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Molecular dynamics simulations of biomolecular complexes consisting of proteins and nucleic acids
Melcr, Josef ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Literature search on the Elongation factor Tu (EF-Tu), which is involved in the process of translation of genetic information, was performed. Further, computational methods as molecular dynamics (MD) and Monte Carlo (MC) were studied. Then, computer programs for MD and MC simulations of a Lennard-Jones gas were developed. MD simulations were further applied to EF-Tu using the NAMD and ACEMD software packages. Multiprocessor PC clusters and programmable NVIDIA GPUs were used. MD simulations of EF-Tu uncovered binding of monovalent ions in nearby of the EF-Tu active site. The impact of Na$^+$ binding on evolutionarily conserved residues (His85, Val20, Ile61, Asp21, Tyr47, Asp87, etc.) was studied in detail.
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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...
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Model membranes studied by advanced fluorescence techniques and molecular dynamics simulations
Melcrová, Adéla ; Hof, Martin (advisor)
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...
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Model membranes studied by advanced fluorescence techniques and molecular dynamics simulations
Melcrová, Adéla ; Hof, Martin (advisor)
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...
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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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...
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor) ; Otyepka, Michal (referee) ; Tarek, Mounir (referee)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Molecular dynamics simulations of biomolecular complexes consisting of proteins and nucleic acids
Melcr, Josef ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Literature search on the Elongation factor Tu (EF-Tu), which is involved in the process of translation of genetic information, was performed. Further, computational methods as molecular dynamics (MD) and Monte Carlo (MC) were studied. Then, computer programs for MD and MC simulations of a Lennard-Jones gas were developed. MD simulations were further applied to EF-Tu using the NAMD and ACEMD software packages. Multiprocessor PC clusters and programmable NVIDIA GPUs were used. MD simulations of EF-Tu uncovered binding of monovalent ions in nearby of the EF-Tu active site. The impact of Na$^+$ binding on evolutionarily conserved residues (His85, Val20, Ile61, Asp21, Tyr47, Asp87, etc.) was studied in detail.
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Mechanisms involved in sodium uptake activation by the Tumor Necrosis Factor-derived TIP peptide
DULEBO, Alexander
The Tumor Necrosis Factor derived-TIP peptide is a small 17 amino acids cyclic peptide with lectin-like activity, that possesses several therapeutically relevant biological activities, among which is activation of alveolar liquid clearance in both healthy and injured lungs in vivo. Accumulation of fluid in the lungs? alveoli and interstitial spaces is a life-threatening condition called pulmonary edema. The mortality rate due permeability pulmonary edema, accompanied by a dysfunction of the alveolar/capillary barrier, is high because no effective treatment lacking side effects exists nowadays. It is known that the TIP peptide is able to activate vectorial Na+ transport ? which mediates lung liquid clearance. However, the mechanism of action of remains elusive. The aim of this thesis was to investigate the initial steps of interaction between the TIP peptide and airway epithelial cells. Numerous novel methods and single-molecule techniques were used to unravel: (i) how the TIP peptide interacts with the molecules on the apical side of the lung epithelial cells; (ii) whether the TIP peptide need to be internalized inside of the cells to trigger its effects; (iii) the nature of the interaction between the TIP peptide and its putative receptor(s); (iv) the putative receptor(s) for the TIP peptide on the apical surface of the lung epithelial cells.
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