The specificity and selectivity of the enzyme Candida antarctica lipase B (CALB) were studiedfor several substrates and applications.With help of molecular modeling, the active site of CALB was redesigned for the ring openingpolymerization of D,D‐lactide. Two mutants, with about 90‐fold increase in activity ascompared to the wild‐type enzyme, were created. Changing a glutamine into alanineaccounted for this increase in both mutants by creating a larger space in the acyl donorpocket. The new space made it possible to accommodate the bulky substrate and improvethe transition state‐active site complementarity during polymer chain propagation.The enantioselectivity of CALB towards secondary alcohols was engineered by rationalredesign of the stereoselectivity pocket in the enzyme active site. A larger space created by asingle point mutation resulted in an 8’300’000 times change in enantioselectivity towards 1‐phenylethanol and the enantiopreference was inverted into S‐preference. The activitytowards the S‐enantiomer increased 64’000 times in the mutant as related to the wild‐type.The solvent and temperature effects on the enantioselectivity were studied for severalsubstrates and revealed the importance of entropy in the change in enantioselectivity.Substrate selectivity is of great importance for the outcome of enzyme catalyzed polymersynthesis. Ring opening polymerization (ROP) of γ‐acyloxy‐ε‐caprolactones will result in apolyester chain with pendant functional groups. CALB was found to have activity not onlytowards the lactone but also towards the γ‐ester leading to rearrangement of the monomersyielding γ‐acetyloxyethyl‐γ‐butyrolactone. This selectivity between the lactone and the γ‐ester was dependent on the type of group in the γ position and determined the ratio ofpolymerization and rearrangement of the monomers. Molecular dynamics simulations wereused to gain molecular understanding of the selectivity between the lactone and γ‐ester.In order to obtain (meth)acrylate functional polyesters we investigated the use of 2‐hydroxyethyl (meth)acrylate (HEA and HEMA) as initiators for ring opening polymerization.We found that, in addition to the ring opening polymerization activity, CALB catalyzed thetransacylation of the acid moiety of the initiators. The selectivity of CALB towards thedifferent acyl donors in the reaction resulted in a mixture of polymers with different endgroups. A kinetic investigation of the reaction showed the product distribution with timewhen using HEA or HEMA with ε‐caprolactone or ω‐pentadecalactone.The high selectivity of CALB towards lactones over (meth)acrylate esters such as ethyleneglycol di(meth)acrylate was used to design a single‐step route for the synthesis ofdi(meth)acrylated polymers. By mixing ω‐pentadecalactone with the ethylene glycoldi(meth)acrylate and the enzyme in solvent free conditions, we obtained >95 % ofdi(meth)acrylated polypentadecalactone.Taking advantage of the high chemoselectivity of CALB, it was possible to synthesizepolyesters with thiol and/or acrylate functional ends. When using a thioalcohol as initiatorCALB showed high selectivity towards the alcohol group over the thiol group as acyl acceptorfor the ROP reaction. The enzymatic ability of catalyzing simultaneous reactions (ROP andtransacylation) it was possible to develop a single‐step route for the synthesis ofdifunctionalized polyesters with two thiol ends or one thiol and one acrylate end by mixingthe initiator, lactone and a terminator. / QC 20101006

In the past few years, the use of nanostructured materials in medical applications hasdramatically increased, both in the research phase and for clinical purposes, due to thepeculiar properties and the ability of such materials to interact at a similar scale withbiological entities. In this thesis, we developed tailored magnetic multifunctionalnanoparticles for diagnostic and therapeutic applications, such as detection ofbiomolecules, simultaneous enhanced magnetic resonance imaging (MRI), fluorescentvisualization and controlled drug release.For sensitive and selective detection of specific biomolecules, thermally blocked ironoxide nanoparticles with tailored magnetic properties were developed. The formation ofsuch nanoparticles has been studied both in terms of size and magnetic behavior in liquidsuspension or in polymer matrixes. These particles with narrow size distribution (averagediameter of 19 nm) were surface functionalized by antigen molecules and were used forthe detection of Brucella antibodies in biological samples. The binding of biomoleculesresults in an increase in the particle’s hydrodynamic diameter, affecting the relaxationbehavior that was monitored by magnetic measurements. This sensing system is a fastand sensitive biosensor with very low detection limits (0.05 μg/mL).Superparamagnetic iron oxide nanoparticles (SPION) have been synthesized withaverage diameter of 10-12 nm, narrow size distribution, high crystallinity and superiormagnetic properties as liquid suspensions or embedded in a bulk transparent magneticnanocomposite. These nanoparticles were synthesized in organic solvents and, after phasetransfer with Pluronic F127 amphiphilic copolymer, show excellent relaxivity properties(high r2/r1 ratio) and great contrast enhancement in T2 weighted MRI, confirmed by invivostudies of rat inner ear.SPION have been used as a component for different multifunctional nanostructures. Thefirst system based on poly (L,L lactide)-methoxy polyethylene glycol (PLLA-mPEG)copolymer has been prepared by an emulsion/evaporation process that lead to polymericnanoparticles containing several imaging agents, such as SPION, quantum dots (QDs)and gold nanorods as well as indomethacin (IMC) as therapeutic payload. With a similarprocedure, but using poly (lactide-co-glycolide) (PLGA-PEG-NH2) copolymer, a secondtype of multifunctional nanoparticles has been obtained. Their size can be tailored from70 to 150 nm varying synthesis parameters, such as the surfactant concentration or waterto oil ratio. Both these polymer-based multifunctional nanoparticles can be visualized byfluorescence microscopy (QDs photoemission) and MRI (SPION magnetization) and theycan be used for photothermal therapy (gold nanorods) and drug delivery. The last systemconsists of SPION nanoparticles coated with PLLA directly on the surface by an in-situpolymerization process. A hydrophobic drug was loaded before the phase transfer withPluronic F127 and these nanoparticles show simultaneous MRI T2 contrast enhancementas well as high drug loading and sustained delivery.Controlling the drug release rate is also a critical parameter for tailored therapeutictreatments, and for this reason we developed a novel drug delivery system based on theintegration of SPION and Pluronic F127 gels. IMC was loaded in the ferrogel (with atailored gelation temperature) and its release rate was triggered by applying an externalmagnetic field owing to the SPION magnetic properties. / QC 20101207

Cytochrome P450 (CYP) constitutes a superfamily of heme- containing enzymes that catalyze the oxidative biotransformation of structurally diverse xenobiotics including pharmaceuticals and drugs. Cytochrome P450 3A4 is not only the most abundant isoform in human liver but is also responsible for metabolizing approximately 60% of therapeutic drugs. This feature makes CYP3A4 highly susceptible to both reversible and irreversible, such as mechanism-based, inhibition. Mechanism-based inhibition is characterized by being time dependent as well as NADPH and concentration dependent, when some drugs are converted by CYPs to reactive metabolites. The inactivation of CYP3A4 can be due to chemical modification of the heme, the protein, or both by covalent binding of modified heme to the protein. Compared to reversible inhibition, mechanism-based inhibition of CYP3A4 more frequently causes unfavourable drug- drug interactions (DDI), as the inactivated CYP3A4 has to be replaced by newly synthesized CYP3A4 protein. DDI can lead to higher exposure of co-administered drugs, sometimes leading to toxicity. For these reasons, drug metabolism groups within pharmaceutical companies need a well established screening assay to assess mechanism-based inactivation of major human P450 enzymes by new chemical substances that are being developed by the company. Historically, adverse drug interactions were found in clinical trials or after the drugs were commercially released. That caused pharmaceutical companies large economical losses, since a large portion of development cost was in vain.Medivir AB is a small pharmaceutical company that would like to set up a screening method to be used to test candidate drugs for CYP3A4 mechanism-based inhibition. The central aim of this master degree project was to set up a screening assay to test irreversible inhibition of CYP3A4 and validate it with known inhibitors. Using the validated assay, a number of in-house project compounds will be measured for inhibition potential and the results analyzed for structure-activity correlations. Relationships between some functional groups and mechanism-based inhibition can provide insight for improvement of drug candidates and inhibition liability. The assay was based on microsomes containing recombinant human CYP3A4 and activity measured by conversion of the substrate dibenzylfluorescein into a fluorescent product. The product was quantified by measurement of fluorescence in a 96-well plate reader. Optimization was achieved by determining the reaction linearity with time and enzyme concentration. When possible the Km for the probe substrate was also determined. The effect of different backgrounds was studied to settle on a compensation for the enzyme activity. The effect of DMSO on CYP3A4 mediated metabolism of the substrate was studied to determine the acceptable solvent concentration. The concentration responsible for 50% inhibition (IC50) was also determined for several known inhibitors and compared with literature data. / The master thesis was performed at Medivir AB, a small pharmaceutical company in Stockholm.

The Thioredoxin (Trx) and Glutaredoxin (Grx) system are two major antioxidant redoxsystems in the cells that prevent and respond to oxidative stress, which is a well known factor in aging and causing several diseases, like neurodegenerative disorders, diabetes and cancer. Oxidative stress also can be described as an imbalance between production of reactive oxygen species (ROS) and the cellular protection. Thioredoxin Reductase (TrxR), a selenoproteine located both in the cytosol and the mitochondria, functioning as an electron donor for Trx, and also its mithochondrial form (TrxR2) it can be an electron donor for Grx2.   Lately, several studies has been showing Selenite, a highly oxidized form of selenium, a well known essential tracemineral and antioxidant,  to be a potential therapeutic drug in cancer treatment by inhibiting tumor growth and induce apoptosis in cytostatic drug-resistant malign cell-lines. Gold, and gold-containing drugs have a long history in medicine, and has been validated as potent TrxR inhibitors. In this study we have combined Selenite and a Goldcompound in treatment of Grx2-overexpressing HeLa cell-lines, and investigated the inhibiting effect on the Thioredoxin and Glutaredoxin system, and also how Grx2 would function without its electron donor, TrxR2. By using a quantitative polymerase chain reaction and for this, we have successfully optimized a TrxR2-primer, measured and compared the expression of mRNA levels of TrxR1, TrxR2, Grx2 and Grx2tot.We have also investigated the enzyme kinetics of Grx1 with selenocysteine, selenodiglutathione and selenomethylselenocystine, to see/ and found that  they could be a substrate for Grx1.

Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e. g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats. / <p>Part of urn:nbn:se:su:diva-8295</p>

In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many transmembrane helices (TMHs) in multispanning membrane proteins are not sufficiently hydrophobic to be recognized as such by the translocon. In this study, we have screened 16 marginally hydrophobic TMHs from membrane proteins of known three-dimensional structure. Indeed, most of these TMHs do not insert efficiently into the endoplasmic reticulum membrane by themselves. To test if loops or TMHs immediately upstream or downstream of a marginally hydrophobic helix might influence the insertion efficiency, insertion of marginally hydrophobic helices was also studied in the presence of their neighboring loops and helices. The results show that flanking loops and nearest-neighbor TMHs are sufficient to ensure the insertion of many marginally hydrophobic helices. However, for at least two of the marginally hydrophobic helices, the local interactions are not enough, indicating that post-insertional rearrangements are involved in the folding of these proteins. / <p>authorCount :12</p>

TOPCONS (http://topcons.net/) is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by approximately 10 percentage points. The web interface allows for constraining parts of the sequence to a known inside/outside location, and detailed results are displayed both graphically and in text format.

Background: In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct environments; a hydrophobic lipid environment inside the membrane, a hydrophilic water environment outside the membrane and an interface region rich in phospholipid head-groups. Therefore, it is energetically favorable for transmembrane proteins to expose different types of residues in the different regions. Results: Investigations of a set of structurally determined transmembrane proteins showed that the composition of solvent exposed residues differs significantly inside and outside the membrane. In contrast, residues buried within the interior of a protein show a much smaller difference. However, in all regions exposed residues are less conserved than buried residues. Further, we found that current state-of-the-art predictors for surface area are optimized for one of the regions and perform badly in the other regions. To circumvent this limitation we developed a new predictor, MPRAP, that performs well in all regions. In addition, MPRAP performs better on complete membrane proteins than a combination of specialized predictors and acceptably on water-soluble proteins. A web-server of MPRAP is available at http://mprap.cbr.su.se/ Conclusion: By including complete a-helical transmembrane proteins in the training MPRAP is able to predict surface accessibility accurately both inside and outside the membrane. This predictor can aid in the prediction of 3D-structure, and in the identification of erroneous protein structures. / <p>authorCount :3</p>

The pea (Pisum sativum) tetrameric short-chain alcohol dehydrogenase-like protein (SAD) family consists of at least three highly similar members (SAD-A, -B, and -C). According to mRNA data, environmental stimuli induce SAD expression. The aim of this study was to characterize the SAD proteins by examining their catalytic function, distribution in pea, and induction in different tissues. In enzyme activity assays using a range of potential substrates, the SAD-C enzyme was shown to reduce one- or two-ring-membered quinones lacking long hydrophobic hydrocarbon tails. Immunological assays using a specific antiserum against the protein demonstrated that different tissues and cell types contain small amounts of SAD protein that was predominantly located within epidermal or subepidermal cells and around vascular tissue. Particularly high local concentrations were observed in the protoderm of the seed cotyledonary axis. Two bow-shaped rows of cells in the ovary and the placental surface facing the ovule also exhibited considerable SAD staining. Ultraviolet-B irradiation led to increased staining in epidermal and subepidermal cells of leaves and stems. The different localization patterns of SAD suggest functions both in development and in responses to environmental stimuli. Finally, the pea SAD-C promoter was shown to confer heterologous wound-induced expression in Arabidopsis (Arabidopsis thaliana), which confirmed that the inducibility of its expression is regulated at the transcriptional level.

Probiotics is a special group of health products on the market. The most common type of  these is live cultures of lactic acid fermenting bacteria from raw milk . These include, among others, yogurt and various trademarks such as Hälsofil ®, Acidophilus ®, Dofilus ® and Kefir ®. Such products are often used by patients who are treated with antibiotics to combat the intestinal flora eliminated, thus causing digestive problems. The present work deals with yet another type of health product, viz. kefir of Tibetan type. A literature review of mainly Russian sources has been made to identify the nutrients and potential health benefits of kefir consumption in humans. The study sought to find data on the nutritional values of this very particular culture of a certain fungus, Zoogloea ramigera and some species of the genus Lactobacillus. However, this has not been found other than the data on the product, which is on the Swedish market under the brand Kefir, which is a product of a different nature than the Tibetan form of kefir. One source indicates, however, that among other things, it contains vitamin D, which would otherwise break down in this type of product. Part of the work is a study of the characteristics of the kefir culture for an intended technological process of production. The study shows that culture can be stored while maintaining viability by freezing to -70 ⁰ C. The culture is not affected by Gentamycin, which is a common antibiotic. Kefir culture tends to grow in the form of granules or lumps, which may be separated and reused for production. It is sensitive to metal ions, so that process equipment, intended for contact with kefir must be manufactured from other materials such as enamel or polymer-coated steel sheets. A study of cultural interaction with three different strains of intestinal bacteria showed very little impact on the cultivation on agar plate. In batch fermentation the pH of the kefir culture decreases to 3.4, which is slightly higher than the pKa of lactic acid. This pH is unfavorable for disease-causing bacteria and can be expected to limit growth of those in the human gastrointestinal tract upon ingestion.