Intact chloroplasts were isolated from Euglena gracilis variety bacillaris, and aliquots were exposed to several different chemical cross-linking reagents. The reagents penetrated the triple membrane of Euglena chloroplasts. This was shown by gradient acrylamide gel electrophoresis under denaturing conditions. The activity of the nonaggregated fatty acid synthetase of Euglena was located within the chloroplast stroma, and the effects of dimethylsuberimidate cross-linking on the activity of the enzyme system were examined. The acyl-carrier protein concentration in the chloroplast was measured at about 0.24 mM.

The 3D structures of proteins may provide important clues to their functions and roles in complex biological pathways. Traditional methods such as X-ray crystallography and NMR are not feasible for all proteins, while theoretical models are typically not validated by experimental data. This project investigates the use of chemical crosslinkers as an experimental means of validating these models. Five target proteins were successfully purified from yeast whole cell extract: Transketolase (TKL1), inorganic pyrophosphatase (IPP1), amidotransferase/cyclase HIS7, phosphoglycerate kinase (PGK1) and enolase (ENO1). These TAP-tagged target proteins from yeast <em>Saccharomyces cerevisiae</em> allowed the protein to be isolated in two affinity purification steps. Subsequent structural analysis used the homobifunctional chemical crosslinker BS³ to join pairs of lysine residues on the surface of the purified protein via a flexible spacer arm. Mass spectrometry (MS) analysis of the crosslinked protein generated a set of mass values for crosslinked and non-crosslinked peptides, which was used to identify surface lysine residues in close proximity. The Automatic Spectrum Assignment Program was used to assign sequence information to the crosslinked peptides. This data provided inter-residue distance constraints that can be used to validate or refute theoretical protein structure models generated by structure prediction software such as SWISS-MODEL and RAPTOR. This approach was able to validate the structure models for four of the target proteins, TKL1, IPP1, HIS7 and ENO1. It also successfully selected the correct models for TKL1 and IPP1 from a protein model library and provided weak support for the HIS7, PGK1 and ENO1 models.

The 3D structures of proteins may provide important clues to their functions and roles in complex biological pathways. Traditional methods such as X-ray crystallography and NMR are not feasible for all proteins, while theoretical models are typically not validated by experimental data. This project investigates the use of chemical crosslinkers as an experimental means of validating these models. Five target proteins were successfully purified from yeast whole cell extract: Transketolase (TKL1), inorganic pyrophosphatase (IPP1), amidotransferase/cyclase HIS7, phosphoglycerate kinase (PGK1) and enolase (ENO1). These TAP-tagged target proteins from yeast <em>Saccharomyces cerevisiae</em> allowed the protein to be isolated in two affinity purification steps. Subsequent structural analysis used the homobifunctional chemical crosslinker BS³ to join pairs of lysine residues on the surface of the purified protein via a flexible spacer arm. Mass spectrometry (MS) analysis of the crosslinked protein generated a set of mass values for crosslinked and non-crosslinked peptides, which was used to identify surface lysine residues in close proximity. The Automatic Spectrum Assignment Program was used to assign sequence information to the crosslinked peptides. This data provided inter-residue distance constraints that can be used to validate or refute theoretical protein structure models generated by structure prediction software such as SWISS-MODEL and RAPTOR. This approach was able to validate the structure models for four of the target proteins, TKL1, IPP1, HIS7 and ENO1. It also successfully selected the correct models for TKL1 and IPP1 from a protein model library and provided weak support for the HIS7, PGK1 and ENO1 models.

This master's thesis deals with gelation of hydroxyethylcellulose and hyaluronan crosslinked with nontoxic crosslinking agent – citric acid. First of all, the optimalization of gelation process of hydroxyethylcellulose took place. After obtaining the product insolube in the ultrapure deionized water, a reaction mixture of hyaluronan and hydroxyethylcellulose in two different weight ratios were prepared. There was prepared solution containing only hyaluronan as the polymeric part too. Citric acid was used in concentrations of 5 %, 10 % and 20 % (w/w of polymer). These solutions of polymers and citric acid were gelated under the same conditions and the products were compared to each other using Differential Scanning Calorimetry, Thermogravimetry and Fourier Transform Infrared Spectroscopy. The products containing hydroxyethylcellulose and hyaluronan with hydroxyethylcellulose in weight ratio equal to 3 : 7 were considered crosslinked.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

Předložená disertační práce shrnuje současné poznatky v oblasti termosenzitivních biodegradabilních kopolymerů, které ve formě vodného solu gelují při teplotě lidského těla. Tyto polymerní materiály jsou použitelné v medicíně pro injekční aplikace jako nosiče léčiv či resorbovatelné implantáty pro regeneraci tkání. V experimentální práci byly pomocí vakuové linky syntetizovány termosenzitivní amfifilní triblokové kopolymery na bázi biodegradabilního hydrofobního polylaktidu a polyglykolidu a biokompatibilního hydrofilního polyethylenglykolu (PLGA–PEG–PLGA). Připravený PLGA–PEG–PLGA kopolymer se dvěma fázovými přechody sol-gel a gel-suspenze byl následně modifikován anhydridem kyseliny itakonové. Výsledný funkcionalizovaný ITA/PLGA–PEG–PLGA/ITA kopolymer obsahuje na koncích řetězců reaktivní dvojné vazby vhodné k další polymeraci či síťování a karboxylové skupiny pro případné modifikace biologicky aktivními látkami. Fyzikální i chemické síťování bylo dále sledováno jak z hlediska poměrů hydrofilního a hydrofobního řetězce, tak i z hlediska množství navázané kyseliny itakonové. Vodné roztoky syntetizovaného ITA/PLGA–PEG–PLGA/ITA kopolymeru gelují v rozmezí teplot 33 - 43 °C. Kritická gelační koncentrace byla 6 % a kritická gelační teplota 34 °C pro kopolymer s poměrem PLGA/PEG = 2,5. Čím je kopolymer více hydrofobní, tím geluje dříve a je více hydrolyticky stabilní. Tuhost gelu stoupá se zvyšujícím se poměrem PLGA/PEG a je závislá na typu rozpouštědla použitého při přečišťování kopolymeru. Připravené ITA/PLGA–PEG–PLGA/ITA makomonomerů byly síťovány pomocí modrého světla bez dalšího síťovadla. Hydrolytická stabilita vzorků modifikovaných pomocí ITA se výrazně zlepšila a zvýšila v přímé úměře jak s rostoucí dobou síťování, tak s množstvím dvojných vazeb na koncích řetězců. Vzorek s 63 mol% ITA síťovaný 40 minut ve vodě zcela zdegradoval po 32 dnech. Protonovou NMR relaxometrií bylo zjištěno, že když vzorek ve vodě nabotnal (po cca 12 hodinách), množství nevázané vody se začalo snižovat a postupně difundovat do kavit na povrchu vzorku a pomalu se měnit na slabě a pevně vázanou vodu na polymerní řetězce. Nicméně, termální stabilita chemicky síťovaných vzorků vzrůstala pouze do 20 minut síťování. Pomocí ATR-FTIR bylo prokázáno, že se přibližně 57 % dvojných vazeb kyseliny itakonové (při vlnové délce 1640 cm-1) přeměnilo na nové jednoduché RR'C-CHR'' vazby při vlnové délce 795 cm-1. Delší čas síťování (nad 30 minut) vedl ke změnám v chemické struktuře pomocí beta-štěpení řetězců a částečné rekombinaci dvojných vazeb. Díky vzniku nových dvojných vazeb v jiných částech řetězce se snížila termální stabilita z 242 °C na 237° C a teplota skelného přechodu z -2,2 na -5.8 °C. Předložená práce popisuje, jak složení polymeru, modifikace funkčními skupinami a fyzikální podmínky ovlivňují fyzikální a chemické síťování připravených amfifilních kopolymerů. Kontrola hydrolytické a termální stability hydrogelů je zapotřebí zejména při uvolňování léčiv a regeneraci tkání.