Enzyme selectivity means that the enzyme´s preferences towards competing substrates will be different. In this thesis, the enzyme selectivity has been studied for utilization in synthesis of functionalized macromonomers. The aim was to study how the inherent –or introduced – selectivity of lipases can be used to introduce thiol‐ or enefunctionalities into short polyesters. Thiol‐ and ene‐functionalized renewable organic precursor molecules in combination with thiol‐ene click chemistry opens up for a sustainable material production. Lipases do not normally affect ene‐moieties and the preference towards thiols is low, enabling introduction of these functional groups for further modifications. In addition, lipases have been shown to be good catalysts in the formation of polyesters, both via ring‐opening and polycondensation polymerization. In paper I Candida antarctica lipase B was used to end‐functionalize poly(ε‐caprolactone) with free thiols in a one‐pot reaction. The advantage of using achemoselective lipase as catalyst was that no protection of the thiol was needed. The chemoselectivity displayed by Candida antarctica lipase B turned out to be 88 000 in favour of the alcohol (paper II). Rhizomucor miehei lipase showed less pronounced chemoselectivity. The largest contribution to the selectivities was derived from the more than two orders of magnitude higer KM towards the thiol compared to the alcohol. Thiols can be cross‐linked with enes in radical reactions to form networks, enabling formation of materials. One promising renewable molecule containing an acrylate moiety is itaconic acid. In paper III the selectivity towards the two esters in dimethyl itaconate was investigated and the active site of Candida antarctica lipase B was redesigned to generate variants with increased and decreased selectivity. One variant showed 14‐fold higher selectivity and could regioselectively add dimethyl itaconate onto a diol. This variant could be used in end‐functionalizations of polymers, introducing acrylate‐ester end‐groups. The enzyme selectivity towards lactones and their corresponding polyesters is of importance when designing a ring‐opening polymerization reaction. In paper IV Candida antarctica lipase B was found to prefer ω‐pentadecalactone and polyesters over ε‐caprolactone ten‐fold, while Humicola insolens cutinase preferred ε‐caprolactone and its corresponding polyester four‐fold over ω‐pentadecalactone and its polyester. From a selectivity point of view, Candida antarctica lipase B and Humicola insolens cutinase would be equally good in ring‐opening polymerization of ω‐pentadecalactone, while in the case of ε‐caprolactone Humicola insolens cutinase would be the preferred choice. / QC 20110608

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<p>Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion.</p><p>Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures.</p><p>In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods.</p><p>The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments.</p><p>An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions.</p><p>An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops.</p><p>Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".</p>

<p>The aim of this work was to determine if the protein Majastridin found in the proteobacterium Rhodobacter blasticus has a functional relative in the hypothetical protein Q1U8S3/ B3XNV1 found in Lactobacillus reuteri. To be able to study the protein, it was overexpressed in  E. coli-cells and purified. As a starting material, the L. reuteri Q1U8S3 gene previously cloned into a pET SUMO vector from Invitrogen was used. The produced protein will be a fusion protein containing a His6-tag, a SUMO-protein and the protein of interest. A nickel column in combination with a gel filtration column was used to purify the protein and after purification, crystallization experiments were set up using standardized kits.</p>

Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion. Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures. In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods. The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments. An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions. An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops. Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".

<p>This thesis presents a novel bioinformatic methodology denoted the bio-chemometric approach. The methodology is designed for generation of detailed descriptions and predictions of biomolecular interactions. It is based on multivariate analysis of the sensitivity of a biomolecular interaction to multiple minor changes in the experimental conditions. In this work, either the chemical environment where the interaction takes place, or the molecular structure of one of the interacting molecules, was varied. The sensitivity of the interaction to the performed variations was presented as a vector called the sensitivity fingerprint. The bio-chemometric approach was tested on several biomolecular interactions. Useful descriptions of the interactions were obtained by measuring binding kinetics for each interaction in 12-20 different buffers and correlating buffer composition to binding kinetics. The obtained chemical sensitivity fingerprints were reproducible, significantly different and showed a weak correlation to binding site properties for the tested interactions. The results indicate that the fingerprints contained useful information about the binding site. The predictive ability of the bio-chemometric approach was tested on two different biomolecular interactions where one of the binding partners was slightly modified into multiple analogues by amino acid exchanges. In one example, interactions of 18 peptide analogues with an antibody gave data that could be used for accurate prediction of the dissociation rates of novel analogues. Reliable predictions of binding kinetics and affinity were also obtained for single domain camel antibody analogues binding to a protein antigen. By using the three-dimensional structure of camel antibodies and data obtained using the bio-chemometric approach, even the importance of non-exchanged amino acids for the binding could be estimated. The bio-chemometric approach can potentially improve the development of peptides and proteins for therapeutic and diagnostic use. It is suggested to be valid for general use in biochemistry.</p>

<p>The aim of this work was to understand the molecular mechanism of translation and the mechanism of translation termination, in particular. Cleavage of peptidyl-tRNA and peptide release terminates translation of mRNA on the ribosome. In prokaryotes, three release factors (RFs) are involved in this process. RF1 and RF2 recognise the three stop codons on mRNA and induce hydrolysis of the ester bond in peptidyl-tRNA. RF3 accelerates the rate of RF1 and RF2 recycling between ribosome in a GTP-dependent manner. We have clarified the mechanism of action of peptide release factor RF3. In the cell, free RF3 is in the GDP conformation. When RF3∙GDP binds to ribosome in complex with RF1 or RF2, these ribosome complexes act as guanine exchange factors for RF3 by inducing rapid dissociation of GDP. If, and only if, the peptide has been removed from tRNA, GDP is quickly replaced by GTP. Binding of GTP to RF3 induces a conformation of the factor with high affinity for the ribosome, which forces RF1 or RF2 to rapidly dissociate. Subsequent hydrolysis of GTP on RF3 induces a factor conformation with low affinity for the ribosome and rapid release of RF3∙GDP. It was further shown how the position of peptidyl-tRNA on the ribosome and the presence or absence of its peptide regulates the binding and GTPase activity of translation factors IF2, EF-G and EF-Tu. The result explains how idling GTPase hydrolysis and negative interference between different translation factors are minimized in living cells. The present biochemical observations, in conjunction with cryo-EM results, lead to new proposals for the role of hybrid sites in translocation of tRNAs, recycling of RF1 and RF2 by RF3 and recycling of post-termination ribosomes back to a new round of initiation.</p>

This thesis presents a novel bioinformatic methodology denoted the bio-chemometric approach. The methodology is designed for generation of detailed descriptions and predictions of biomolecular interactions. It is based on multivariate analysis of the sensitivity of a biomolecular interaction to multiple minor changes in the experimental conditions. In this work, either the chemical environment where the interaction takes place, or the molecular structure of one of the interacting molecules, was varied. The sensitivity of the interaction to the performed variations was presented as a vector called the sensitivity fingerprint. The bio-chemometric approach was tested on several biomolecular interactions. Useful descriptions of the interactions were obtained by measuring binding kinetics for each interaction in 12-20 different buffers and correlating buffer composition to binding kinetics. The obtained chemical sensitivity fingerprints were reproducible, significantly different and showed a weak correlation to binding site properties for the tested interactions. The results indicate that the fingerprints contained useful information about the binding site. The predictive ability of the bio-chemometric approach was tested on two different biomolecular interactions where one of the binding partners was slightly modified into multiple analogues by amino acid exchanges. In one example, interactions of 18 peptide analogues with an antibody gave data that could be used for accurate prediction of the dissociation rates of novel analogues. Reliable predictions of binding kinetics and affinity were also obtained for single domain camel antibody analogues binding to a protein antigen. By using the three-dimensional structure of camel antibodies and data obtained using the bio-chemometric approach, even the importance of non-exchanged amino acids for the binding could be estimated. The bio-chemometric approach can potentially improve the development of peptides and proteins for therapeutic and diagnostic use. It is suggested to be valid for general use in biochemistry.

The aim of this work was to understand the molecular mechanism of translation and the mechanism of translation termination, in particular. Cleavage of peptidyl-tRNA and peptide release terminates translation of mRNA on the ribosome. In prokaryotes, three release factors (RFs) are involved in this process. RF1 and RF2 recognise the three stop codons on mRNA and induce hydrolysis of the ester bond in peptidyl-tRNA. RF3 accelerates the rate of RF1 and RF2 recycling between ribosome in a GTP-dependent manner. We have clarified the mechanism of action of peptide release factor RF3. In the cell, free RF3 is in the GDP conformation. When RF3∙GDP binds to ribosome in complex with RF1 or RF2, these ribosome complexes act as guanine exchange factors for RF3 by inducing rapid dissociation of GDP. If, and only if, the peptide has been removed from tRNA, GDP is quickly replaced by GTP. Binding of GTP to RF3 induces a conformation of the factor with high affinity for the ribosome, which forces RF1 or RF2 to rapidly dissociate. Subsequent hydrolysis of GTP on RF3 induces a factor conformation with low affinity for the ribosome and rapid release of RF3∙GDP. It was further shown how the position of peptidyl-tRNA on the ribosome and the presence or absence of its peptide regulates the binding and GTPase activity of translation factors IF2, EF-G and EF-Tu. The result explains how idling GTPase hydrolysis and negative interference between different translation factors are minimized in living cells. The present biochemical observations, in conjunction with cryo-EM results, lead to new proposals for the role of hybrid sites in translocation of tRNAs, recycling of RF1 and RF2 by RF3 and recycling of post-termination ribosomes back to a new round of initiation.