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Distribution of ions at surfaces of hydrated proteins
Heyda, Jan ; Barvík, Ivan (referee) ; Jungwirth, Pavel (advisor)
By means of molecular dynamics simulations we have systematically investigated the behavior of positively charged amino acids - arginine, lysine, and histidine in salt solutions. Salt always contained potassium cation and anions from the halide group. Both simple salts and binary salt solutions were investigated. Primarily, we have quantified the level of interaction of anions with amino acids. Also, the interaction sites were defined together with their role in cumulative interactions. The interaction was quantified by means of density maps, contacts, and cumulative sums with respect to individual parts of the amino acid. All simulations were done both with nonpolarizable and polarizable force fields. A significant difference in behavior between fluoride and other halides was observed in all cases. Fluoride preferentially interacted with the charged part of amino acids, while interactions of other halides were spread over the whole amino acid.
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Molecular Simulations of Surfaces of Aqueous Solutions
Vácha, Robert ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee) ; Barvík, Ivan (referee)
This thesis consists of 18 papers, in which we investigated the behavior of molecules and ions at aqueous interfaces by means of molecular dynamics (MD) simulations. We started our simulations with the surface of neat water, where we investigated the behavior of hydronium and hydroxide ions, i.e., the products of autolysis of water that are of 10�7M concentration in pure water. The results, ranging from ab initio high level calculations on water clusters and ab initio dynamics on small systems to statistically converged classical molecular dynamics simulations are mutually consistent47,48,50. The observed surface adsorption of hydronium is also consistent with the surface selective spectroscopy experiments (VSFG, SHG, PES)45,51,55{59, surface tension measurements60, and with _-potential measurements of acidic solutions62,63. The spectroscopy and surface tension experiments are also in agreement with the weak surface repulsion/non-accumulation of hydroxide observed in our simulations. However, there are macroscopic measurements, such as higher pH electrophoretic mobility measurements, titration of oil emulsions, and thin _lm stability experiments that indicate a negative charge on air/water and oil/water interfaces 61{71. Even though these experiments do not directly reveal the chemical nature or...
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Molecular dynamics simulations of complexes consisting of proteins and nucleic acids
Zíma, Vlastimil ; Barvík, Ivan (advisor) ; Jungwirth, Pavel (referee)
At first, numerical integration algorithms was studied. Main objective was a study of active sites of HCV and HIV polymerases in complexes with a natural substrate and in complexes where an approaching nucleosidetriphosphate was replaced with inhibitors (S)-HMPMGpp and (S)-HMPMApp respectively. Further, an ABF method was used to obtain free energy profiles of water and methane molecules passing through a boundary between water and vacuum. Finally, the same method was used to obtain free energy profiles of water, methane and guanosine molecules passing through a lipid bilayer.
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MD simulations of complexes between nucleic acids and RNase H
Bartek, Tomáš ; Burda, Jaroslav (referee) ; Barvík, Ivan (advisor)
The aim of this diploma thesis was to study interactions between human Rase H enzyme and a natural and modified substrate using molecular dynamics simulations (altogether 9 MD runs ere produced). Conformational preferences of internucleotide linkages (undergoing contacts with the RNase H enzyme) were studied using several versions of the AMBER force field. Either one or two copies of RNase H were included into the simulated system. As the most important DNA-binding residues were recognized Trp93 and Ser101 in the first DNA binding site and Thr49 and Arg47 in the second DNA binding site. Further, the AMBER force field was re-parameterized slightly using ab initio calculations to produce force constants for the modified phosphonate internucleotide linkage. Biologically active version of the modified internucleotide linkage C3-O3-P-C-O5-C5 was able to bind Arg47 using two hydrogen bonds within the 10 ns MD run (even more effciently than in the case of MD runs with natural internucleotide linkages). On the other hand, the biologically inactive C3-O3-C-P-O5-C5 internucleotide linkage lose contacts with Arg47 quickly.
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