The bacterial enzyme t-RNA (m1G37) methyltransferase (TrmD) is an ideal anti-microbial drug target since it is found in all eubacteria, serves an essential role during protein synthesis, and shares very little sequence or structural homology with its eukaryotic counterpart, Trm5. TrmD, a homodimeric protein, methylates the G37 nucleotide of tRNA using S-adenosyl-L-methionine (SAM) as the methyl donor and thus enables proper codon-anticodon alignment during translation. The two deeply buried binding sites for SAM seen in X-ray crystallography suggest that significant conformational changes must occur for substrate binding and catalytic turnover. Results from molecular dynamics simulations implicate a flexible loop region and a halo-like loop which may be gating the entrance to the active site. Analysis of simulation trajectories indicates an alternating pattern of active site accessibility between the two SAM binding sites, suggesting a single site mechanism for enzyme activity. Isothermal titration calorimetry (ITC), demonstrates that binding of SAM to TrmD is an exothermic reaction resulting from sequential binding at two sites. A similar mode of binding at higher affinities was observed for the product, S-adenosyl-L-homocysteine (SAH) suggesting that product inhibition may be important in vivo. ITC reveals that tRNA binding is an endothermic reaction in which one tRNA molecule binds to one TrmD dimer. This further supports the hypothesis of a single site mechanism for enzyme function. However, mutational analysis using hybrid mutant proteins suggests that catalytic integrity must be maintained in both active sites for maximum enzymatic efficiency. Mutations impeding flexibility of the halo loop were particularly detrimental to enzyme activity. Noncompetitive inhibition of TrmD was observed in the presence of bis-ANS, an extrinsic fluorescent dye. In silico ligand docking of bis-ANS to TrmD suggests that dye interferes with mobility of the flexible linker above the active site. Because SAM is a ubiquitous cofactor in methyltransferase reactions, analogs of this ligand may not be suitable for drug development. It is therefore important to investigate allosteric modes of inhibition. These experiments have identified key, mobile structural elements in the TrmD enzyme important for activity, and provide a basis for further research in the development of allosteric inhibitors for this enzyme.

<p>The increase in shale gas exploitation has motivated the studies towards new processes for converting light alkanes into higher valuable chemicals, including fuels. The works in this dissertation focuses on two processes: propane dehydrogenation and ethylene oligomerization. The former involves the conversion of propane into propylene and hydrogen, while the latter converts light alkenes into higher molecular weight products, such as butylene and hexene. </p> <p>The thesis project focuses on understanding the effect of geometric effects of Pt alloy catalysts for propane dehydrogenation and the methodologies for their characterization. Pt-Co bimetallic catalysts were synthesized with increasing Co loadings, characterized and evaluated for its propane dehydrogenation performance. In-situ synchrotron X-Ray Powder Diffraction (XRD) and X-Ray Absorption (XAS) were used to identify and differentiate between the intermetallic compound phases in the nanoparticle surface and core. Difference spectra between oxidized and reduced catalysts suggested that, despite the increase in Co loading, the catalytic surface remained the same, Pt₃Co in a Au₃Cu structure, while the core became richer in Co, changing from a monometallic Pt fcc core at the lowest Co loading to a PtCo phase in a AuCu structure at the highest loading. Co^II single sites were also observed on the surface, due to non-reduced Co species. The catalytic performance towards propane dehydrogenation reinforced this structure, as propylene selectivity was around 96% for all catalysts, albeit the difference in composition. The Turnover Rate (TOR) of these catalysts was also similar to that of monometallic Pt catalysts, around 0.9 s^-1, suggesting Pt was the active site, while Co atoms behaved as non-active, despite both atoms being active in their monometallic counterparts.</p> <p>In the second project, a single site Co^II catalyst supported on SiO₂ was evaluated for ethylene oligomerization activity. The catalyst was synthesized, evaluated for propane dehydrogenation, propylene hydrogenation and ethylene oligomerization activities and characterized <i>in-situ</i> by XAS and EXAFS and H₂/D₂ exchange experiments. The catalysts have shown negligible conversion at 250^oC for ethylene oligomerization, while a benchmark Ni/SiO₂ catalyst had about 20% conversion and TOR of 2.3x10^-1 s^-1. However, as the temperature increased to above 300^oC, ethylene conversion increased significantly, reaching about 98% above 425^oC. <i>In-situ</i> XANES and EXAFS characterization suggested that H₂ uptake under pure H₂ increased in about two-fold from 200^oC to 500^oC, due to the loss of coordination of Co-O bonds and formation of Co-H bonds. This was further confirmed by H₂/D₂ experiments with a two-fold increase in HD formation per mole of Co. <i>In-situ</i> XAS characterization was also performed with pure C­₂H₄ at 200^oC showed a similar trend in Co-O bond loss, suggesting the formation of Co-alkyl, similarly to that of Co-H. The <i>in-situ</i> XANES spectra showed that the oxidation state remained stable as a Co²⁺ despite the change in the coordination environment, suggesting that the reactions occurs through a non-redox mechanism. These combined results allowed the proposition of a reaction pathway for dehydrogenation and oligomerization reactions, which undergo a similar reaction intermediate, a Metal-alkyl or Metal-Hydride intermediates, activating C-H bonds at high temperatures.</p>

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K. Kaprová (2019): Revealed preferences for outdoor recreation in natural areas - Czech and European perspective Abstract of the Doctoral Dissertation The dissertation thesis focuses on the investigation and synthesis of recreation welfare benefits associated with natural areas in the Czech Republic and in Europe. The dissertation thesis consists of five case studies. These represent various geographic levels of analysis: the level of one single recreation locality, the national level that takes into account large natural recreation sites in the Czech Republic (including protected areas), and a synthesis of results of studies on the European level. The methodological approach is based on the theory of environmental economics and employs non-market valuation techniques based on methods of revealed preferences, namely the hedonic pricing method and two types of travel cost modelling. In Study I, we examine how the presence and characteristics of urban greenery affect property prices in Prague. The results confirm that proximity to greenery and its area are important determinants of housing prices in Prague, which means that residents realize the positive values provided by urban greenery, including recreational ecosystem service. Benefits to residents differ with the type of greenery. Urban forests have the...