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Protein-protein interactions are involved in various biological processes and detailed characterization of their structural basis by the means of structural biology is often instrumental for rigorous understanding of underlying molecular mechanisms. This information is important not only for fundamental biology but also plays an important role in search for sites amenable for therapeutic intervention. Nuclear magnetic resonance spectroscopy is alongside X-ray crystallography and single-particle cryo-electron microscopy one of the key high-resolution techniques in structural biology. Although its applicability to larger systems has a well-known physical limit, it offers unique capabilities in addressing highly dynamic or inherently heterogeneous systems. In this doctoral thesis, the solution-based NMR approach was used for detailed structural characterization of selected biologically important proteins and their complexes that provided important insights into their biological roles. In three distinct projects, I (i) studied the relationship between the structural effects of particular modifications in the insulin-like growth factor II (IGF-II) and their selectivity to the insulin axis receptors; (ii) the specific binding mechanism of the SH3 domain from the Crk-associated substrate (CAS); (iii) and...

In the first part of this work, a series of site-specific artificial metallonucleases (AMNs) was developed conjugating clamped-phenanthroline (Clip-Phen) copper complexes to triplex- forming oligonucleotides (TFOs). Several synthetic routes were explored for the synthesis of the TFO-AMNs hybrids, all sharing a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction as the key step. As a consequence, building blocks for enzymatic or chemical synthesis of oligonucleotides (ONs) containing clickable groups, or already conjugated to the Clip-Phen ligand via CuAAC, were prepared. Two new alkynyl-linked nucleoside-5'-O-triphosphates (dNTPs) were designed and developed in order to obtain an efficient polymerase incorporation of clickable alkynyl-tethers into ONs and, at the same time, enhance the efficiency of CuAAC reactions on modified DNA. The relative 3'-O- phosphormaidites were also prepared in order to insert the same alkynyl-linkers into ONs via solid-phase synthesis. The AMN was linked at the 5'- or 3'-ends or in the middle of the TFO stretch, using diverse likers. The hybridization of all the synthesized TFOs with a target DNA duplex was studied. Finally, an extensive study of cleavage efficiency and specificity of the TFO-AMN conjugates towards the target DNA was performed, exploring the...

The aim of this Master Thesis is to synthesize and study new macrocyclic ligands containing fluorine atoms for use as potencial contrast agents in 19 F magnetic resonance imaging. New ligands were designed as analogues of ligands used in contrast agents already utilized in clinical practice - macrocyclic ligand for complexation of trivalent lanthanide ions based on DOTA skeleton and series of macrocyclic ligands for complexation of divalent nickel ion based on cyclam skeleton. All designed ligands were synthesized a characterized. The complexes [LnIII (dotptfe )]− were tested in vitro and in vivo to study 19 F NMR relaxation times enhancements.

Carotenoids are an extensive group of natural pigments employed by a majority of organisms on earth. They are present in most organisms, including humans, but can be synthesized only by plants and microorganisms. They perform two major roles in photosynthesis, often in partnership with the more prevalent chlorophylls (Chls) / bacteriochlorophylls (BChls): light-harvesting and photoprotection. Carotenoids absorb radiation in a spectral region inaccessible to Chls and BChls and transfer the absorbed energy to (B)Chls which, in turn, funnel it into the photosynthetic reaction center (RC). It is determined that the structures and dynamics of excited states of carotenoids found in photosynthetic proteins provide an explanation of their roles as light-harvesting and photoprotective agents. The conjugation length and the type of carotenoids play a big part in understanding the energy transfer from carotenoids to Chls and BChls, because excited-state properties of carotenoids are affected by number of conjugated C=C bonds and their structures. An accurate description of these states is, therefore, the crucial first step in explaining carotenoid photochemistry and understanding the interactions between carotenoids and other molecules in photobiological processes. The research in this thesis, femtosecond ultrafast transient absorption spectroscopy was used to study the light-harvesting function of carotenoids both in solvent and protein environment. The findings were supported with computational methods. Based on spectroscopic indications, the light-harvesting function of carotenoids has a bearing on their structures, and specific light-harvesting strategies are explicitly dependent with the structure of the light-harvesting complexes.

In an effort to increase the thermodynamic stability and the kinetic inertness of the complexes, the five new azamacrobicyclic ligands derived from TACN, cyclen, and cyclam have been prepared. The ligands were decorated with phosphinate or phosphonate pendant arms to maintain fast complexation. Since the ascending importance of targeted diagnostic and therapy, the bone-targeted non-bridged cyclam derivative with phosphinate-bis(phosphonate) pendant arm (H5TE1PBP) has also been synthesized. The ligands were studied with respect to their application. The bridged TACN (H2bpbtacn) and cyclen (H4bpbcen) ligands show high macrocyclic basicity (logK1 = 12.25 and 12.70, respectively). The thermodynamic stability of H2bpbtacn with Cu(II) ion is more than ten orders of magnitude lower than that of the NOTA ligand. The stability constants of H4bpbcen with Cu(II) and Zn(II) ions are comparable to those given for the DOTA. The stability of Ln(III)-bpbcen complexes is 7-10 orders of magnitude lower compared to DOTA complexes. For both ligands, the lower thermodynamic stability of the complexes is attributed to the high rigidity of the ligand structure. The bridged cyclam derivatives with phosphonate (H4TE2P), bis(phosphinate) (H4TE2bpin), or phosphinate (H2TE2PH) pendants are characterized by high stability of...

Mass spectrometry with electrospray ionization is an excellent method for structural analysis of coordination compounds with outstanding sensitivity and selectivity. However, it fails to detect some low-polar rhenium complexes. This master thesis describes derivatization method of non-ionizable rhenium complexes with 1,2-dihydroxybenzene and 2,3- dihydroxytoluenene. Fragmentation mechanisms and structure of prepared complexes was studied using high resolution mass spectrometry and collision-induced dissociation (CID). Furthermore, density functional theory (DFT) computational method was used for prediction of bond cleavage based on bond lengthening.

Present methods for diagnosis of neurodegenerative diseases are rather limited and in clinical practise are missing. This thesis is focused on utilization of the positron emission tomography using isotope 64 Cu(II). For the project, two contrast agents were proposed containing ligand for Cu (II) coordination and thioflavine T derivative as fluorescent dye, also as a targeting compound. Structure of the thioflavine T derivative was defined by X-ray structural analysis. The selected fluorescent dye has a high affinity for incipient amyloids and, when bound to their structure, has enhanced fluorescent properties. The proposed ligands are tetraazacyclic. The first one is a diamide, where the thioflavin T derivative is part of a macrocyclic ring. The second selected ligand is linked to the thioflavin T derivative via a linker. Key words: complexes; pharmaceuticals; transition metals

Modern diagnostic method magnetic resonance imaging (MRI) usually uses contrast agents T1-type, which are based on Gd3+ complexes. Due to severe toxicity of free Gd3+ , it is desired to have thermodynamically stable and kinetically inert complexes with fast elimination from the body. This work summarizes information about a novel contrast agent based on ligand DO3AP (1,4,7,10-tetraazacyclododecane-1-methyl(alkyl)phosphinic-4,7,10- triacetic acid) with pendant hydrophobic dibenzylamino group which is able to interact hydrophobically with the macromolecule of serum albumin. The stability of supracomplex is dependent on pH value, i.e. on the protonation of the pendant amino group of the complex (pKA = 5.6) and this interaction was confirmed from 1 H-NMRD profile and fluorescent analysis. The compound was tested for its angiographic properties in vivo on rat model. Furthermore, other complexes of the ligand with trivalent lanthanides (Nd3+ , Eu3+ , Tb3+ , Dy3+ , Er3+ ) were characterized by various methods (XRD, luminescence, UV-VIS, 1 H-, 17 O- and 31 P-NMR). The cleavage of the benzyl groups affords ligand whose Ln3+ complexes possess pH dependent PARACEST effect. These complexes were characterized by XRD, luminescence and 1 H- and 31 P-NMR. Moreover, the novel ligands with modified length of pendant...

Two linear aminodiphosphinates (H3L1 , H5L2 ) and one cyclic aminodiphosphinate (H2L3 ) were prepared and studied. Newly prepared compounds were characterized by NMR, MS and EA (elemental analysis). Acid-base and coordination properties of ligands were studied. Protonation constants and stability constants of complexes with Zn2+ , Ni2+ and Cu2+ metal ions were determined by potentiometry. Keywords Ligands, dissociation constants, potentiometry, phosphinates, complexes.