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Interactions of Proteins with Nucleic Acids: from Structure to Specificity
Jakubec, Dávid ; Vondrášek, Jiří (advisor) ; Šponer, Jiří (referee) ; Zagrovic, Bojan (referee)
Sequence-specific interactions between proteins and nucleic acids play an essential role in the cell biology. While several molecular mechanisms contributing to the binding speci- ficity have been identified empirically, no general protein-DNA recognition code has been described to date. In this thesis, I explore selected characteristics of protein-DNA inter- actions using computational methods. First, the pairwise interactions between the basic biomolecular building blocks-amino acids and nucleotides-are investigated. It is shown that several statistically enriched, biologically relevant interaction motifs correspond to the most energetically favorable configurations of the respective binding partners. In ad- dition, a relationship between the physico-chemical properties of the amino acid residues found at the protein-DNA interface and the local geometric features of the DNA helix is presented. Next, the applicability of molecular dynamics-based setups to the description of binding equilibria in protein-DNA systems is investigated. Discrepancies are observed between the description offered by the computer simulations and experimental results, as well as between the results obtained using two molecular mechanical force fields. Finally, the more general evolutionary aspects of protein organization...
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Non - covalent interactions in fundamental biological processes
Klusák, Vojtěch ; Rulíšek, Lubomír (advisor) ; Burda, Jaroslav (referee) ; Šponer, Jiří (referee)
Charles University in Prague Faculty of Science Department of Physical and Macromolecular Chemistry Non-covalent interactions in fundamental biological processes Doctoral Thesis Abstract Mgr. Vojtěch Klusák Supervisor: Mgr. Lubomír Rulíšek, CSc. Institute of Organic Chemistry and Biochemistry AS CR Center for Biomolecules and Complex Molecular Systems Praha 2010 2 3 Universita Karlova v Praze Přírodovědecká fakulta Katedra fyzikální a makromolekulární chemie Nekovalentní interakce v základních biologických procesech Souhrn disertační práce Mgr. Vojtěch Klusák Školitel: Mgr. Lubomír Rulíšek, CSc. Ústav organické chemie a biochemie AV ČR Centrum biomolekul a komplexních molekulárních systémů Praha 2010 4 5 Introduction Understanding inter- and intra-molecular interactions is the key for our insight into the properties of the biomolecular systems which, in turn, maintain and govern virtually all the processes in biology. Attempts to draw the structure-function relationship at the atomistic or electronic level bring us quite often beyond experimental resolution and capabilities. Modern tools of computational chemistry enable us to focus with satisfactory degree of reliability on the details of the studied process, gather additional (often complementary) information and ascribe particular structural features to...
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