|
|
Model membranes studied by advanced fluorescence techniques and molecular dynamics simulations
Melcrová, Adéla ; Hof, Martin (advisor) ; Heyda, Jan (referee) ; Konopásek, Ivo (referee)
In this thesis, we start with the description of the biophysical properties of the plasma membrane models upon signaling processess such as the increased cytoso- lic concentration of calcium ions, or posttranslational modifications of membrane proteins. Calcium signaling is characterized by a rapid increase of its cytosolic concentration. We identify calcium binding sites and characterize the binding in the plasma membrane models of increasing complexity from pure phospholipid bilayers, through cholesterol and peptide rich lipid membranes, to membranes ex- tracted from HEK293 cells. We use Time-Dependent Fluorescent Shift method, which provides direct information on hydration and mobility in defined regions of a lipid bilayer, accompanied with molecular dynamic (MD) simulations, which give molecular details of the studied interactions. The initial step of signaling mediated by PAG protein is its double palmi- toylation. We investigate changes of the biophysical properties of both the lipid membrane and the peptide itself upon the incorporation of the palmitoyls. Em- ploying all atom MD simulations, we study inter- and intramolecular interactions as well as changes in membrane hydration, thickness, or lipid ordering. The second part of the thesis, realized in a direct collaboration with a phar- macological...
|
|
|
Effect of acid-base equilibria on the association behaviour of polyelectrolytes
Staňo, Roman ; Košovan, Peter (advisor) ; Heyda, Jan (referee)
Title: Effect of acid-base equilibria on the association behaviour of polyelec- trolytes Author: Roman Staňo Department: Department of physical and macromolecular chemistry Supervisor: RNDr. Peter Košovan, Ph.D., Department of physical and macro- molecular chemistry Abstract: Macromolecules bearing charged monomeric units are omnipresent in the nature. Living systems utilize complex mechanisms to regulate the charge on biomacromolecules, hence controlling their structure or activity. Recently, there has been a surge in the preparation of bioinspired macromolecular mate- rials, such as drug delivery systems or self-healing hydrogels, possessing a high degree of responsivity to the external stimuli, such as pH. However, the fundamen- tal understanding of pH-based charge regulation in both natural and synthetic systems seems to be lacking, presumably because of the deficiency of suitable theoretical models and computational methods. Herein, we used coarse-grained simulations to shed light on the underyling physical principles of the relation between the pH, ionization, multivalency and structure of macromolecules. We presented a novel model of complex coacervates, and used it to describe phase equilibria and ion partitioning in such systems. Next, we explored the effects of multivalent ions and charged...
|
|
|
Ion-Protein Interactions
Heyda, Jan
Title: Ion-Protein Interactions Author: Mgr. et Mgr. Jan Heyda Department: Physical and Macromoleculer Chemistry Advisor: Prof. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: Conventional molecular dynamics simulations in combination with ad- vanced methods of analyses were used to improve the understanding of the interac- tion between ions and proteins in salt solutions. Thus systems of diverse complexity and size were investigated, starting with simple (and molecular) salt solutions with small fragments that mimic the various functional groups of amino acids such as N-methylacetamide representing the peptide bond or alkylated ammonium cations. Continuing with individual positively charged amino acids (arginine, histidine, ly- sine) a strong binding interaction with small fluoride anion that is significantly weak- ened for larger halides (Cl− , Br− , I− ) was described. This observation was extended by detecting the strong sensitivity of fluoride to charge distribution on ammonium, lysine side chain, and the N-terminal of glycine while sensitivity of iodide was found to be low. Later it was shown that the attractive side chain-side chain interactions are significant for short positively charged peptide fragments in polyarginine and dihistidine, while...
|
|
|
Effect of acid-base equilibria on the association behaviour of polyelectrolytes
Staňo, Roman ; Košovan, Peter (advisor) ; Heyda, Jan (referee)
Title: Effect of acid-base equilibria on the association behaviour of polyelec- trolytes Author: Roman Staňo Department: Department of physical and macromolecular chemistry Supervisor: RNDr. Peter Košovan, Ph.D., Department of physical and macro- molecular chemistry Abstract: Macromolecules bearing charged monomeric units are omnipresent in the nature. Living systems utilize complex mechanisms to regulate the charge on biomacromolecules, hence controlling their structure or activity. Recently, there has been a surge in the preparation of bioinspired macromolecular mate- rials, such as drug delivery systems or self-healing hydrogels, possessing a high degree of responsivity to the external stimuli, such as pH. However, the fundamen- tal understanding of pH-based charge regulation in both natural and synthetic systems seems to be lacking, presumably because of the deficiency of suitable theoretical models and computational methods. Herein, we used coarse-grained simulations to shed light on the underyling physical principles of the relation between the pH, ionization, multivalency and structure of macromolecules. We presented a novel model of complex coacervates, and used it to describe phase equilibria and ion partitioning in such systems. Next, we explored the effects of multivalent ions and charged...
|
|
|
Model membranes studied by advanced fluorescence techniques and molecular dynamics simulations
Melcrová, Adéla ; Hof, Martin (advisor) ; Heyda, Jan (referee) ; Konopásek, Ivo (referee)
In this thesis, we start with the description of the biophysical properties of the plasma membrane models upon signaling processess such as the increased cytoso- lic concentration of calcium ions, or posttranslational modifications of membrane proteins. Calcium signaling is characterized by a rapid increase of its cytosolic concentration. We identify calcium binding sites and characterize the binding in the plasma membrane models of increasing complexity from pure phospholipid bilayers, through cholesterol and peptide rich lipid membranes, to membranes ex- tracted from HEK293 cells. We use Time-Dependent Fluorescent Shift method, which provides direct information on hydration and mobility in defined regions of a lipid bilayer, accompanied with molecular dynamic (MD) simulations, which give molecular details of the studied interactions. The initial step of signaling mediated by PAG protein is its double palmi- toylation. We investigate changes of the biophysical properties of both the lipid membrane and the peptide itself upon the incorporation of the palmitoyls. Em- ploying all atom MD simulations, we study inter- and intramolecular interactions as well as changes in membrane hydration, thickness, or lipid ordering. The second part of the thesis, realized in a direct collaboration with a phar- macological...
|
|
|
Interaction of weak polyelectrolytes with multivaltent ions
Staňo, Roman ; Košovan, Peter (advisor) ; Heyda, Jan (referee)
By means of molecular simulations, we study dissociative behavior of weak polyacids with added mutlivalent salt. Weak polyacids are macromolecules that bear weak acid groups, therefore, their ionization varies with pH. The titration curve of such an acid deviates from the ideal one - its ionization is suppressed because of the strong repulsion between charged groups on the polyacid contour. The presence of salt in solution of a polyacid enhances the ionzation due to the effects of electrostatic screening and counterion condensation. Up to now, the influence of the salt valency on the weak polyacid ionization has not been explored, although it plays an important role in biological processes. In this thesis, we examine weak polyacid solutions with added salt of various cation valencies (+1,+2,+3) at fixed charge ratio of salt cations to po- lymer segments. We show that increasing the salt valency promotes the polyelectrolyte ionization in a manner which is different from the effect of increasing ionic strength. A higher counterion valency leads to a lower value of the critical Manning parameter, initiating strong counterion condensation which results in additional ionization due to ion-ion correlations between the condensed counterions and charged groups of the polyelectrolytes.
|
|
| |
|
|
Automatic data analysis in capillary zone electrophoresis
Ördögová, Magda ; Dubský, Pavel (advisor) ; Heyda, Jan (referee)
Evaluating data in capillary zone electrophoresis usually involves many steps that require using several different programmes. Apart from evaluating the electrophoreogram itself, it is usual to process the obtained data in some other way. For example, a suitable model is fit to the data in order to obtain physical and chemical parameters of the separation (e.g. stability constant in case of complexation). It is also important to know the accuracy of the evaluation (the calculation error). In this work, new parts of the Eval programme, originally developed for electrophoreogram evaluation, were implemented. The programme now automatically estimates the Haarhoff-van der Linde function (solution of continuity equation in capillary) parameters for analyte peak. Complexing agents are often used to improve the separation in the capillary zone electrophoresis. Complexation in the capillary can be described by its physical and chemical parameters. A new part was added to the Eval programme that allows the user to fit a rectangular hyperbole function to the obtained data. Thus, the regression parameters of this dependence can be gained. The programme can also draw profile diagrams for these parameters, from which the confidence intervals can be read. An option that allows two dependencies to be fitted at...
|
|
|
Ion-Protein Interactions
Heyda, Jan
Title: Ion-Protein Interactions Author: Mgr. et Mgr. Jan Heyda Department: Physical and Macromoleculer Chemistry Advisor: Prof. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: Conventional molecular dynamics simulations in combination with ad- vanced methods of analyses were used to improve the understanding of the interac- tion between ions and proteins in salt solutions. Thus systems of diverse complexity and size were investigated, starting with simple (and molecular) salt solutions with small fragments that mimic the various functional groups of amino acids such as N-methylacetamide representing the peptide bond or alkylated ammonium cations. Continuing with individual positively charged amino acids (arginine, histidine, ly- sine) a strong binding interaction with small fluoride anion that is significantly weak- ened for larger halides (Cl− , Br− , I− ) was described. This observation was extended by detecting the strong sensitivity of fluoride to charge distribution on ammonium, lysine side chain, and the N-terminal of glycine while sensitivity of iodide was found to be low. Later it was shown that the attractive side chain-side chain interactions are significant for short positively charged peptide fragments in polyarginine and dihistidine, while...
|
|
|
Ion - Protein Interaction
Heyda, Jan ; Jungwirth, Pavel (advisor) ; Hof, Martin (referee) ; Ettrich, Rüdiger (referee)
Title: Ion-Protein Interactions Author: Mgr. et Mgr. Jan Heyda Department: Physical and Macromoleculer Chemistry Advisor: Prof. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: Conventional molecular dynamics simulations in combination with ad- vanced methods of analyses were used to improve the understanding of the interac- tion between ions and proteins in salt solutions. Thus systems of diverse complexity and size were investigated, starting with simple (and molecular) salt solutions with small fragments that mimic the various functional groups of amino acids such as N-methylacetamide representing the peptide bond or alkylated ammonium cations. Continuing with individual positively charged amino acids (arginine, histidine, ly- sine) a strong binding interaction with small fluoride anion that is significantly weak- ened for larger halides (Cl− , Br− , I− ) was described. This observation was extended by detecting the strong sensitivity of fluoride to charge distribution on ammonium, lysine side chain, and the N-terminal of glycine while sensitivity of iodide was found to be low. Later it was shown that the attractive side chain-side chain interactions are significant for short positively charged peptide fragments in polyarginine and dihistidine, while...
|
guest ::
RSS feed.