This thesis aimed at studying mechanisms involved in control of tissue fluid homeostasis during inflammation. The interstitial fluid pressure (PIF) is of importance for control of tissue fluid balance. A lowering of PIF in vivo will result in a transport of fluid from the circulation into the tissue, leading to edema. Loose connective tissues that surround blood vessels have an intrinsic ability to take up fluid and swell. The connective tissue cells exert a tension on the fibrous network of the tissues, thereby preventing the tissues from swelling. Under normal homeostasis, the interactions between the cells and the fibrous network are mediated by β1 integrins. Connective tissue cells are in this way actively controlling PIF. Here we show a previously unrecognized function for the integrin αVβ3, namely in the control of PIF. During inflammation the β1 integrin function is disturbed and the connective tissue cells release their tension on the fibrous network resulting in a lowering of PIF. Such a lowering can be restored by platelet-derived growth factor (PDGF) -BB. We demonstrated that PDGF-BB restored PIF through a mechanism that was dependent on integrin αVβ3. This was shown by the inability of PDGF-BB to restore a lowered PIF in the presence of anti-integrin β3 IgG or a peptide inhibitor of integrin αVβ3. PDGF-BB was in addition unable to normalize a lowered PIF in β3 null mice. Furthermore, we demonstrated that extracellular proteins from Streptococcus equi modulated αVβ3-mediated collagen gel contraction. Because of the established concordance between collagen gel contraction in vitro and control of PIF in vivo, a potential role for these proteins in control of tissue fluid homeostasis during inflammation could be assumed. Sepsis and septic shock are severe, and sometimes lethal, conditions. Knowledge of how bacterial components influence PIF and the mechanisms for tissue fluid control during inflammatory reactions is likely to be of clinical importance in treating sepsis and septic shock.

Heparan sulfate (HS) is an unbranched and negatively charged polysaccharide of the glycosaminoglycan family, based on the repeated (GlcNAcα1-4GlcAβ1-4) disaccharide structure. The HS backbone is modified by epimerization and sulfation in various positions. HS chains are composed of N-sulfated (NS) domains – predominant locations for further modification steps –, the poorly modified N-acetylated (NA) domains and the alternating NA/NS-domains. HS is present at the cell surface and in the extra-cellular matrix and interacts at these sites with various proteins involved in numerous biological processes, such as angiogenesis. Both pro- and anti-angiogenic proteins can interact with HS and this study was focused on how HS binds to the anti-angiogenic proteins endostatin (ES) and histidine-rich glycoprotein (HRGP) and to pro-angiogenic fibroblast growth factors (FGFs). Here we show that ES recognizes NS-domains in HS spaced by NA-disaccharides, and that binding to ES is abolish through cleavage at these NA-disaccharides. HRGP335, a peptide derived from the His/Pro-rich domain of HRGP is shown to bind to heparin and HS to the same extent as full-size HRGP, in a Zn2+-dependent manner. Moreover, the ability of HRGP to inhibit endothelial cell migration is located to the same region of the protein. We analyzed HS structure in respect to binding to HRGP335 and FGF-2, and show that the ability of HS to bind to those proteins depends on chain length and composition. Finally, the role of HS in FGF–HS–FGF receptor ternary complexes is evaluated using biosynthetic analogs of NS-domains. For stabilization of such complexes the overall sulfation degree of HS seems to play a more pronounced role than the exact distribution of sulfate groups. The results presented in this thesis contribute to a greater understanding of the role of HS in angiogenesis and may provide valuable information for the development of cures against angiogenesis-related disorders.

One of the most challenging tasks remaining in the field of biochemistry is the one of understanding how the information within the amino acid sequence of proteins translates into a unique structure. Solving this problem would lead to endless possibilities for application in the medical and biotechnology industry. Many decades ago scientists realized that the process that facilitates the folding of a polypeptide chain could not be random and happen by chance; there needs to be direction in the folding free energy landscape. This landscape is defined by the thermodynamic factors entropy and enthalpy. The contribution made by enthalpy i.e. the contact energies from intra- and intermolecular interactions have been extensively investigated by various mutational studies. The influence of entropy on the other hand, is less well understood. My work focuses on the effect of altering the entropic components of forming the various parts of a known protein scaffold. This is done by genetic engineering in combination with biophysical characterisation and analysis. The results show effects on protein folding rates as well as on the pathway for nucleation and emphasis the ability of the folding landscape to readjust to entropic variations. Proteins are therefore not required to fold along a unique route to their final structure but can do so in several ways. The folding pathways we observe today have hence likely evolved as an adaptation to biological demands.

Lipoprotein lipase (LPL) is an enzyme to hydrolyze triglycerides in lipoproteins and thereby make the fatty acids available for cellular metabolic reactions. Short-term fasting down-regulates LPL activity in adipose tissue. This regulation is through post-translational mechanism. The objective of this work was to investigate (1) The molecular mechansim for regulation of LPL activity in adipose tissue; (2) The basis for the tissue-specific regulation of LPL in adipose tissue, heart and skeletal muscle. LPL in adipose tissue can be found both inside (intracellular) and outside adipocytes (extracellular). Within adipocytes, neither LPL mass nor the distribution of LPL between active and inactive forms changed on fasting. Extracellular LPL mass also did not change significantly, but shifted from predominantly active to predominantly inactive. Activie, extracellular LPL was distributed in a similar way in the two nutritional states. The down-regulation during fasting is due to a decline of extracellular LPL activity. The up-regulation of LPL activity induced by re-feeding did not need new mRNA. The down-regulation of LPL activity induced by fasting did not occur when mRNA synthesis was inhibited. LPL activity in adipose tissue from fasted rats was fully restored by actinomycin. So fasting switches on a gene, whose product suppresses LPL activity. Similar results were also obtained in experiments on mice. When food was removed from young rats in the early morning, adipose tissue TNF-α activity increased and LPL activity decreased within six hours. There was a negative correlation between TNF-α and LPL activities. Pentoxifylline, that inhibits biosynthesis of TNF-α, almost abolished the rise of TNF-α and the decrease of LPL activity. Actinomycin D virtually abolished the response of LPL activity to fasting or exogenous TNF-α. This study suggests that fasting signals via TNF-α to a gene whose product causes a rapid shift of newly-synthesized LPL molecules towards an inactive form.

Fibroblasts continuously strive to organize and compact the surrounding extracellular matrix (ECM). Recent data suggest that this cellular contractility controls interstitial fluid homeostasis in loose connective tissues (CT). The aim of this thesis was to study the effects of prostaglandins on fibroblast contractility and to investigate whether fibroblasts in the interstitial CT surrounding the human endolymphatic duct (ED) can modulate inner ear fluid pressure and endolymph resorption. Paper I shows that prostaglandin E1 (PGE1) and prostacyclin inhibit fibroblast-mediated collagen matrix compaction in vitro and lower the interstitial fluid pressure in vivo in rat dermis. Paper II demonstrates that the inhibition of collagen matrix compaction by PGE1 is protein kinase A-dependent. Furthermore, PGE1 induces a complete but reversible actin depolymerization in human dermal fibroblasts by affecting the phosphorylation state of regulatory actin-binding proteins. Paper III describes that the cells of the interstitial CT encompassing the human ED are organized in a network based on intercellular- and cell-ECM contacts. Paper IV shows that two distinct cell phenotypes populate this interstitial CT: one expressing the lymph endothelial marker podoplanin and the other a fibroblast marker. Furthermore, CT cells isolated from human ED tissues exhibited the same tissue compacting properties in vitro as dermal fibroblasts. In conclusion, PGE1 inhibits fibroblast contractility by interfering with the stability and dynamics of the actin cytoskeleton, which leads to a loss of integrin-mediated adhesion to the ECM. These mechanisms are supposedly involved in edema formation in skin during inflammation and might be involved in the formation of endolymphatic hydrops in the inner ear of patients with Ménière’s disease.

This thesis is based on studies, described in four papers, in which the folding energy landscape of MerP was investigated by various techniques. MerP is a water-soluble 72 amino acid protein with a secondary structure consisting of four anti-parallel β-strands and two α-helices on one side of the sheet in the order β1α1β2β3α2β4. The first paper describes the use of CD and fluorescence analysis to examine the folding/unfolding process of MerP. From these experiments it was found that the protein folds according to a two-state model in which only the native and unfolded forms are populated without any visible intermediates. With a rate constant of 1.2 s-1, the folding rate was found to be unusually slow for a protein of this size. The studies presented in the second and third papers were based on measurements of native-state amide proton exchange at different temperatures (Paper II) and GuHCl concentrations (Paper III) in the pre-transitional region. In these studies partially unfolded forms were found for MerP which are essentially unrelated to each other. Thus, in the folding energy landscape of MerP, several intermediates seem to occur on different folding trajectories that are parallel to each other. The slow folding rate of MerP might be coupled to extensive visitation of these conformations. Hydrogen exchange in MerP did also reveal structure-dependent differences in compactness between the denatured states in GuHCl and H2O. In the last paper multivariate data analysis was applied to 2-dimensional NMR data to detect conformational changes in the structure of MerP induced by GuHCl. From this analysis it was suggested that regions involved in the most flexible part of the protein structure are disrupted at rather low denaturant concentrations (< 2.1 M GuHCl) while the native structures of the most stable parts are still not completely ruptured at 2.9 M GuHCl. Finally, the stability, kinetics, contact order and folding nuclei of six proteins with similar topology (MerP, U1A, S6, ADA2h, AcP and HPr) were compared. In this analysis it was found that their folding properties are quite diverse, despite their topological similarities, and no general rules that have been formulated yet can adequately predict their folding behaviour.

Fish has for a long time been a very important source of protein for human kind and with the world population at an all-time high, 7.5 billion and rapidly growing, the demand for fish as a food source is also at an all-time high and rapidly increasing. This has in turn led to overexploitation of many of the fish stocks of the world ocean’s and in many cases to depletion of fish stocks. The demand for sustainable food sources and sustainable usage of the world ocean’s fish stocks is therefore a subject with great deal of interest today. Much of the fish caught today are used for production of fish meal for usage as fish food at fish farms, which also increases the depletion of fish stocks around the globe. One way of dealing with this problem is to replace the fish meal as protein source in fish feed with protein from agricultural crops which in many cases are done today by usage of soy bean protein. This however poses another problem as the agricultural crops take up vast amount of land, in many cases obtained by diminishing the rainforests in the area. Another usage for the soybean would be as a direct human food source. Agricultural products are also dependent on environmental conditions to ensure reasonable production. The problems related to production of fish meal and soy has sparked the idea of using microorganisms for production of Single cell protein for usage as protein source in fish feed. Single cell protein can be produced in closed fermentation vessels and can be produced at a controlled rate and under controlled manners, while taking up negligible land space. During this thesis, the production of single cell protein from spent sulfite liquor using the filamentous fungi Paecilomyces variotii was examined. The aim of the project was to examine the effect of cultivation parameters (i.e., pH, temperature and nutrients) on the production of biomass as well as the protein content of the biomass. The correlation of the biomass growth and protein content have also been examined. The project was carried out by performing several experiment cultivations using spent sulfite liquor provided by Domsjö Fabriker in Örnsköldsvik. This process enables the utilization of a residual stream from the pulp industry which gives this process a huge environmental upside compared to similar processes as for example the commercial production of Quorn (a Single cell based food product) which utilizes pure glucose. The results showed that the protein content will steadily decrease as the biomass production increases hence it is desirable to keep the cultivation time at a minimum while maximizing biomass production during that time frame. It also points towards that the highest protein content is present in the young cell mass. The key conclusion from this thesis is however that it is possible to lower the pH of the cultivation from pH 6 down to pH 4.5 while still maintaining the biomass production and increasing the protein content. The highest obtained protein content was 62.7% at pH 4.5. The high protein content might be due to a slightly longer lag phase in the beginning of the cultivation which yields a higher number of younger cells in the final broth thus increasing protein content. Running the process at a lower pH is a huge advantage for industrial implementation as this on large scale means significant lower amounts of chemicals needed for pH adjusting of the spent sulfite liquor which renders the process much more economical. This is because pH adjustment today is one of the most costly process steps in the production of bioethanol from spent sulfite liquor.

<p> </p><p>In a time when the amount of biological data present in the public domain is becoming increasingly vast, the need for good classification systems has never been greater. In the field of glycoscience the necessity of a good classification for the enzymes involved in the biosynthesis, modification and degradation of polysaccharides is even more pronounced than in other fields. This is due to the complexity of the substrates, the polysaccharides, as the theoretical number of possible hexa-oligosaccharides from only hexoses exceeds 10¹² isomers! </p><p>An initiative to classify enzymes acting on carbohydrates began around 1990 by the French scientist Bernard Henrissat. The resulting database, the Carbohydrate Active enzymes database (CAZy), classifies enzymes by sequence similarity into families allowing the inference of structure and catalytic mechanism. What CAZy <em>does not </em>provide however, are means to understand how members of a family are related, and in what way they differ from each other. The top-down approach used in this thesis, combining phylogenetic analysis of whole CAZy families, or sub-families, with structural determinations and detailed kinetic analysis allows for exactly that.  </p><p>Finding determinants for transglycosylation <em>versus </em>hydrolysis within the <em>xth </em>gene product family of GH16 as well as restricting the hydrolytic enzymes to a well defined clade are integral parts of paper I. In paper II a new bacterial sub-clade within CE8 was discovered. The structural determination of the<em>Escherichia coli </em>outer membrane lipoprotein YbhC from from the new sub-clade explained the difference in specificity. The information provided in the two papers of this thesis gives a better understanding of the development of different specificities of diverse CAZY families as well as it aids in future gene product annotations. Furthermore this work has begun to fill the white spots uncovered in the phylogenetic trees.</p><p> </p><p> </p>

Ribonucleotide reductase (RNR) is a key enzyme in the de novo biosynthesis and homeostatic maintenance of all four DNA building blocks by being able to make deoxyribonucleotides from the corresponding ribonucleotides. It is important for the cell to control the production of a balanced supply of the dNTPs to minimize misincorporations in DNA. Because RNR is the rate-limiting enzyme in DNA synthesis, it is an important target for antimicrobial and antiproliferative molecules. The enzyme RNR has one of the most sophisticated allosteric regulations known in Nature with four allosteric effectors (ATP, dATP, dGTP, and dTTP) and two allosteric sites. One of the sites (s-site) controls the substrate specificity of the enzyme, whereas the other one (a-site) regulates the overall activity.  The a-site binds either dATP, which inhibits the enzyme or ATP that activates the enzyme. In eukaryotes, ATP activation is directly through the a-site and in E. coli it is a cross-talk effect between the a and s-sites. It is important to study and get more knowledge about the overall activity regulation of RNR, both because it has an important physiological function, but also because it may provide important clues to the design of antibacterial and antiproliferative drugs, which can target RNR. Previous studies of class I RNRs, the class found in nearly all eukaryotes and many prokaryotes have revealed that the overall activity regulation is dependent on the formation of oligomeric complexes. The class I RNR consists of two subunits, a large α subunit, and a small β subunit. The oligomeric complexes vary between different species with the mammalian and yeast enzymes cycle between structurally different active and inactive α6β2 complexes, and the E. coli enzyme cycles between active α2β2 and inactive α4β4 complexes. Because RNR equilibrates between many different oligomeric forms that are not resolved by most conventional methods, we have used a technique termed gas-phase electrophoretic macromolecule analysis (GEMMA). In the present studies, our focus is on characterizing both prokaryotic and mammalian class I RNRs. In one of our projects, we have studied the class I RNR from Pseudomonas aeruginosa and found that it represents a novel mechanism of overall activity allosteric regulation, which is different from the two known overall activity allosteric regulation found in E. coli and eukaryotic RNRs, respectively.  The structural differences between the bacterial and the eukaryote class I RNRs are interesting from a drug developmental viewpoint because they open up the possibility of finding inhibitors that selectively target the pathogens. The biochemical data that we have published in the above project was later supported by crystal structure and solution X-ray scattering data that we published together with Derek T. Logan`s research group. We have also studied the effect of a novel antiproliferative molecule, NSC73735, on the oligomerization of the human RNR large subunit. This collaborative research results showed that the molecule NSC73735 is the first reported non-nucleoside molecule which alters the oligomerization to inhibit human RNR and the molecule disrupts the cell cycle distribution in human leukemia cells.

<p>Kinases and phosphatases are key regulatory proteins in the cell. The disruption of their activities leads ultimately to the abolishment of the homeostasis of the cell, and is frequently correlated with cancer. EphB1 is a member of the largest family of receptor tyrosine kinases. It is associated with neurogenesis, angiogenesis, and cancer. The cytosolic part of the human EphB1 receptor is composed of two domains. Successful generation of soluble constructs, using a novel random construct screening approach, led to the structure determination of the kinase domain of this receptor. The native structure and the complex structure with an ATP analogue revealed novel features in the regulation of the Eph family of kinases.</p><p>The structure of PTPA, an activator of protein phosphatase 2 A, a tumor suppressor and a key phosphatase in the cell was solved. The structure revealed a novel fold containing a conserved cleft predicted to be involved in interaction with PP2A.</p><p>Finally, the structure of YegS, an <i>Escherichia coli</i> protein annotated as a putative diacylglycerol kinase, has been determined. Beside the elucidation of its atomic structure, a phosphatidylglycerol (PG) kinase activity, never seen before, has been assigned to YegS based on biochemical studies. The YegS structure shows resemblance to the fold previously seen in NAD kinases. The structure also revealed the existence of a novel metal site that could potentially play a regulatory role. The YegS structure has important implications for understanding related proteins in pathogenic organisms and is the first homologue of a human lipid kinase for which the structure has been elucidated.</p>