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In-vitro binding analysis of bovine serum albumin with sulindac/chlorpromazine: Spectroscopic, calorimetric and computational approaches. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112124] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Zhang X, Sisamakis E, Sozanski K, Holyst R. Nanoscopic Approach to Quantification of Equilibrium and Rate Constants of Complex Formation at Single-Molecule Level. J Phys Chem Lett 2017; 8:5785-5791. [PMID: 29131951 DOI: 10.1021/acs.jpclett.7b02742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Equilibrium and rate constants are key descriptors of complex-formation processes in a variety of chemical and biological reactions. However, these parameters are difficult to quantify, especially in the locally confined, heterogeneous, and dynamically changing living matter. Herein, we address this challenge by combining stimulated emission depletion (STED) nanoscopy with fluorescence correlation spectroscopy (FCS). STED reduces the length-scale of observation to tens of nanometres (2D)/attoliters (3D) and the time-scale to microseconds, with direct, gradual control. This allows one to distinguish diffusional and binding processes of complex-formation, even at reaction rates higher by an order of magnitude than in confocal FCS. We provide analytical autocorrelation formulas for probes undergoing diffusion-reaction processes under STED condition. We support the theoretical analysis of experimental STED-FCS data on a model system of dye-micelle, where we retrieve the equilibrium and rates constants. Our work paves a promising way toward quantitative characterization of molecular interactions in vivo.
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Affiliation(s)
- Xuzhu Zhang
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | | | - Krzysztof Sozanski
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | - Robert Holyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
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Jelińska A, Zagożdżon A, Górecki M, Wisniewska A, Frelek J, Holyst R. Denaturation of proteins by surfactants studied by the Taylor dispersion analysis. PLoS One 2017; 12:e0175838. [PMID: 28426809 PMCID: PMC5398553 DOI: 10.1371/journal.pone.0175838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/01/2017] [Indexed: 11/29/2022] Open
Abstract
We showed that the Taylor Dispersion Analysis (TDA) is a fast and easy to use method for the study of denaturation proteins. We applied TDA to study denaturation of β-lactoglobulin, transferrin, and human insulin by anionic surfactant sodium dodecyl sulfate (SDS). A series of measurements at constant protein concentration (for transferrin was 1.9 x 10−5 M, for β- lactoglobulin was 7.6 x 10−5 M, and for insulin was 1.2 x 10−4 M) and varying SDS concentrations were carried out in the phosphate-buffered saline (PBS). The structural changes were analyzed based on the diffusion coefficients of the complexes formed at various surfactant concentrations. The concentration of surfactant was varied in the range from 1.2 x 10−4 M to 8.7 x 10−2 M. We determined the minimum concentration of the surfactant necessary to change the native conformation of the proteins. The minimal concentration of SDS for β-lactoglobulin and transferrin was 4.3 x 10−4 M and for insulin 2.3 x 10−4 M. To evaluate the TDA as a novel method for studying denaturation of proteins we also applied other methods i.e. electronic circular dichroism (ECD) and dynamic light scattering (DLS) to study the same phenomenon. The results obtained using these methods were in agreement with the results from TDA.
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Affiliation(s)
- Aldona Jelińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Zagożdżon
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Jadwiga Frelek
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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Characterization of the interaction of glycyrrhizin and glycyrrhetinic acid with bovine serum albumin by spectrophotometric-gradient flow injection titration technique and molecular modeling simulations. Int J Biol Macromol 2017; 102:92-103. [PMID: 28377238 DOI: 10.1016/j.ijbiomac.2017.02.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 01/19/2023]
Abstract
In this research, the interactions of glycyrrhizin (GL) and glycyrrhetinic acid (GA) with bovine serum albumin (BSA) have been investigated by the novel method of spectrophotometric- gradient flow injection titration technique. The hard-modeling multivariate approach to binding was used for calculation of binding constants and estimation of concentration-spectral profiles of equilibrium species. The stoichiometric ratio of binding was estimated using eigenvalue analysis. Results showed that GL and GA bind BSA with overall binding constants of KGL-BSA=3.85 (±0.09)×104Lmol-1, KGA-BSA=3.08 (±0.08)×104Lmol-1. Ligand-BSA complexes were further analyzed by combined docking and molecular dynamics (MD) simulations. Docking simulations were performed to obtain a first guess on the binding structure of the GL/GA-BSA complex, and subsequently analyzed by 20 ns MD simulations in order to evaluate interactions of GL/GA with BSA in detail. Results of MD simulations indicated that GL-BSA complex forms mainly on the basis of hydrogen bonds, while, GA-BSA complex forms on the basis of hydrophobic interactions. Also, water molecules can bridge between the ligand and protein by hydrogen bonds, which are stable during the entire simulation and play an important role in stabilization of the GL/GA-BSA complexes.
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Hołyst R, Poniewierski A, Zhang X. Analytical form of the autocorrelation function for the fluorescence correlation spectroscopy. SOFT MATTER 2017; 13:1267-1275. [PMID: 28106203 DOI: 10.1039/c6sm02643e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) can provide information about diffusion coefficients and rate constants of chemical reactions in small systems of interacting molecules. However, the interpretation of FCS experiments depends crucially on the model of the autocorrelation function for the fluorescence intensity fluctuations. In this theoretical work, we consider a system of fluorescent molecules that diffuse and interact with massive particles, e.g. surfactant micelles. Using the general formalism of FCS, we derive a new analytical approximation of the autocorrelation function for systems in which both diffusion and a binary reaction occur. This approximation provides a smooth interpolation between the limit of fast reaction (much faster than diffusion), and the opposite limit of slow reaction. Our studies of noncovalent interactions of micelles with dyes by FCS provided an experimental case to which the approximate autocorrelation function was successfully applied [X. Zhang, A. Poniewierski, A. Jelińska, A. Zagożdżon, A. Wisniewska, S. Hou and R. Hołyst, Soft Matter, 2016, 12, 8186-8194].
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Affiliation(s)
- Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Xuzhu Zhang
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Zhang X, Poniewierski A, Jelińska A, Zagożdżon A, Wisniewska A, Hou S, Hołyst R. Determination of equilibrium and rate constants for complex formation by fluorescence correlation spectroscopy supplemented by dynamic light scattering and Taylor dispersion analysis. SOFT MATTER 2016; 12:8186-8194. [PMID: 27714379 DOI: 10.1039/c6sm01791f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The equilibrium and rate constants of molecular complex formation are of great interest both in the field of chemistry and biology. Here, we use fluorescence correlation spectroscopy (FCS), supplemented by dynamic light scattering (DLS) and Taylor dispersion analysis (TDA), to study the complex formation in model systems of dye-micelle interactions. In our case, dyes rhodamine 110 and ATTO-488 interact with three differently charged surfactant micelles: octaethylene glycol monododecyl ether C12E8 (neutral), cetyltrimethylammonium chloride CTAC (positive) and sodium dodecyl sulfate SDS (negative). To determine the rate constants for the dye-micelle complex formation we fit the experimental data obtained by FCS with a new form of the autocorrelation function, derived in the accompanying paper. Our results show that the association rate constants for the model systems are roughly two orders of magnitude smaller than those in the case of the diffusion-controlled limit. Because the complex stability is determined by the dissociation rate constant, a two-step reaction mechanism, including the diffusion-controlled and reaction-controlled rates, is used to explain the dye-micelle interaction. In the limit of fast reaction, we apply FCS to determine the equilibrium constant from the effective diffusion coefficient of the fluorescent components. Depending on the value of the equilibrium constant, we distinguish three types of interaction in the studied systems: weak, intermediate and strong. The values of the equilibrium constant obtained from the FCS and TDA experiments are very close to each other, which supports the theoretical model used to interpret the FCS data.
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Affiliation(s)
- Xuzhu Zhang
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Aldona Jelińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Anna Zagożdżon
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Agnieszka Wisniewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Sen Hou
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength. PLoS One 2016; 11:e0161409. [PMID: 27536866 PMCID: PMC4990340 DOI: 10.1371/journal.pone.0161409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/04/2016] [Indexed: 11/19/2022] Open
Abstract
We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales-from diffusion of molecular probes to macroscopic viscous flow-we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid.
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Chamieh J, Biron JP, Cipelletti L, Cottet H. Monitoring Biopolymer Degradation by Taylor Dispersion Analysis. Biomacromolecules 2015; 16:3945-51. [DOI: 10.1021/acs.biomac.5b01260] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph Chamieh
- Institut des Biomolécules
Max Mousseron (IBMM, UMR 5247 CNRS, Université de Montpellier,
Ecole Nationale Supérieure de Chimie de Montpellier), Campus Triolet, Place Eugène Bataillon,
CC 1706, 34095 Montpellier
Cedex 5, France
| | - Jean Philippe Biron
- Institut des Biomolécules
Max Mousseron (IBMM, UMR 5247 CNRS, Université de Montpellier,
Ecole Nationale Supérieure de Chimie de Montpellier), Campus Triolet, Place Eugène Bataillon,
CC 1706, 34095 Montpellier
Cedex 5, France
| | - Luca Cipelletti
- Laboratoire Charles
Coulomb (L2C), UMR 5221 CNRS, Université de Montpellier, Montpellier, F-France
| | - Hervé Cottet
- Institut des Biomolécules
Max Mousseron (IBMM, UMR 5247 CNRS, Université de Montpellier,
Ecole Nationale Supérieure de Chimie de Montpellier), Campus Triolet, Place Eugène Bataillon,
CC 1706, 34095 Montpellier
Cedex 5, France
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