No description available.

Chemical complementation is a general system for detecting protein-small molecule interactions, and linking that interaction to genetic selection. In this chemical complementation system, the interaction of a nuclear receptor and a ligand is essential for yeast survival. In first generation chemical complementation, a two-component assay was developed where the Gal4 DNA-binding domain is fused to the ligand binding domains of nuclear receptors, and expressed in the strain S.cerevisiae PJ69-4A. The Gal4 DNA binding domain binds to a Gal4 response element controlling transcription of a selective marker, and the nuclear receptor ligand-binding domain binds its ligand. This system was developed using the retinoid X receptor, the pregnane X receptor, and the liver X receptor and their ligands 9-cis retinoic acid, paclitaxel, and oxysterols, respectively. Yeast survive on selective plates only in the presence of both components: a nuclear receptor and the corresponding ligand. Growth was observed at the highest concentration of ligand (10-5 M) and, compared to Gal4-activated growth, the growth density was less and growth time was more. The second generation chemical complementation system is a three-component system comprising a nuclear receptor ligand-binding domain fused to the Gal4 DNA binding domain, the ligand, and a nuclear receptor coactivator fused to the yeast Gal4 activation domain. This system was developed using the retinoid X receptor and has been extended to several other nuclear receptors. The sensitivity of chemical complementation is increased 1000-fold, and growth time and density are equivalent to Gal4-activated growth. An assay was developed to provide a quantitative high-throughput assay for evaluating nuclear receptor- ligand interactions, and measuring EC50 values for the ligand-receptor pairs. Chemical complementation can be used in a variety of applications, such as drug discovery for nuclear receptor-based disease, providing a high-throughput assay for the discovery of potential nuclear receptor agonists, and with the use of the negative chemical complementation system, the discovery of nuclear receptor antagonists. Chemical complementation is used for protein engineering, specifically engineering receptors to bind and activate in response to other ligands. Chemical complementation is also used for deciphering and assembling biosynthetic pathways.

Biocatalysis is an ever evolving field that uses enzymes or microorganisms for chemical synthesis. By utilizing enzymes that generally have evolved for specific reactions under mild conditions and temperatures, biocatalysis can be a more environmentally friendly option compared to traditional chemistry. Amide-type chemistries are important and bond formation avoiding poor atom economy is of high priority in organic chemistry. Biocatalysis could potentially be a solution but restricted substrate scope is a limitation. Esterases/lipases usually display broad substrate scope and catalytic promiscuity but are poor at hydrolyzing amides compared to amidases/proteases. The difference between the two enzyme classes is hypothesized to reside in one key hydrogen bond present in amidases, which facilitates the transition state for nitrogen inversion during catalysis. In this thesis the work has been focused on introducing a stabilizing hydrogen bond acceptor in esterases, mimicking that found in amidases, to develop better enzymatic catalysts for amide-based chemistries. By two strategies, side-chain or water interaction, variants were created in three esterases that displayed up to 210-times increased relative amidase specificity compared to the wild type. The best variant displayed reduced activation enthalpy corresponding to a weak hydrogen bond. The results show an estimated lower limit on how much the hydrogen bond can be worth to catalysis. MsAcT catalyze kinetically controlled N-acylations in water. An enzymatic one-pot one-step cascade was developed for the formation of amides from aldehydes in water that gave 97% conversion. In addition, engineered variants of MsAcT with increased substrate scope could synthesize an amide in water with 81% conversion, where the wild type gave no conversion. Moreover, variants of MsAcT displayed up to 32-fold change in specificity towards amide synthesis and a switch in reaction preference favoring amide over ester synthesis. / <p>QC 20161125</p>

Enzyme engineering relies on changes in the amino acid sequence of an enzyme to give rise to improvements in catalytic activity, substrate specificity, thermostability, and enantioselectivity. However, beneficial amino acid substitutions in proteins are difficult to rationally predict. Large numbers of enzyme variants containing random amino acid substitutions are screened in a high throughput manner to isolate improved enzymes. Identifying improved enzymes from the resulting library of randomized variants is a current challenge in protein engineering. This work focuses on the development of high-throughput screens for a class of enzymes called hydrolases, and in particular, proteases and esterases. In the first part of this work, we have developed an assay for detecting protease activity in the cytoplasm of Escherichia coli by exploiting the SsrA protein degradation pathway and flow cytometry. In this method, a protease-cleavable linker is inserted between a fusion protein consisting of GFP and the SsrA degradation tag. The SsrA-tagged fusion protein is degraded in the cell unless a co-expressed protease cleaves the linker conferring higher cellular fluorescence. The assay can detect specific cleavage of substrates by TEV protease and human caspase-8. To apply the screen for protease engineering, we sought to evolve a TEV protease variant that has altered P1 specificity. However, in screening enzyme libraries, the clones we recovered were found to be false positives in that they did not express protease variants with the requisite specificities. These experiments provided valuable information on physiological and chemical parameters that can be employed to optimize the screen for directed evolution of novel protease activities. In the second part of this work, single bacterial cells, expressing an esterase in the periplasm, were compartmentalized in aqueous droplets of a water-in-oil emulsion also containing a fluorogenic ester substrate. The primary water-in-oil emulsion was then re-emulsified to form a water-in-oil-in-water double emulsion which was capable of being analyzed and sorted by flow cytometry. This method was used to enrich cells expressing an esterase with activity towards fluorescein dibutyrate from an excess of cells expressing an esterase with no activity. A 50-fold enrichment was achieved in one round of sorting, demonstrating the potential of this method for use as a high-throughput screen for esterase activity. This method is suitable for engineering esterases with novel catalytic specificities or higher stabilit / text

The creation of artificial enzymes to catalyze desired reactions is a major goal of computational protein design. However, de novo enzymes display low catalytic efficiencies, requiring the introduction of activity-enhancing active site and distal mutations through directed evolution. A better understanding of how mutations introduced by directed evolution contribute to increased enzymatic activity will guide the development of design methods such that efficient enzymes can be designed de novo. Here, we evaluate the structural, functional, and dynamical impacts of active site and distal mutations introduced by directed evolution of the de novo retro-aldolase RA95, an enzyme that presents an important case study in enzyme design due to the significant structural remodelling that was observed during evolution. We observe that the variant RA95-Core, containing only active site mutations introduced by directed evolution, displays activity within one order of magnitude of the fully evolved variant. This suggests that computational enzyme design methods can be improved to create much more efficient enzymes than what was previously achieved in RA95. However, structural changes induced by distal mutations prevent computational recapitulation of the evolved active site on the original design template, indicating that the optimized active site identified through directed evolution could not have been designed de novo using current design methodologies. We suggest strategies for the incorporation of backbone remodelling into design procedures that would allow recapitulation of the evolved retro-aldolase active site, as well as the de novo design of highly efficient enzymes without the need for optimization by directed evolution.

Raman spectroscopy records the inelastic scattering of photons originating from striking a sample with monochromatic light. Inelastic, or Raman, scattered photons shift in wavelength due to excitation of the vibrational modes of molecules struck by the incident light. The Raman scattered photons are representative of all of the covalent bonds contained within a sample. Raman spectra taken of biological systems such as proteins, bacterial colonies, and liquid waste, are difficult to interpret due to the complexity of their covalent bond landscape and mixtures of molecules in highly variable concentrations. Rather than deconstructing Raman spectra to attempt assignment of specific bonds and functional groups to wavenumber peaks, here we have developed a chemometric analysis pipeline for quantifying the similarities and differences among a set of Raman spectra. This quantification aids in both classification of samples, and in measuring how samples change over time. The chemometric approach for interpretation of Raman spectra was made freely available in a user-friendly format via a MATLAB add-on called the Raman Data Analysis (RDA) Toolbox. Demonstrations of the RDA Toolbox functionalities on Raman spectra taken of various common biological systems are included, such as determination of protein concentration and monitoring bacterial culture growth. The RDA Toolbox and Raman spectroscopy are also used to initiate research in novel areas. Fast and accurate evaluation of enzyme specific activity is required for engineering enzymes, and results of Raman assays, evaluated in the RDA Toolbox, are successfully correlated to absorbance activity assays of an enzyme WT and mutant library. Further development of this research could alleviate the bottleneck of screening mutant libraries in enzyme engineering projects. The Toolbox is then used in a distinctly different application for evaluating urine and spent dialysate samples from patients with end stage renal disease. Categorization between samples from healthy volunteers and patients is accomplished with close to 100% accuracy, and evidence indicating that Raman spectroscopy can serve as an early diagnostic tool for infections of the peritoneal membrane is presented. / PHD / Raman spectroscopy, unlike other forms of spectroscopy, provides a complete picture of the chemical make-up of a sample. However, Raman spectra of biological samples are very difficult to interpret due to the complex mixture of molecules in living systems. Rather than trying to discern what specific molecules are in a sample, we have developed a method for measuring the similarities and differences among a set of Raman spectra. These measurements help us classify samples and monitor how samples change over time. We made a MATLAB add-on called the Raman Data Analysis (RDA) Toolbox to automate our method for interpreting Raman spectra, and made it available online for anyone to download and use. Raman spectroscopy and the RDA Toolbox are used to measure enzyme reaction speed, and the results compare favorably with a traditional method for measuring enzyme reaction speed. The final part of this dissertation focuses on using Raman spectroscopy and the RDA Toolbox to evaluate the health of patients with end stage renal disease (ESRD) by scanning urine and spent dialysate samples to detect failing kidney function or the onset of infection.

No description available.

The use of enzymes as catalysts for chemical transformations has emerged as a “greener” alternative to traditional organic synthesis. An issue to solve though, is that enzymes are designed by nature to catalyze reactions in a living cell and therefore, in many cases, do not meet the requirements of a suitable biocatalyst. By mimicking Darwinian evolution these problems can be addressed in vitro by different types of directed evolution strategies. α-Hydroxy aldehydes and α-hydroxy ketones are important building blocks in the synthesis of natural products, fine chemicals and pharmaceuticals. In this thesis, two alcohol dehydrogenases, FucO and ADH-A, have been studied. Their potentials to serve as useful biocatalysts for the production of these classes of molecules have been investigated, and shown to be good. FucO for its strict regiospecificity towards primary alcohols and that it strongly prefers the S-enantiomer of diol substrates. ADH-A for its regiospecificity towards secondary alcohols, its enantioselectivity and that is has the ability to use a wide variety of bulky substrates. The kinetic mechanisms of these enzymes were investigated using pre-steady state kinetics, product inhibition, kinetic isotope effects and solvent viscosity effects, and in both cases, the rate limiting steps were pin-pointed to conformational changes occurring at the enzyme-nucleotide complex state. These characterizations provide an important foundation for further studies on these two enzymes.   FucO is specialized for activity with small aliphatic substrates but is virtually inactive with aryl-substituted compounds. By the use of iterative saturation mutagenesis, FucO was re-engineered and several enzyme variants active with S-3-phenylpropane-1,2-diol and phenylacetaldehyde were obtained. It was shown that these variants capability to act on larger substrates are mainly due to an enlargement of the active site cavity. Furthermore, several amino acids which are important for catalysis and specificity were identified. Phe254 interacts with aryl-substituted substrates through π-π stacking and may be essential for activity with these larger substrates. One mutation caused a loss in the interactions made between the enzyme and the nucleotide and thereby enhanced the turnover number for the preferred substrate

The substrate selectivities for different serine hydrolases were utilized in various applications, presented in papers I-VI. The articles are discussed in the thesis in view of the kinetics of the enzyme catalysis involved. In paper I the enantioselectivities towards a range of secondary alcohols were reversed for Candida antarctica lipase B by site directed mutagenesis. The thermodynamic components of the enantioselectivity were determined for the mutated variant of the lipase. In papers II-III Candida antarctica lipase B was engineered for selective monoacylation using two different approaches. A variant of the lipase created for substrate assisted catalysis (paper II) and three different variants with mutations which decreased the volume of the active site (paper III) were evaluated. Enzyme kinetics for the different variants were measured and translated into activation energies for comparison of the approaches. In papers IV and V three different enzymes were used for rapid analysis of enantiomeric excess and conversion of O-acylated cyanohydrins synthesized by a defined protocol. Horse liver alcohol dehydrogenase, Candida antarctica lipase B and pig liver esterase were sequentially added to a solution containing the O-acylated cyanohydrin. Each enzyme caused a drop in absorbance from oxidation of NADH to NAD+. The product yield and enantiomeric excess was calculated from the relative differences in absorbance. In paper VI a method for C-terminal peptide sequencing was developed based on conventional Carboxypeptidase Y digestion combined with matrix assisted laser desorption/ionization mass spectrometry. An alternative nucleophile was used to obtain a stable peptide ladder and improve sequence coverage. / QC20100629

Enzymes are gaining increasing importance as catalysts for selective transformations in organic synthetic chemistry. The engineering and design of enzymes is a developing, growing research field that is employed in biocatalysis. In the present thesis, combinatorial protein engineering methods are applied for the development of Candida antarctica lipase A (CALA) variants with broader substrate scope and increased enantioselectivity. Initially, the structure of CALA was deduced by manual modelling and later the structure was established by X-ray crystallography. The elucidation of the structure of CALA revealed several biocatalytically interesting features. With the knowledge derived from the enzyme structure, enzyme variants were produced via iterative saturation mutagenesis (ISM), a powerful protein engineering approach. Several of these variants were highly active and enantioselective towards bulky esters. Furthermore, an extensively combinatorial protein engineering approach was developed and investigated. A CALA variant with a spacious substrate binding pocket that can accommodate an unusually bulky substrate, an ester derivate of the non-steroidal anti-inflammatory drug (S)-ibuprofen, was obtained with this approach. / At the time of the doctoral defence the following paper was unpublished and had a status as follows: Paper nr. 5: Manuscript