Single cell migration in artificial collagen gels as an in vitro model system in the context of cancer are studied. Cell and matrix mechanical properties are determined using atomic force microscopy and an advanced analysis method. Matrix pore-size is studied using a novel approach and analysis method. A novel, minimally invasive approach to determine the amount of displacement of the cell microenvironment due to force generation of single cells during migration in artificial 3D collagen gels is introduced. An automated analysis and user friendly software to analyze high-throughput cell invasion is introduced. These methods are used to study cell migration and mechanical properties of the breast cancer cell lines MDA-MB-231 and MCF-7 and the influence of cell nuclear elasticity is investigated. Using mouse embryonic fibroblasts, the role of focal adhesion kinase (FAK) during cell migration is studied using FAK deficient knock-out cell lines FAK-/- and control FAK+/+ as well as kinase-dead mutants FAKR454/R454 and control FAKWT/WT.:Abstract i Acknowledgements iii 1 Introduction 1 2 Background 5 2.1 Cancer — An ever-changing Disease 5 2.1.1 Carcinogenesis and Neoplasm 6 2.1.2 Hallmarks of Cancer 7 2.1.3 Metastasis— The malignant Progression of Cancer 7 2.1.4 Metastatic Cascade 9 2.2 The Cell— Where it begins 10 2.2.1 Actomyosin Complex 12 2.2.1.1 Actin Monomer 12 2.2.1.2 Polymerization 12 2.2.1.3 Structures 14 2.2.1.4 Actin Cortex 15 2.2.1.5 Filopodia 16 2.2.1.6 Lamellipodium 16 2.2.1.7 Invadopodium 17 2.2.1.8 Stress Fibers 17 2.2.1.9 Actin in Cancer and Metastasis 17 2.2.1.10 Myosin and Actin 18 2.2.2 Focal Adhesions 19 2.2.3 Microtubules 20 2.2.4 Intermediate Filaments 21 2.2.5 Cellular Stiffness 22 2.2.6 Nuclear Deformability 23 2.3 The Extracellular Matrix— Where it happens 24 2.3.1 Components and Structure 25 2.3.2 Collagen as a Model System 26 2.3.2.1 Collagen I Fibril Formation 27 2.3.2.2 The Rat/Bovine-Collagen-Mix Model System 28 2.4 Single Cell Migration— Why it spreads 29 3 Materials and Methods 31 3.1 Cell Culture 31 3.1.1 Cancer Cells 31 3.1.2 Mouse fibroblasts 32 3.1.3 Pharmacological treatment 34 3.2 Collagen matrices 34 3.3 Cell Elasticity 36 3.3.1 Atomic Force Microscopy 36 3.3.2 Preparation 37 3.3.3 Data Aquisition 38 3.3.4 Data Analysis 38 3.4 Matrix Stiffness 40 3.4.1 Preparation 40 3.4.2 Data Aquisition 41 3.4.3 Data Analysis 41 3.5 Invasion Assay 42 3.5.1 Preparation 42 3.5.2 Data aquisition 44 3.5.3 Data Analysis 44 3.6 Matrix Topology 48 3.6.1 Preparation 49 3.6.2 Data Acquisition 50 3.6.3 Data Analysis 51 3.6.3.1 Binarization 51 3.6.3.2 Pore-Size 53 3.6.3.3 Fiber Thickness 54 3.7 Fiber Displacement 55 3.7.1 Preparation 56 3.7.2 Data Aquisition 56 3.7.3 Data analysis 57 3.7.3.1 Fiber Displacement 59 3.7.3.2 Cell Segmentation 60 3.7.3.3 Shell Analysis 61 3.8 A toolset to understand Single Cell Migration and what influences it 62 4 Results 65 4.1 Cell Elasticity 65 4.1.1 Example Force-Distance Curves 66 4.1.2 Single Cell Elasticity 67 4.2 Matrix Stiffness 69 4.3 Invasion 71 4.4 Matrix Topology 75 4.5 Influence of Cell Nucleus on Cell Migration 79 4.5.1 Cellular Elasticity 79 4.5.2 Invasion 81 4.6 Fiber Displacement 89 4.7 Effect of FAK on Cell Invasion and Fiber Displacement 93 4.7.1 FAK Knock-Out 93 4.7.2 Kinase-dead FAK Mutant 96 5 Discussion 103 References 107 / Die Einzelzellmigration in künstlichen Kollagennetzwerken als ein in vitro Modellsystem im Kontext von Krebs wurde studiert. Mechanische Eigenschaften von Zellen und der verwendeten Kollagennetzwerke wurden mithilfe der Atomic Force Microscopy (AFM) und weiterentwickelten Analysemethoden bestimmt. Die Porengröße der verwendeten Kollagennetzwerke wurde mit einer neuentwickelten Auswertemethode analysiert. Eine neuartige, minimal-invasive Methode zur Bestimmung der Verformung der Mikroumgebung von Zellen während der Migration verursacht durch Kräftegenerierung der Zelle wird beschrieben. Die Analyse des Invasions-Assays wurde automatisiert und eine nutzerfreundliche Software entwickelt, mit der große Datenmengen ausgewertet werden können. Diese Methoden wurden verwendet, um mechanische Eigenschaften und Migration der humanen Brustkrebszellinien MDA-MB-231 und MCF-7 zu studieren. Die Rolle der focal adhesion kinase (FAK) wurde mithilfe von embryonalen Maus-Fibroblasten studiert. Sowohl eine FAK knock-out Zellinie FAK-/- und Kontrolle FAK+/+, als auch eine kinase-dead Mutante FAKR454/R454 und Kontrolle FAKWT/WT wurden hinsichtlich ihrer Invasion und Verformung der Mikroumgebung analysiert.:Abstract i Acknowledgements iii 1 Introduction 1 2 Background 5 2.1 Cancer — An ever-changing Disease 5 2.1.1 Carcinogenesis and Neoplasm 6 2.1.2 Hallmarks of Cancer 7 2.1.3 Metastasis— The malignant Progression of Cancer 7 2.1.4 Metastatic Cascade 9 2.2 The Cell— Where it begins 10 2.2.1 Actomyosin Complex 12 2.2.1.1 Actin Monomer 12 2.2.1.2 Polymerization 12 2.2.1.3 Structures 14 2.2.1.4 Actin Cortex 15 2.2.1.5 Filopodia 16 2.2.1.6 Lamellipodium 16 2.2.1.7 Invadopodium 17 2.2.1.8 Stress Fibers 17 2.2.1.9 Actin in Cancer and Metastasis 17 2.2.1.10 Myosin and Actin 18 2.2.2 Focal Adhesions 19 2.2.3 Microtubules 20 2.2.4 Intermediate Filaments 21 2.2.5 Cellular Stiffness 22 2.2.6 Nuclear Deformability 23 2.3 The Extracellular Matrix— Where it happens 24 2.3.1 Components and Structure 25 2.3.2 Collagen as a Model System 26 2.3.2.1 Collagen I Fibril Formation 27 2.3.2.2 The Rat/Bovine-Collagen-Mix Model System 28 2.4 Single Cell Migration— Why it spreads 29 3 Materials and Methods 31 3.1 Cell Culture 31 3.1.1 Cancer Cells 31 3.1.2 Mouse fibroblasts 32 3.1.3 Pharmacological treatment 34 3.2 Collagen matrices 34 3.3 Cell Elasticity 36 3.3.1 Atomic Force Microscopy 36 3.3.2 Preparation 37 3.3.3 Data Aquisition 38 3.3.4 Data Analysis 38 3.4 Matrix Stiffness 40 3.4.1 Preparation 40 3.4.2 Data Aquisition 41 3.4.3 Data Analysis 41 3.5 Invasion Assay 42 3.5.1 Preparation 42 3.5.2 Data aquisition 44 3.5.3 Data Analysis 44 3.6 Matrix Topology 48 3.6.1 Preparation 49 3.6.2 Data Acquisition 50 3.6.3 Data Analysis 51 3.6.3.1 Binarization 51 3.6.3.2 Pore-Size 53 3.6.3.3 Fiber Thickness 54 3.7 Fiber Displacement 55 3.7.1 Preparation 56 3.7.2 Data Aquisition 56 3.7.3 Data analysis 57 3.7.3.1 Fiber Displacement 59 3.7.3.2 Cell Segmentation 60 3.7.3.3 Shell Analysis 61 3.8 A toolset to understand Single Cell Migration and what influences it 62 4 Results 65 4.1 Cell Elasticity 65 4.1.1 Example Force-Distance Curves 66 4.1.2 Single Cell Elasticity 67 4.2 Matrix Stiffness 69 4.3 Invasion 71 4.4 Matrix Topology 75 4.5 Influence of Cell Nucleus on Cell Migration 79 4.5.1 Cellular Elasticity 79 4.5.2 Invasion 81 4.6 Fiber Displacement 89 4.7 Effect of FAK on Cell Invasion and Fiber Displacement 93 4.7.1 FAK Knock-Out 93 4.7.2 Kinase-dead FAK Mutant 96 5 Discussion 103 References 107

Malonyl-thioesters are reactive at the thioester carbonyl and the carboxylate moieties, as seen in acyl transfer or hydrolysis and decarboxylation. Enzymes use these reactive centers to perform different enzyme chemistry throughout metabolism. This enzyme chemistry coupled with the inherent reactivity of malonyl-thioesters makes structure-function studies difficult. When malonyl-thioesters are used for structure-function studies, it usually results in a hydrolyzed or decarboxylated product. There are examples, however, where this is overcome, many of which are discussed throughout this thesis. To overcome the inherent reactivity of malonyl-thioesters and enzymes, analogs have been synthesized to perform structure-function studies. Initial studies focused on altering the thioester carbonyl to limit hydrolysis and decarboxylation; however, these studies revealed the importance of retaining the thioester carbonyl to be positioned in the oxyanion hole. My thesis work focused on the synthesis, characterization, and use in structure-function studies of malonyl-thioester analogs that either preserve the thioester carbonyl or alter it to an ester or amide, and alter the carboxylate to a sulfonate or nitro group. After synthesizing the methylmalonyl-CoA analogs, we performed structure-function studies with methylmalonyl-CoA decarboxylase. This case study revealed the potential of these analogs to both inhibit decarboxylase activity and their use in structure-function studies to gain mechanistic insights. This successful study prompted us to continue these structure-function studies in enzymes with different chemistries such as an epimerase or bi-functional acyltransferase/decarboxylase. The widespread use of these methylmalonyl-CoA analogs also motivated us to add more malonyl-thioester analogs to our toolbox. I have preliminary data that these malonyl-thioester analogs inhibit β-keto-acyl-synthase III, an enzyme involved in fatty acid production in <i>E. coli</i>. This inhibition gives us confidence that these analogs will be useful in structure-function studies that will reveal answers to long standing mechanism and protein-protein interaction questions in the polyketide and fatty acid synthase field.

Os óleos essenciais da Pimenta pseudocaryophyllus (Gomes) Landrum de planta de populações naturais de três ecossistemas, localizados na Ilha de Cananéia, região de restinga, no Morro da Cataia, cidade de Cajati, região de encosta, ambas em área de Mata Atlântica, e na Reserva Natural Morro Grande, cidade de Caldas, região de campos montanos, foram avaliados como promotores de permeação cutânea do diclofenaco de potássio. Os óleos essenciais foram extraídos de partes aéreas das plantas e o rendimento do processo foi entre 0,90% (p/p) e 2,7% (p/p). A análise da composição química mostrou diferenças, indicando tratar-se de três quimiotipos diferentes. A interação dos óleos essenciais e dos componentes majoritários com membrana biológica natural foi avaliada por FT-Raman e ATR- FTIR, indicando a interação com as porções lipídicas do tecido. Foram desenvolvidas seis membranas biológicas artificiais, compostas por ceramidas, ácidos graxos e colesterol em proporções equimolares, que foram caracterizadas por espectroscopia Raman confocal e foram consideradas semelhantes. As membranas foram utilizadas no desenvolvimento do sistema PAMPA (Parallel Artificial Membrane Permeability Assay) para avaliar a segurança e eficácia dos óleos essenciais e componentes majoritário como promotores de permeação do diclofenaco de potássio. Os resultados dos ensaios com o sistema PAMPA foram estatisticamente avaliados. A segurança foi avaliada com o critério de permeação mínima dos óleos através das membranas do sistema PAMPA, verificada pela absorbância mínima do eugenol na solução aceptora. Os óleos essenciais e componentes majoritários foram utilizados no pré-tratamento das membranas, nas concentrações de 0,125%, 0,25%, 0,50% e 2,00% (v/v) em etano!. Ensaios de permeação do diclofenaco de potássio no sistema PAMPA indicaram efeito de promoção da permeação para todos os compostos avaliados. O método de doseamento do fármaco por UV foi validado e utilizado para os ensaios de permeação de formulações de gel em base aquosa contendo o diclofenaco de potássio (1,0% p/p). As amostras de gel foram preparadas com o óleo procedente de Morro Grande, selecionado na etapa de avaliação de segurança, a 0,125% (p/v). Adicionalmente, foram preparadas formulações com citronelol e etanol, na mesma concentração. O óleo essencial da Reserva Natural Morro Grande teve efeito de promoção da permeação superior ao do citronelol e etanol, que foram equivalentes. / The essential oils of the species Pimenta pseudocaryophyllus (Gomes) Landrum collected from natural populations of three existing ecosystems in the Cananéia Island, located at sea level, Cajati city, located in hillside region, both in the Atlantic Forest areas, as well as species collected in the Morro Grande Natural Reserve, region of montane fields, were evaluated as skin permeation enhancers of potassium diclofenac. Essential oils were extracted from the aerial parts of the plants and the process yield was between of 0.90% (w/w) and 2.7% (w/w). The chemical composition analysis showed differences between the plants of three origins, indicating that they are different chemotypes. The interaction of the essential oils and their major components with natural biological membrane was evaluated by FT- Raman and ATR-FTIR, indicating interaction with the Iipid portions of the natural membrane. Six artificial biological membranes have been developed, consisting of ceramides, cholesterol and fatty acids in equimolar proportions, which were characterized by confocal Raman spectroscopy and found to be similar. The membranes were used in developing the PAMPA (Parallel Artificial Membrane Permeability Assay) system to evaluate the safety of the potential permeation enhancers. The test results with PAMPA system were statistically evaluated. Safety was evaluated with the criterion of minimum permeation of the essential oil through the membranes, checked by the minimum absorbance of eugenol in the acceptor solution. The essential oils and the major components were used in the pretreatment of the membranes, at concentrations of 0.125%, 0.25%, 0.50% and 2.00% (v/v) in ethanol. Results indicated permeation enhancement effect for ali compounds evaluated. The analytical method for the quantification of potassium diclofenac was validated and used for the evaluation of the permeation of aqueous based gel formulations containing potassium diclofenac (1.0% w/w). The gel samples were prepared with the oil from Morro Grande Natural Reserve, selected in the safety evaluation step, at 0.125% (w/v). In addition, formulations were prepared with citronellol and ethanol at the same concentration. The essential Gil of Morro Grande Natural Reserve was more efficient as permeation enhancer than citronellol and ethanol under the test conditions.

Os óleos essenciais da Pimenta pseudocaryophyllus (Gomes) Landrum de planta de populações naturais de três ecossistemas, localizados na Ilha de Cananéia, região de restinga, no Morro da Cataia, cidade de Cajati, região de encosta, ambas em área de Mata Atlântica, e na Reserva Natural Morro Grande, cidade de Caldas, região de campos montanos, foram avaliados como promotores de permeação cutânea do diclofenaco de potássio. Os óleos essenciais foram extraídos de partes aéreas das plantas e o rendimento do processo foi entre 0,90% (p/p) e 2,7% (p/p). A análise da composição química mostrou diferenças, indicando tratar-se de três quimiotipos diferentes. A interação dos óleos essenciais e dos componentes majoritários com membrana biológica natural foi avaliada por FT-Raman e ATR- FTIR, indicando a interação com as porções lipídicas do tecido. Foram desenvolvidas seis membranas biológicas artificiais, compostas por ceramidas, ácidos graxos e colesterol em proporções equimolares, que foram caracterizadas por espectroscopia Raman confocal e foram consideradas semelhantes. As membranas foram utilizadas no desenvolvimento do sistema PAMPA (Parallel Artificial Membrane Permeability Assay) para avaliar a segurança e eficácia dos óleos essenciais e componentes majoritário como promotores de permeação do diclofenaco de potássio. Os resultados dos ensaios com o sistema PAMPA foram estatisticamente avaliados. A segurança foi avaliada com o critério de permeação mínima dos óleos através das membranas do sistema PAMPA, verificada pela absorbância mínima do eugenol na solução aceptora. Os óleos essenciais e componentes majoritários foram utilizados no pré-tratamento das membranas, nas concentrações de 0,125%, 0,25%, 0,50% e 2,00% (v/v) em etano!. Ensaios de permeação do diclofenaco de potássio no sistema PAMPA indicaram efeito de promoção da permeação para todos os compostos avaliados. O método de doseamento do fármaco por UV foi validado e utilizado para os ensaios de permeação de formulações de gel em base aquosa contendo o diclofenaco de potássio (1,0% p/p). As amostras de gel foram preparadas com o óleo procedente de Morro Grande, selecionado na etapa de avaliação de segurança, a 0,125% (p/v). Adicionalmente, foram preparadas formulações com citronelol e etanol, na mesma concentração. O óleo essencial da Reserva Natural Morro Grande teve efeito de promoção da permeação superior ao do citronelol e etanol, que foram equivalentes. / The essential oils of the species Pimenta pseudocaryophyllus (Gomes) Landrum collected from natural populations of three existing ecosystems in the Cananéia Island, located at sea level, Cajati city, located in hillside region, both in the Atlantic Forest areas, as well as species collected in the Morro Grande Natural Reserve, region of montane fields, were evaluated as skin permeation enhancers of potassium diclofenac. Essential oils were extracted from the aerial parts of the plants and the process yield was between of 0.90% (w/w) and 2.7% (w/w). The chemical composition analysis showed differences between the plants of three origins, indicating that they are different chemotypes. The interaction of the essential oils and their major components with natural biological membrane was evaluated by FT- Raman and ATR-FTIR, indicating interaction with the Iipid portions of the natural membrane. Six artificial biological membranes have been developed, consisting of ceramides, cholesterol and fatty acids in equimolar proportions, which were characterized by confocal Raman spectroscopy and found to be similar. The membranes were used in developing the PAMPA (Parallel Artificial Membrane Permeability Assay) system to evaluate the safety of the potential permeation enhancers. The test results with PAMPA system were statistically evaluated. Safety was evaluated with the criterion of minimum permeation of the essential oil through the membranes, checked by the minimum absorbance of eugenol in the acceptor solution. The essential oils and the major components were used in the pretreatment of the membranes, at concentrations of 0.125%, 0.25%, 0.50% and 2.00% (v/v) in ethanol. Results indicated permeation enhancement effect for ali compounds evaluated. The analytical method for the quantification of potassium diclofenac was validated and used for the evaluation of the permeation of aqueous based gel formulations containing potassium diclofenac (1.0% w/w). The gel samples were prepared with the oil from Morro Grande Natural Reserve, selected in the safety evaluation step, at 0.125% (w/v). In addition, formulations were prepared with citronellol and ethanol at the same concentration. The essential Gil of Morro Grande Natural Reserve was more efficient as permeation enhancer than citronellol and ethanol under the test conditions.

La thérapie génique et l'interférence par l'ARN sont des méthodes pleines de promesses pour le traitement de nombreux troubles génétiques et infections virales, mais ce sont aussi des outils polyvalents pour l'étude des mécanismes génétiques et épigénétiques à la base du bon fonctionnement ou dysfonctionnement des cellules et des organismes complexes. Toutefois, la délivrance intracellulaire d'acides nucléiques reste un obstacle majeur pour la mise en œuvre de ces thérapies. En dépit des progrès récents dans le domaine, il existe un nombre limité d'agents de transfection non viraux qui ont passé à la phase clinique de la mise au point de médicaments. Un agent de transfection efficace forme un complexe (généralement non-covalent) avec des acides nucléiques, qui est stable dans l'environnement extracellulaire, en particulier dans le plasma sanguin. En outre, il doit favoriser la délivrance cellulaire en interagissant avec la membrane plasmique ou avec des glycosaminoglycanes chargés négativement et induire l'absorption par endocytose du complexe de transfection. Enfin, l’agent de transfection devrait améliorer l'échappement de l'endosome et le dépaquetage des acides nucléiques à partir du complexe. Les peptides amphiphiles et cationiques, qui ont la capacité de pénétrer dans les cellules, possèdent toutes les caractéristiques ci-dessus nommées. En effet, ils s’associent aux acides nucléiques via des liaisons électrostatiques, ils se lient de manière efficace et traversent la membrane plasmique en favorisant l'absorption de la cargaison. LAH4-L1 est le peptide de la famille LAH4 riche en lysines et histidines, possédant une activité de transfection d’ADN et de pARNi prometteuse. Ce qui a été montré dans des expériences biologiques sur des cellules en culture. Le peptide LAH4-L1 présente des modes d'interaction différents avec les membranes à pH neutre et acide, ce qui est l'une des caractéristiques les plus importantes puisqu’elle assure une libération efficace des acides nucléiques dans le cytoplasme. Ce travail est dédié à l'étude des caractéristiques structurales et thermodynamiques de l'association LAH4-L1 avec des membranes modèles et des acides nucléiques, comme l'ADN générique et de pARNi. Une grande variété de techniques biophysiques, telles que la résonance magnétique nucléaire, le dichroïsme circulaire, la calorimétrie de titration isotherme, la diffusion dynamique de la lumière et le dosage d'efflux de la calcéine, a été utilisée pour élucider le mécanisme de la transfection cellulaire efficace par le peptide LAH4-L1. / Gene and RNA-based therapies have a great promise as the methods for the treatment of variety of the genetic disorders and viral infections, but also it is a versatile tool for the investigation of the genetic and epigenetic mechanisms underlying the proper functioning or dysfunctioning of the cells and complex organisms. However, intracellular delivery of nucleic acids remains a major hurdle for the implementation of these therapies. In spite of the recent progress in the field, there is limited number of the non-viral transfection agents that passed to the clinical phase of the drug development.An efficient transfection agent forms a complex (usually non-covalent) with nucleic acids, which is stable in the extracellular environment, in particular in the blood plasma. Furthermore, it should promote the cellular delivery by interacting with the plasma membrane or negatively charged glycosaminoglycans and inducing the endocytic uptake of the transfection complex. Finally transfection agent should enhance the endosomal escape and unpacking of the nucleic acids from the complex.Cationic amphipathic cell-penetrating peptide comprise all above-named features as they associate electrostatically with the nucleic acids, they bind efficiently and translocate plasma membrane promoting the cargo uptake. LAH4-L1 is the lysine and histidine-rich designed peptide from LAH4 family, possessing a promising DNA and siRNA transfection activity, which was shown in biological experiments on the cell culture. LAH4-L1 peptide displays different modes of interaction with the membranes at neutral and acidic pH, which is one of the most important features that assure an efficient nucleic acid release to the cytoplasm.This works is dedicated to the investigation of structural and thermodynamic characteristics of the LAH4-L1 association with model membranes and nucleic acids, such as generic DNA and siRNA. The variety of the biophysical techniques, as nuclear magnetic resonance, circular dichroism, isothermal titration calorimetry, dynamic light scattering and calcein efflux assay, were used to unravel the mechanism of efficient cellular transfection by LAH4-L1 peptide.

N-glycosylation is the most common eukaryotic post-translational modification, impacting on protein stability, folding, and protein-protein interactions. More broadly, N-glycans play biological roles in reaction kinetics modulation, intracellular protein trafficking, and cell-cell communications. The machinery responsible for the initial stages of N-glycan assembly and processing is found on the membrane of the endoplasmic reticulum. Following N-glycan transfer to a nascent glycoprotein, the enzyme Processing α-Glucosidase I (GluI) catalyzes the selective removal of the terminal glucose residue. GluI is a highly substrate-specific enzyme, requiring a minimum glucotriose for catalysis; this glycan is uniquely found in biology in this pathway. The structural basis of the high substrate selectivity and the details of the mechanism of hydrolysis of this reaction have not been characterized. Understanding the structural foundation of this unique relationship forms the major aim of this work. To approach this goal, the S. cerevisiae homolog soluble protein, Cwht1p, was investigated. Cwht1p was expressed and purified in the methyltrophic yeast P. pastoris, improving protein yield to be sufficient for crystallization screens. From Cwht1p crystals, the structure was solved using mercury SAD phasing at a resolution of 2 Å, and two catalytic residues were proposed based upon structural similarity with characterized enzymes. Subsequently, computational methods using a glucotriose ligand were applied to predict the mode of substrate binding. From these results, a proposed model of substrate binding has been formulated, which may be conserved in eukaryotic GluI homologs.

N-glycosylation is the most common eukaryotic post-translational modification, impacting on protein stability, folding, and protein-protein interactions. More broadly, N-glycans play biological roles in reaction kinetics modulation, intracellular protein trafficking, and cell-cell communications. The machinery responsible for the initial stages of N-glycan assembly and processing is found on the membrane of the endoplasmic reticulum. Following N-glycan transfer to a nascent glycoprotein, the enzyme Processing α-Glucosidase I (GluI) catalyzes the selective removal of the terminal glucose residue. GluI is a highly substrate-specific enzyme, requiring a minimum glucotriose for catalysis; this glycan is uniquely found in biology in this pathway. The structural basis of the high substrate selectivity and the details of the mechanism of hydrolysis of this reaction have not been characterized. Understanding the structural foundation of this unique relationship forms the major aim of this work. To approach this goal, the S. cerevisiae homolog soluble protein, Cwht1p, was investigated. Cwht1p was expressed and purified in the methyltrophic yeast P. pastoris, improving protein yield to be sufficient for crystallization screens. From Cwht1p crystals, the structure was solved using mercury SAD phasing at a resolution of 2 Å, and two catalytic residues were proposed based upon structural similarity with characterized enzymes. Subsequently, computational methods using a glucotriose ligand were applied to predict the mode of substrate binding. From these results, a proposed model of substrate binding has been formulated, which may be conserved in eukaryotic GluI homologs.