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Intermolecular interactions in proteins
Kysilka, Jiří ; Vondrášek, Jiří (advisor) ; Ettrich, Rüdiger (referee) ; Banáš, Pavel (referee)
Intermolecular Interactions in Proteins - Abstract Mgr. Jiří Kysilka Non-covalent interactions are responsible for the protein folding and the molecular recognition during the protein interaction with other molecules, including various ligands, other proteins and solvent molecules. In order to understand these processes, exhibited by protein molecules, a proper description of non-covalent interactions is needful. Most methods that are computationally available for the systems of biological interest have difficulties handling with the dispersion term. In this thesis, a density functional theory / coupled clusters (DFT/CC) correction scheme is utilized for a set of small molecules, interacting with a graphitic surface. The results serve as a benchmark for the interaction of the functional groups of proteins with hydrophobic environment. In the following part of this thesis, the role of non-covalent interactions in proteins was studied for the processes of protein-protein interaction and protein hydration. Interaction interfaces has been localized in a set of 69 protein dimers and their composition has been characterized. Interfaces has been shown to prefer branched-chain hydrophobic amino acids (Ile, Leu, Val), aromatic amino acids (Phe, Tyr) and exclude the charged amino acids except of Arg. It was...
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Modelling mechanical properties of RNA and DNA
Dršata, Tomáš ; Lankaš, Filip (advisor) ; Banáš, Pavel (referee) ; Schneider, Bohdan (referee)
Structural and mechanical properties of nucleic acids play a key role in a wide range of biological processes, as well as in the field of nucleic acid nanotechnology. The thesis presents results of several studies focused on modelling these properties. Extensive unrestrained atomic-resolution molecular dynamics (MD) simulations are used to investigate structural dynamics of nucleic acids, and to parametrize their mechanical models. The deformation energy is assumed to be a general quadratic function of suitably chosen internal coordinates. Two types of models are employed which differ in the level of coarse- graining. The first one is based on the description of conformation at the level of individual bases and the second, coarser one is used to study global bending and twisting flexibility. The models are applied to explain mechanical properties of A-tracts in the context of DNA looping and nucleosome positioning, to characterize twist-stretch cou- pled deformations in DNA and RNA, and to predict changes in the properties of damaged DNA that are likely to be relevant for damage recognition and repair. Besides that, we propose a general model of DNA allostery, applied to study the effect of minor groove binding of small ligands and the allosteric coupling between proteins mediated by the DNA. A careful...
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Intermolecular interactions in proteins
Kysilka, Jiří ; Vondrášek, Jiří (advisor) ; Ettrich, Rüdiger (referee) ; Banáš, Pavel (referee)
Intermolecular Interactions in Proteins - Abstract Mgr. Jiří Kysilka Non-covalent interactions are responsible for the protein folding and the molecular recognition during the protein interaction with other molecules, including various ligands, other proteins and solvent molecules. In order to understand these processes, exhibited by protein molecules, a proper description of non-covalent interactions is needful. Most methods that are computationally available for the systems of biological interest have difficulties handling with the dispersion term. In this thesis, a density functional theory / coupled clusters (DFT/CC) correction scheme is utilized for a set of small molecules, interacting with a graphitic surface. The results serve as a benchmark for the interaction of the functional groups of proteins with hydrophobic environment. In the following part of this thesis, the role of non-covalent interactions in proteins was studied for the processes of protein-protein interaction and protein hydration. Interaction interfaces has been localized in a set of 69 protein dimers and their composition has been characterized. Interfaces has been shown to prefer branched-chain hydrophobic amino acids (Ile, Leu, Val), aromatic amino acids (Phe, Tyr) and exclude the charged amino acids except of Arg. It was...
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