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Measuring of conformational properties of nucleic acids
Hrazdilová, Ivana ; Renčiuk,, Daniel (referee) ; Maděránková, Denisa (advisor)
This thesis gives a brief characteristic of the most important conformations of nucleic acids. It describes alternative conformations that are different from canonical B-DNA helix, such as A-DNA, Z-DNA, triplex structures, or guanine and cytozin quadruplex structures. In the next part it presents most common methods used for determing secondary structure of nucleic acids, which are nuclear magnetic resonance (NMR), measurement of circular dichroism (CD), X-ray diffraction, computational methods, measurements of ultraviolet absorbance and its utilization for analysis of thermal melting curves. In MATLAB was created algorithm with graphical user interface, which analyze melting curves and graphically computes thermodynamic parameters, which are melting temperature and transition enthalpy, which defines stability of examined sample.
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Molecular organization of humic acids in solutions
Chytilová, Aneta ; Enev, Vojtěch (referee) ; Klučáková, Martina (advisor)
The diverse structure and content of the highly varied functional groups of humic acids determine these substances as a worthwhile study material for a number of scientific institutions. Above all, the structure causes a wide range of their interesting properties, especially spectral, colloidal, electrochemical, ion-exchange and adsorption properties. Humic acids have variety of utilization in the industry while they have been the subject of a range of further research and development. The character of these complex heterogeneous polydisperse substances is mainly cyclic and aromatic, which according to some studies results in their brown color. Generally, there are multiple theories assuming their potential secondary structure. The aim of this study is the analysis of structure and conformation of humic acids in aqueous solutions. For the purposes mentioned above a concentration series of humic acids have been prepared in four different mediums: 0,1 M NaOH, humic acids in water with pH modified to 12 (basic medium), 0,1 M NaOH + 0,1 M HCl, 0,1 M NaCl (neutral medium). In order to study conformations several analytic methods have been used: ultraviolet and visible spectroscopy, dynamic light scattering, electrophoretic light scattering, potentiometric determination of pH and direct conductimetry. Throughout the experimentation the emphasis was mainly on the purity of humic acids extracted from lignite.
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Conformation and molecular organization of humic acids in aqueous solutions
Věžníková, Kateřina ; Pospíšilová, Ľubica (referee) ; Klučáková, Martina (advisor)
This diploma thesis deals with the conformation and molecular organization of humic acids in aqueous solutions. Humic substances have heterogeneous and polydisperse nature, therefore their secondary chemical structure has not yet been defined properly, neither has their conformational arrangement. The conformation of humic substances in the solutions is mainly stabilized by weak disperse forces, such as Van der Waals, -, CH- interactions and hydrogen bonds. Humic substances in the solutions tend to form aggregates that are held together mostly by the intermolecular hydrophobic interactions. Concentration series of humic acids were prepared in three different mediums of constant ionic strength: NaOH and NaCl (prepared either by neutralization NaOH by HCl or direct dilution by solution of NaCl). Several analytical methods have been used to determine conformation and molecular organization of humic acids: potentiometric determination of pH, direct conductometry, ultraviolet and visible spectroscopy, density measurement, dynamic light scattering, laser Doppler velocimetry and high resolution ultrasound spectrometry. It was confirmed that the conformation and molecular organization of humic acids in aqueous solutions depend not only on pH of medium, but they also depend on chemical nature and concentration with the same pH. Results showed that hydrodynamic diameter of particles is significantly increasing in NaCl medium prepared by neutralization NaOH by HCl, particularly at low concentrations, which corresponds to higher values of zeta potential obtained. Concentration dependencies of ultrasonic velocity and compressibility also indicate the changes in conformation and molecular organization corresponding with results from other methods used.
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Fractionation and molecular organization of humic acids
Chytilová, Aneta ; Enev, Vojtěch (referee) ; Klučáková, Martina (advisor)
Humic acids are part of the natural organic matter occurring all around us. The aim of this thesis is to study the molecular organization, conformation of humic acids in aqueous solutions, that always raise a number of questions. For a long time, the scientists all over the world argue, if humic acid are polymers, micelles or supramolecules. Over time, thanks to new technologies, their opinions are moving away from a polymer model and tend rather to supramolecular arrangement of humic acids. Studying humic complex systems is not easy, because they are polydisperse and heterogeneous, which significantly complicates any characterization. Moreover, its molecular organization is affected by many factors such as e.g. pH, ionic strength and etc. For the study of the conformation of humic acids, concentration series of IHSS (International humic substances asociation) Leonardite humic acids stamdards in four different mediums were prepared: 0,1 M NaOH, humic acids in water with pH modified to 12 (basic medium), 0,1 M NaOH + 0,1 M HCl, 0,1 M NaCl (neutral environment). Furthermore it has been performed the fractionation of humic acids for the purpose of simplifying the complicated structure. Prepared concentration series were characterized with several analytical methods such as ultraviolet and visible spectroscopy, dynamic light scattering, electrophoretic light scattering, microrheology, gel permeation chromatography, potentiometric pH determination and direct conductometry. Diploma thesis is built on the previous bachelor thesis in which different sample of humic acids was studied. The measured results indicate that the studied systems show supramolecular behavior and in some cases are subject to aggregation into larger units (micelles).
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The influence of alcohols on the flow properties of sodium hyaluronate
Habartová, Lucie ; Pekař, Miloslav (referee) ; Smilek, Jiří (advisor)
This bachelor’s thesis examines the influence of alcohol presence on the conformation of sodium hyaluronate aqueous solutions primarily about the use of flow methods utilizing. Two molecule masses of sodium hyaluronan were studied, namely 1500-1750 kDa further referred to as high-molecular sodium hyaluronan and 500-750 kDa referred to as low-molecular. The flow and viscosity properties of high-molecular sodium hyaluronate have been studied in the presence of methanol, ethanol, isopropyl alcohol and terc-butanol in the concentration range 0-80 wt. %. Low-molecular sodium hyaluronate, and above all its flow and viscosity properties, were measured in the presence of ethanol and isopropyl alcohol in the concentration range 0-80 wt. %. Based on measured data, viscosities were assessed at infinitesimal stresses consistent with zero-rate viscosity. The high-molecular sodium hyaluronate ranged up to 327 mPas in terc-butanol solution. Viscosity values increased with the increasing length of the alcohol chain. The low-molecular sodium hyaluronate reached a maximum of 39 mPas in an isopropyl alcohol solution. The viscosity curves of low-molecular sodium hyaluronate were close to that of the Newtonian liquid.
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Study of structural features of single stranded DNA by biophysical techniques and crystallography
Svoboda, Jakub ; Schneider, Bohdan (advisor) ; Pavlíček, Jiří (referee)
DNA is the fundamental molecule in all domains of life, its role in heredity is well established. Although the famous double helical complementary form is indispensable for replication mechanism DNA can occupy wide range of conformations. In the past studies performed in the laboratory, DNA oligomers related to single stranded bacterial Repetitive Extragenic Palindromic (REP) showed spectral behavior suggesting complex equilibria including double helical, hairpin, and tetraplex conformations. The studies presented in this thesis extended the scope of analyzed sequences and employed circular dichroism spectroscopy and X-ray crystallography. We report spectral data and X-ray structures of three successfully crystalized oligonucleotides. All three structures acquire double helical architecture with two consecutive T- T mismatches in the center. To improve the convergence of the refinement process of the crystal structures we used novel dinucleotide conformational classes, NtC classes. The NtC class classification was also used to analyze geometries of selected non-canonical base pairs in all DNA crystal structures in the Protein Data Bank. We measured the fit between geometries of the dinucleotides involved in the non-canonical base pairing and the NtC classes and correlated this fit to the electron...
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The influence of alcohols on the flow properties of sodium hyaluronate
Habartová, Lucie ; Pekař, Miloslav (referee) ; Smilek, Jiří (advisor)
This bachelor’s thesis examines the influence of alcohol presence on the conformation of sodium hyaluronate aqueous solutions primarily about the use of flow methods utilizing. Two molecule masses of sodium hyaluronan were studied, namely 1500-1750 kDa further referred to as high-molecular sodium hyaluronan and 500-750 kDa referred to as low-molecular. The flow and viscosity properties of high-molecular sodium hyaluronate have been studied in the presence of methanol, ethanol, isopropyl alcohol and terc-butanol in the concentration range 0-80 wt. %. Low-molecular sodium hyaluronate, and above all its flow and viscosity properties, were measured in the presence of ethanol and isopropyl alcohol in the concentration range 0-80 wt. %. Based on measured data, viscosities were assessed at infinitesimal stresses consistent with zero-rate viscosity. The high-molecular sodium hyaluronate ranged up to 327 mPas in terc-butanol solution. Viscosity values increased with the increasing length of the alcohol chain. The low-molecular sodium hyaluronate reached a maximum of 39 mPas in an isopropyl alcohol solution. The viscosity curves of low-molecular sodium hyaluronate were close to that of the Newtonian liquid.
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Effect of pH on initiation of viral infection
Vomáčka, Petr ; Španielová, Hana (advisor) ; Šmahelová, Jana (referee)
In organisms, acidic pH occurs either in the intracellular or extracellular environment. Intracellularly an acidic pH is found in particular cellular compartments, such as early and late endosomes or lysosomes. In the extracellular space, the acidic pH is found in hypoxic tissues, or in tissues where inflammation or tumour growth occurs. The value of the pH is usually in the range of approximately from 5.5 up to 6.5. This work focuses on the description of the conformation changes of viral proteins, which occur due to a decreased pH and lead to escape of viral components from membrane compartments. Changes in pH in organelles of endocytic pathways as well as changes in extracellular pH affect significantly the infection of many viruses. Research on the role of pH during the viral can bring important information for the development of antiviral and anticancer treatment. Key words: virus, conformation, pH, receptor, endocytosis
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Computational study of short peptides and miniproteins in different environments
Vymětal, Jiří ; Vondrášek, Jiří (advisor) ; Svozil, Daniel (referee) ; Berka, Karel (referee)
Apart from biological functions, peptides are of uttermost importance as models for un- folded, denatured or disordered state of the proteins. Similarly, miniproteins such as Trp-cage have proven their role as simple models of both experimental and theoretical studies of protein folding. Molecular dynamics and computer simulations can provide an unique insight on processes at atomic level. However, simulations of peptides and minipro- teins face two cardinal problems-inaccuracy of force fields and inadequate conformation sampling. Both principal issues were tackled in this theses. Firstly, the differences in several force field for peptides and proteins were questioned. We demonstrated the inability of the used force fields to predict consistently intrinsic conformational preferences of individual amino acids in the form of dipeptides and the source of the discrepancies was traced. In order to shed light on the nature of conformational ensembles under various denatur- ing conditions, we studied host-guest AAXAA peptides. The simulations revealed that thermal and chemical denaturation by urea produces qualitatively different ensembles and shift propensities of individual amino acids to particular conformers. The problem of insufficient conformation sampling was dealt by introducing gyration- and...
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Fractionation and molecular organization of humic acids
Chytilová, Aneta ; Enev, Vojtěch (referee) ; Klučáková, Martina (advisor)
Humic acids are part of the natural organic matter occurring all around us. The aim of this thesis is to study the molecular organization, conformation of humic acids in aqueous solutions, that always raise a number of questions. For a long time, the scientists all over the world argue, if humic acid are polymers, micelles or supramolecules. Over time, thanks to new technologies, their opinions are moving away from a polymer model and tend rather to supramolecular arrangement of humic acids. Studying humic complex systems is not easy, because they are polydisperse and heterogeneous, which significantly complicates any characterization. Moreover, its molecular organization is affected by many factors such as e.g. pH, ionic strength and etc. For the study of the conformation of humic acids, concentration series of IHSS (International humic substances asociation) Leonardite humic acids stamdards in four different mediums were prepared: 0,1 M NaOH, humic acids in water with pH modified to 12 (basic medium), 0,1 M NaOH + 0,1 M HCl, 0,1 M NaCl (neutral environment). Furthermore it has been performed the fractionation of humic acids for the purpose of simplifying the complicated structure. Prepared concentration series were characterized with several analytical methods such as ultraviolet and visible spectroscopy, dynamic light scattering, electrophoretic light scattering, microrheology, gel permeation chromatography, potentiometric pH determination and direct conductometry. Diploma thesis is built on the previous bachelor thesis in which different sample of humic acids was studied. The measured results indicate that the studied systems show supramolecular behavior and in some cases are subject to aggregation into larger units (micelles).
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