreszenz durch Intersystem Crossing verband. [2] Lewis und Kasha folgerten, dass bei allen von ihnen beobachteten Molekülen der phosphoreszierende Zustand ein Triplettzustand war, unabhängig davon, ob dieses Molekül einfach oder komplex, organisch oder anorganisch war. Auch kann die Kasha-Regel, die beschreibt, dass jeder strahlende elektronische Zustand einer gegebenen Multiplizität der tiefstliegende elektronisch angeregte Zustand dieser Multiplizität ist, [3] in jedem Lehrbuch der physikalischen Chemie oder der Molekülspektroskopie gefunden werden. Außerdem zeigte Kasha, dass die Wechselwirkung mit schweren Atomen bei organischen Molekülen Absorption durch Singulett-Triplett-Übergänge sowie Phosphoreszenz ermçglichen kann-der externe Schweratomeffekt oder auch Kasha-Effekt. [4] Kasha war derjenige, der die quantenmechanischen Theorien der Excitonen und des Energietransfers durch Induktionsresonanz verband. [5] Er entdeckte, dass Singulett-Sauerstoff durch chemische Reaktionen erzeugt werden kann, und untersuchte die Chemilumineszenz molekularen Sauerstoffs, [6] die sich bei späteren Untersuchungen als bedeutend für die Biologie herausstellte. Daneben klärte er die Rolle der Antennenpigmente in der Photosynthese. [7] Er war ein Pionier bei der Untersuchung von Systemen mit Protonentransfer im angeregten Zustand, egal ob intramolekular, mit doppeltem Protonentransfer oder durch das Lçsungsmittel vermittelt, [8] und er entwickelte das Vierstufendiagramm für diese Prozesse und bewies ihre Verbindung zu elektronischen Ladungstransfers. Mit jeder einzelnen dieser Vielzahl an Entdeckungen hätte er sich einen Platz in der Wissenschaftsgeschichte verdient. In diesem Essay mçchten wir persçnliche Erinnerungen nutzen, um zum biographischen Material beizutragen [9] und folgende Frage zu beantworten: Wer war dieser Mann, der so viele herausragende Beiträge leistete?

Research paper thumbnail of Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels

Frontiers in Chemistry, 2020

Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quanti... more Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).

Research paper thumbnail of Dual emissive analogue of deoxyuridine as a sensitive hydration-reporting probe for discriminating mismatched from matched DNA and DNA/DNA from DNA/RNA duplexes

Journal of Materials Chemistry C, 2016

Herein, we report the incorporation in DNA of a tailored dual emissive probe with exquisite sensi... more Herein, we report the incorporation in DNA of a tailored dual emissive probe with exquisite sensitivity to hydration.

Research paper thumbnail of Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues

RSC Advances, 2015

We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration... more We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.

Research paper thumbnail of Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers

The Scientific World Journal, 2013

A remarkable flexibility is observed in biological membranes, which allows them to form the struc... more A remarkable flexibility is observed in biological membranes, which allows them to form the structures of different curvatures. We addressed the question of intrinsic ability of phospholipid membranes to form highly curved structures and the role of cholesterol in this process. The distribution of cholesterol in the highly curved asymmetric DOPC/DOPS lipid bilayer was investigated by the coarse-grained molecular dynamics simulations in the membrane patches with large aspect ratio. It is shown that cholesterol induces uneven membrane curvature promoting the formation of extended flattened regions of the membrane interleaved by sharp bends. It is shown that the affinity of cholesterol to anionic DOPS or neutral DOPC lipids is curvature dependent. The cholesterol prefers DOPS to DOPC in either planar or highly curved parts of the membrane. In contrast, in the narrow interval of moderate membrane curvatures this preference is inverted. Our data suggest that there is a complex self-consistent interplay between the membrane curvature and cholesterol distribution in the asymmetric lipid bilayers. The suggested new function of cholesterol may have a biological relevance.

Research paper thumbnail of Clustering Monte Carlo simulations of the hierarchical protein folding on a simple lattice model

Biopolymers and Cell, 2004

A role of specific collective motions and clustering behavior In protein folding was investigated... more A role of specific collective motions and clustering behavior In protein folding was investigated using simple 2D lattice models. Two model peptides, which have the sequences of hierarchical and non-hierarchical design, were studied comparatively. Simulations were performed using three methods: Metropolis Monte Carlo with the local move set, Metropolis Monte Carlo with unspeclflc rigid rotations, and the Clustering Monte Carlo (CMC) algorithm that has been recently described by the authors. The latter was developed with particular aim to provide a realistic description of cluster dynamics. We present convincing evidence that the folding pathways and kinetics of hierarchically folding sequence are not adequately described in conventional MC simulations. In this case the account for cluster dynamics provided by CMC algorithm reveals important features of folding of hierarchically organized sequences. Our data suggest that the methods, which enable specific cluster motions, should be used for realistic description of hierarchical folding.

Research paper thumbnail of Apoptosis and eryptosis: Striking differences on biomembrane level

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2018

The cell plasma membrane plays an essential role in programmed cell death of nucleated cells (apo... more The cell plasma membrane plays an essential role in programmed cell death of nucleated cells (apoptosis) and erythrocytes (eryptosis), and its changes due to loss of transmembrane asymmetry are quite similar. However, nucleated cells possess the network of intracellular membranes, which are missing in erythrocytes. Providing comparative studies with series of molecular probes, we observe dramatic differences in membrane lipid order in the course of apoptosis and eryptosis. In contrast to nucleated cells, in which a significant drop of the lipid order in the plasma membrane is observed, the erythrocyte membrane retains the relatively high level of the lipid order. Observation in nucleated cells of significant differences between inner and plasma membranes and detection of apoptotic bodies with different organization suggest that the decrease in the lipid order of their plasma membrane could be at least partially explained by the phospholipid and/or cholesterol exchange between membranes. Such features are absent in erythrocytes.

Research paper thumbnail of MOESM1 of Visualization and detection of live and apoptotic cells with fluorescent carbon nanoparticles

Additional file 1. Fluorometry and flow cytometry measurements.

Research paper thumbnail of Characterization of Alpha-Synuclein Early Aggregates by Atomic Force Microscopy

Biophysical Journal, 2010

such amyloid fibrils in vitro. However, it exhibits poor sensitivity and reproducibility, require... more such amyloid fibrils in vitro. However, it exhibits poor sensitivity and reproducibility, requires sampling, and is insensitive to the early stages of aggregation. We introduced a new sensor molecule for the continuous monitoring of AS aggregation, denoted AS-140HC, consisting of the AS mutant (A140C, C-terminus) labeled with the 3-hydroxychromone dye MFC [1]. MFC exhibits two fluorescence bands (N* and T*) arising from Excited State Intramolecular Proton Transfer (ESIPT) [2]. The intensity ratio of (I T* /I N*) reflects the microenvironment of the probe. Addition of AS-140HC in the range of 0.5-5% to wild type AS allows the monitoring of aggregation via the strong increase of I T* /I N* (panel A), which occurs at a much earlier stage of aggregation than the ThT response (panel B). See also refs [3-6].

Research paper thumbnail of New Fluorescent Probe for Continuous Monitoring of Alpha-Synuclein Aggregation

Biophysical Journal, 2010

Research paper thumbnail of En Route to White-Light Generation Utilizing Nanocomposites Composed of Ultrasmall CdSe Nanodots and Excited-State Intramolecular Proton Transfer Dyes

ACS Applied Materials & Interfaces, 2011

Research paper thumbnail of Excited-state intramolecular proton-transfer reaction demonstrating anti-Kasha behavior

Research paper thumbnail of Fluorescent Few-Atom Clusters of Silver Formed in Organic Solvents on Polymeric Supports

Few-atom silver clusters are fluorophores with a set of attractive properties including sub-nanom... more Few-atom silver clusters are fluorophores with a set of attractive properties including sub-nanometer size, high quantum yield and large Stokes shift. Sharing high photostability with semiconductor quantum dots but being of much smaller size, lacking blinking and with expected lack of toxicity, they are especially attractive for biological imaging, down to single molecules. No less promising are their applications in chemical sensing and biosensing as well as for molecular optic and electronic devices on a single molecular level. We demonstrate that it is not a unique property of water that can provide the formation and stability of silver clusters. They can be produced on photoreduction in different organic solvents using the same polymeric template. Unique photophysical properties of these clusters share both similarities and differences to that of organic dyes.

Research paper thumbnail of Excited-state intramolecular proton-transfer reaction demonstrating anti-Kasha behavior

We report unusual photophysical properties observed on two newly designed 3-hydroxychromone deriv... more We report unusual photophysical properties observed on two newly designed 3-hydroxychromone derivatives exhibiting the excited-state intramolecular proton transfer (ESIPT) reaction. The efficiency of ESIPT reaction is greatly enhanced upon excitation with high energy quanta to Sn (n > 1) levels in lowpolarity solvents. Based on detailed analyses of excitation and emission spectra as well as time-resolved emission kinetics we derive that conditions, in which this phenomenon contradicting Kasha's rule is observed, are quite different from that for observation of anti-Kasha emission.