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Bonding and non-bonding interaction potentials for simulations of coarse-grained protein models
Pavlíková, Markéta ; Nová, Lucie (advisor) ; Bačová, Petra (referee)
Protein folding involves the transformation of an amino acid chain to a unique 3D structure. The conformation of a protein is determined by its amino acid sequence. Understanding the process of protein folding and dynamics is crucial since protein function is closely related to its structure and dynamics. These processes can be investigated by means of molecular simulations. Coarse- grained models, which are used in molecular simulations, provide a favorable trade-off between computational efficiency and accuracy. To employ such mod- els, a reasonable force field is necessary. The force field includes both bonding and non-bonding interaction potentials, which are derived either from atomistic simulations or from known, experimentally determined protein structures. We derived such potentials using dataset of more than 4,500 structures from PDB database. 1
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Influence of aminoacid side-chain ionization on protein structure
Tomanová, Ema ; Nová, Lucie (advisor) ; Muzdalo, Anja (referee)
Protein folding is governed by many different types of interactions. Aside from the formation of hydrophobic cores and hydrogen bonding, Coulombic forces are believed to play an important role in this process. Their importance arises mainly in partially unfolded states and pH sensitive regions where ionization of amino acid side chains may trigger conformational changes. Better understanding of the role of ionizable residues in folding thereby provides us with new opportunities in protein design and property-enhancing protein modifications.
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Study of self-assembly and degree of ionization of block copolymers using transmission electron microscopy and molecular simulations
Illés, Peter ; Nová, Lucie (advisor) ; Štěpánek, Miroslav (referee)
Responsive systems, such as block copolymers with solvent-affine blocks, can undergo self-assembly into structures like micelles or vesicles. These assem- blies are highly sensitive to slight changes in external conditions, like pH or temperature, leading to the formation or dissolution of micelles. When one of the polymer blocks is a weak polyelectrolyte, its degree of ionization depends not only on the external conditions but also on the association state. This study focuses on investigating the size and degree of ionization of micellar struc- tures formed by polymer chains containing thermoresponsive and pH-responsive blocks. The investigation combines high-resolution transmission electron mi- croscopy and Hamiltonian Monte Carlo simulations to provide a comprehensive understanding of these micellar structures. 1
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