Modelling of interactions of proteins and peptides with metal ions Ondrej Gutten - Diploma thesis Keywords: Metalloproteins, metal ion selectivity, in silico prediction Abstract: An approach for in silico prediction and estimation of selectivity properties of metal-binding peptides is suggested. An in-depth analysis is performed to disclose the justifiability and limitations of this approach. The study is divided into three parts. First part investigates the soundness of two quantum chemical methods (MP2 and DFT) for their use in the set-up quest. The testing includes comparison with CCSD(T), effect of basis selection, performance of the two methods in geometry optimizations and effect of implicit solvent model. Second part foreshadows the approach of searching for a metal selective peptide by thoroughly investigating the ability of simple representative systems, derived from their metalloprotein templates, to retain the property of interest. Final part describes the initial step of extensive combinatorial approach towards examination of vast number of simple systems that represent metal-binding sites, and which are to be used for prediction of metal-selectivity through exploitation of the described approach and, ultimately, to the de novo design of metalloproteins with desired properties.

(in English) This diploma thesis deals with coin finds and their contexts in church interiors in Bohemia. It evaluates this issue and methodology and puts emphasis on usage of metal detectors in archeology. Coin finds are divided according to their relevant locations to two categories - mass findings or single findings. The knowledge is then evaluated in terms of church interiors and also in wider context. For easier orientation, in the total context, a history of every mentioned church is drawn in connection with coin finds. Integral part of diploma thesis is a well arranged catalogue of coin finds in churches interiors in Bohemia. At the end, coin finds are evaluated from several different points of view.

Metal ions are a tempting tool for organisms thanks to the diversity of func- tions they have to offer, if they can be distinguished properly. Examining metal-ion selectivity computationally is challenging mainly due to complex- ity of electronic structure and solvation effects. A DFT-based protocol for predicting metal-ion selectivity of metal-binding systems was developed. The most essential part of the thesis is discussion of the magnitudes and sources of inherent errors, both for metal-ion complexes and small peptides. The thesis connects the work of four original papers. It includes computational and ex- perimental benchmarks, a case-study validating the computational protocol for obtaining energetic and structural insights, and attempts applying the protocol to peptidic systems. ii

The aim of this master thesis is to study the influence of metallic atoms on nitrogen post-discharge. Pure nitrogen post-discharge is a subject study of many works dealing with kinetic processes in plasma. Unfortunately, there are only a few published works that present influence of various traces on nitrogen post-discharge kinetics. This master thesis deals with problems of nitrogen post-discharge containing mercury traces. All experimental data were obtained using optical emission spectroscopy of a DC discharge in a flowing mode, which can achieve appropriate temporal resolution in the order of milliseconds. Spectra emitted during the post-discharge were recorded in the range of 320-780 nm and the following molecular spectral systems were identified: • 1. positive system of nitrogen: N2(B) -> N2(A), • 2. positive system of nitrogen: N2(C) -> N2(B), • 1. negative system of nitrogen: N2+(C) -> N2+(X), • NO-beta system: NO(B) -> NO(X). Besides them we were able to record the mercury line at 254 nm, only (in the spectrum of the first as well as in the second order); no other mercury lines were observed. The mercury vapor was introduced into the system at selected post-discharge time. Dependence of selected molecular band head intensities as well as mercury line intensity on experimental conditions (pressure, discharge power, wall temperature, time of mercury vapor introduction) were observed in time evaluation. The data obtained in pure nitrogen were used as a reference. The obtained results showed very high sensitivity of kinetic processes on mercury atoms presence. If mercury was introduced into the post-discharge the mercury line was observable around the site where mercury vapor was introduced into the discharge. The experimental data showed that mercury line intensity was directly proportional to the mercury atoms concentration and saturation effect could be observed. The energy level diagram demonstrates that the observed mercury line can be excited by collisions with nitrogen ground state molecule excited to vibrational level 18. Thus the mercury can be used for the monitoring of population at this vibrational level. Finally we obtained the population profile at this nitrogen metastable level during the post-discharge. The presented work demonstrates possibility of mercury atoms application for the monitoring of one nitrogen metastable state. Unfortunately, the contemporary data are not sufficient for the measurement of metastable absolute concentration. However, complex understanding of nitrogen post-discharge kinetics is still an open problem. Therefore a lot of future work should be done although the presented work brings a good fundament for such research.

3 Abstract Yeast Saccharomyces cerevisiae belongs to important models for alkali-metal-cation homeostasis research. As other cells, certain intracellular content of K+ is necessary for S. cerevisiae, but Na+ or other alkali metal cations (Li+ , Rb+ ) are toxic for yeast cells. Uniporters Trk1 and Trk2 are responsible for K+ accumulation, while efflux of Na+ , Li+ , Rb+ and K+ is ensured by Ena ATPases, Na+ (K+ )/H+ antiporter Nha1 and K+ specific channel Tok1. Several regulators of K+ (Na+ ) transporters are already known, but reciprocal regulation between transporters and overall picture of the maintenance of alkali-metal-cation homeostasis is still unclear. In this work, K+ circulation (simultaneous uptake and export of K+ ) was shown to be important in alkali-metal-cation homeostasis maintenance. K+ circulation is maintained using reciprocal regulation and interactions between K+ exporters and importers. Though obtained results showed that the alkali-metal-cation homeostasis and associated physiological parameters (e.g. membrane potential, cell size, salt sensitivity) are strain specific, Nha1p was verified to be important for cell survival in ever-changing natural environment. Furthermore, two novel positive regulators of Nha1p activity were found, 14-3-3 proteins and Cka1 kinase. 14-3-3 proteins...

The diploma thesis is focused on the creation and use of chemical computer game (adventure) in chemistry teaching, specifically in practice of metals. The aim of this game is to motivate, activate and develop crosscurricular relationships among students of the second grade of elementary schools and lower grades of multi-year grammar school. Adventure brings players to the city of Jihlava, where they learn about the history and monuments of this city.

The diploma thesis is focused on hand metalworking in Technical Education, which is taught at Upper Primary School, in 6th and 7th classes. Content and range of this thesis is adapted for pupils of 6th and 7th class at Primary School. The work includes descriptions of particular training of hand metalworking supplemented by author's photographic material. There are fourteen videos as a multimedia material in the appendix. The created videos contain demonstrations of technique of hand metalworking which are mentioned in the thesis. This created multimedia material could be used not only by pupils in the lesson of Technical Education but also by uncertificated teachers, who taught this subject.

The general aim of Master’s thesis is to design and execute electronics in the SMT device view for thin film gas sensors and to study principle of gas sensor functionality based on semiconducting oxides. The SMT device contains temperature controller and electronics which is able to scan the concentration of gas on the sensor surface. It is designed for controlling of four sensors and has to communicate with computer for setting of initial conditions and scanning of concentration of gas. The practical part of Master’s thesis contains design and construction of electronics and software making.

The master thesis deals with a construction proposal for a vibrating sorter of cartridges. The thesis contains the theoretical part characterizing various sorter types of cartridges and describes the principle of sorting with the help of the vibrating sorters. The practical part includes a draft of a drive, calculation of a vibrating sorter, a proposal of compression springs bearing vibration frame and a control calculation of these springs. A complete vibrating sorter of the cartridges is created in a 3D modeling program. The thesis is attached by the drawings of the individual assemblies, subassemblies and individual parts.

This diploma thesis is focused on the study of diffusion of metal ions in hydrogel of humic acid. The objective of this thesis was to investigate the effect of the concentration of metal ions supply source and duration of diffusion on transport through the gel using method of diffusion couple. Cupric, nickel and cobalt ions were esed like the diffusion medium. All these ions were selected thanks to their high affinity for the humic acids and because they are ideal to investigate the diffusion through the humic gel. Chloride salts of these metals, namely CuCl2, NiCl2 and CoCl2, were used like supply sources. Three different concentrations of each solution were compared, specifically 0,05M, 0,1M and 1M, and also were three different durations of diffusion, specifically 10 hours, 1 day and 3 days. Metal ions were compared with each other in order to determine which one has the best transport properties through the humic hydrogel. The data, necessary for calculation, were obtained by UV-VIS spectrophotometry. Diffusion coefficients and duffusive flux of individual metal ions were determined from measured data.