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Non-covalent interactions of tryptophan in protein structure
Sokol, Albert ; Fišer, Radovan (advisor) ; Jurkiewicz, Piotr (referee)
A thorough knowledge of non-covalent amino acid interactions within a protein structure is essential for a complete understanding of its conformation, stability and function. Among all the amino acids that usually make up a protein, tryptophan is distinguished both by its rarity and size of its side chain formed by an indole group. It is able to provide various types of indispensable interactions within the protein and between different polypeptide chains, but also between the protein and a biological membrane. In addition, it is the most commonly used natural fluorophore. Databases of solved protein structures are commonly used to study amino acid interactions and allow more or less complex analyzes of the issue. Thus many non-covalent interactions that may occur between tryptophan and other amino acids have been found. However, most of these analyzes focus on specific interactions and do not follow up the tryptophan's environment as a whole, where all amino acids interact. Some newly developed methods have been used in this Thesis, specifically the occurrence profiles of the individual amino acids around the indole group of tryptophan and the results were compared with an available literature. The amino acid that has the greatest preference for tryptophan turned out to be tryptophan again, and...
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Salts of 2-aminoethanol and ferrocene-based acids
Zábranský, Martin ; Štěpnička, Petr (advisor) ; Němec, Ivan (referee)
Combination of the compact but sterically flexible ferrocene scaffold with intermolecular binding potential and conformational variability of (2-hydroxyethyl)ammonium structural motif was utilised in the construction of solid crystalline materials. Crystallisation in systems containing ferrocenecarboxylic, 2-ferrocenylacetic, 3-ferrocenylpropionic, 3-ferrocenyl- acrylic, 3-ferrocenylacrylic, 3-ferrocenylpropiolic, ferrocene-1,1'-dicarboxylic or ferrocene- sulfonic acid with 2-aminoethanol afforded crystals of the corresponding salts. The resulting crystalline products were characterised with the usual methods (proton nuclear magnetic resonance, infrared spectroscopy, elemental analysis) and their crystal structures were determined by means of single-crystal X-ray diffraction analysis. The crystal structures of the salts mentioned above usually contain rather complicated two dimensional networks of charge-assisted hydrogen bonds. With the aim of studying potentially more simple hydrogen-bonded structures, additional crystallisation experiments were conducted in systems of ferrocenecarboxylic acid and 2-(methylamino)ethanol or 2-(dimethylamino)ethanol. These experiments yielded simple salt of the former amine and adducts of salts of both bases with ferrocenecarboxylic acid in the ratio of 1:1. The...
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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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Studies on interactions between NKR-P1D and Clrb membrane receptors
Hanč, Pavel ; Novák, Petr (advisor) ; Brdička, Tomáš (referee)
Studies on interactions between NKR-P1D and Clrb membrane receptors Interaction between murine NKR-P1D and Clrb receptors was originally described as a novel type of "MHC class-I independent missing-self recognition" and was shown to confer protection from killing by natural killer cells.[1] However, further study brought conflicting results suggesting that NKR-P1D does not binds Clrb strongly if it does at all.[2] In order to address the issues arising from these conflicting results, we have recombinantly expressed the extracellular domains of both receptors in E. coli cells and refolded the proteins in vitro. The quality of refolding was confirmed both by determining the disulphide bonding pattern using FTMS and measuring 1 H/15 N-HSQC spectra. By means of size exclusion chromatography and analytical ultracentrifuge we were unable to provide convincing results for the interaction itself. However, using SPR technique, a weak, specific, pH-dependent interaction was observed. Interaction between the proteins in solution was immobilized using chemical cross-linking technique. Three cross-linking reagents, EDC, DSG and DSS were used. The reaction mixture was separated by means of SDS-PAGE and protein bands corresponding to dimers were digested in gel. Using FT-MS we were able to find peptides from both...
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Computational Studies of Interactions of Small Molecules with their Biological Targets
Nekardová, Michaela ; Hobza, Pavel (advisor) ; Berka, Karel (referee) ; Kabeláč, Martin (referee)
The thesis specializes in the computational description of pharmaceutically important compounds. A substantial number of pharmaceutical drugs are small molecules that are bound to an active site of an enzyme by the "lock (binding site) and key (drug)" model through non-covalent interactions. The association of enzymes with drugs cause an increase or decrease in the activity of enzymes. The main topic is focused on the computational elucidation of the structural basis for the interactions of the purine-like compounds with the enzyme cyclin- dependent kinase 2 that belongs to the protein-kinase enzyme family. These enzymes play an important role in the cell cycle regulation; their increased activity significantly contributes to the loss of control over cell proliferation, which is one of the primary causes of cancer cell formation. The study describes the binding motifs of roscovitine, which shows an inhibitory effect on the function of cyclin-dependent kinases, and its analogues containing bioisosteric central heterocycles in the complex with cyclin-dependent kinase 2. The binding affinity between the cyclin-dependent kinase 2 enzyme and the inhibitors was quantified as calculated binding scores and evaluated in relation to the conformation of the optimized structures. The hybrid model combining the...
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Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design
Kříž, Kristian ; Řezáč, Jan (advisor) ; Klimeš, Jiří (referee) ; Kolář, Michal (referee)
Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...
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Computational Studies of Interactions of Small Molecules with their Biological Targets
Nekardová, Michaela ; Hobza, Pavel (advisor) ; Berka, Karel (referee) ; Kabeláč, Martin (referee)
The thesis specializes in the computational description of pharmaceutically important compounds. A substantial number of pharmaceutical drugs are small molecules that are bound to an active site of an enzyme by the "lock (binding site) and key (drug)" model through non-covalent interactions. The association of enzymes with drugs cause an increase or decrease in the activity of enzymes. The main topic is focused on the computational elucidation of the structural basis for the interactions of the purine-like compounds with the enzyme cyclin- dependent kinase 2 that belongs to the protein-kinase enzyme family. These enzymes play an important role in the cell cycle regulation; their increased activity significantly contributes to the loss of control over cell proliferation, which is one of the primary causes of cancer cell formation. The study describes the binding motifs of roscovitine, which shows an inhibitory effect on the function of cyclin-dependent kinases, and its analogues containing bioisosteric central heterocycles in the complex with cyclin-dependent kinase 2. The binding affinity between the cyclin-dependent kinase 2 enzyme and the inhibitors was quantified as calculated binding scores and evaluated in relation to the conformation of the optimized structures. The hybrid model combining the...
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Non-covalent interactions of tryptophan in protein structure
Sokol, Albert ; Fišer, Radovan (advisor) ; Jurkiewicz, Piotr (referee)
A thorough knowledge of non-covalent amino acid interactions within a protein structure is essential for a complete understanding of its conformation, stability and function. Among all the amino acids that usually make up a protein, tryptophan is distinguished both by its rarity and size of its side chain formed by an indole group. It is able to provide various types of indispensable interactions within the protein and between different polypeptide chains, but also between the protein and a biological membrane. In addition, it is the most commonly used natural fluorophore. Databases of solved protein structures are commonly used to study amino acid interactions and allow more or less complex analyzes of the issue. Thus many non-covalent interactions that may occur between tryptophan and other amino acids have been found. However, most of these analyzes focus on specific interactions and do not follow up the tryptophan's environment as a whole, where all amino acids interact. Some newly developed methods have been used in this Thesis, specifically the occurrence profiles of the individual amino acids around the indole group of tryptophan and the results were compared with an available literature. The amino acid that has the greatest preference for tryptophan turned out to be tryptophan again, and...
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Nonclassical noncovalent interactions in proteins and their importance for design of novel specific viral enzyme inhibitors
Kříž, Kristian ; Lepšík, Martin (advisor) ; Novotný, Marian (referee) ; Kabeláč, Martin (referee)
Noncovalent interactions are vital for functioning of biological systems. For instance, they facilitate DNA base pairing or protein folding. Recently, in addition to classical noncovalent interactions such as hydrogen bond, nonclassical noncovalent interactions have been discovered. An example of these interactions is halogen bond belonging to the class of σ-hole interactions, the knowledge of which is already being useful for medical compound design. The aim of this work is to find out if the chalcogen bond, also a σ-hole interaction, plays a role in the binding of existing viral inhibitors, too. Following that, we are also interested whether or to what extent can these existing chalcogen bonds be optimized for a greater affinity of the inhibitor binding. Several protein-ligand crystal structures exhibiting geometrical properties favoring a chalcogen bond have been found in the PDB database. We examined the interaction energies and the interaction energy geometrical dependencies of model systems derived from these crystal structures by means of quantum chemical calculations. Further we have optimized their strength by a series of substitutions. We thus propose that chalcogen bond can become a player in rational design of inhibitors of viral enzymes and their protein target. Keywords: Noncovalent...
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Salts of 2-aminoethanol and ferrocene-based acids
Zábranský, Martin ; Štěpnička, Petr (advisor) ; Němec, Ivan (referee)
Combination of the compact but sterically flexible ferrocene scaffold with intermolecular binding potential and conformational variability of (2-hydroxyethyl)ammonium structural motif was utilised in the construction of solid crystalline materials. Crystallisation in systems containing ferrocenecarboxylic, 2-ferrocenylacetic, 3-ferrocenylpropionic, 3-ferrocenyl- acrylic, 3-ferrocenylacrylic, 3-ferrocenylpropiolic, ferrocene-1,1'-dicarboxylic or ferrocene- sulfonic acid with 2-aminoethanol afforded crystals of the corresponding salts. The resulting crystalline products were characterised with the usual methods (proton nuclear magnetic resonance, infrared spectroscopy, elemental analysis) and their crystal structures were determined by means of single-crystal X-ray diffraction analysis. The crystal structures of the salts mentioned above usually contain rather complicated two dimensional networks of charge-assisted hydrogen bonds. With the aim of studying potentially more simple hydrogen-bonded structures, additional crystallisation experiments were conducted in systems of ferrocenecarboxylic acid and 2-(methylamino)ethanol or 2-(dimethylamino)ethanol. These experiments yielded simple salt of the former amine and adducts of salts of both bases with ferrocenecarboxylic acid in the ratio of 1:1. The...
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