Surface proteins on microorganisms that build up the oral biofilm are key players in the formation of the biofilm. Antigen I/II proteins are surface adhesins found on virtually all oral streptococci and share a conserved multi-domain architecture. These adhesins bind surface components on other bacteria and on host cells. Thus, they are crucial for the development of the biofilm.     The objective of this thesis work is the structural characterization of the large multi-domain Antigen I/II protein SspB from the primary colonizing commensal bacterium Streptococcus gordonii. The crystal structure of the variable domain of SspB was determined to 2.3 Å resolution. The domain comprises a β-supersandwich and a putative binding cleft stabilized by a calcium ion. Despite high similarity in the overall structure, the cleft within SspB is significantly smaller than the cleft within the homologous protein from Streptococcus mutans, indicating that different substrates may bind in the clefts. A screen for carbohydrate binding resulted in no hits for interaction with the SspB variable domain suggesting that the cleft may not be suitable for binding sugars. This thesis also presents the high resolution 1.5 Å structure of a truncated C-terminal domain of SspB, the first of an Antigen I/II C-domain. The structure contains two structurally related domains, each containing one calcium ion and one intramolecular isopeptide bond. The SspB protein shares the feature of intramoleular isopeptide bonds with other surface proteins from Gram positive bacteria, such as pili from Streptococcus pyogenes and Corynebacterium diphtheriae. Intramolecular isopeptide bonds are suggested to be a common feature for retaining stability in a harsh environment. The SspB adherence region, shown to be the recognition motif for Porphyromonas gingivalis attachment to S. gordonii, protrudes from the core protein as a handle available for recognition. In conclusion, this thesis work has provided new knowledge about the SspB protein and increased the understanding of the common structure of AgI/II proteins.

Starting with the structure analysis of ConA in the 70s, the crystal structures of hundreds of different lectins and their carbohydrate complexes have been determined. Lectins, multivalent carbohydrate-binding proteins which specifically bind different sugar structures, have received considerable attention in recent times on account of the realization of the importance of protein−sugar interactions, especially at the cell surface, in biological recognition. They occur in plants, animals, fungi, bacteria and viruses. Plant lectins constitute about 40% of the lectins of known structure. They can be classified into five structural groups, each characterized by a specific fold. Among them, legume lectins constitute the most extensively investigated group. Peanut lectin is a legume lectin which has been studied thoroughly in this laboratory. These studies have provided a wealth of structural and functional information. However, some gaps still exist in our understanding of the structure, interactions and multivalency of peanut lectin. The work presented here addresses these gaps. The hanging drop method was used for crystallizing PNA and its complexes. Intensity data were collected on Mar Research imaging plates mounted on Rigaku RU-200 or ULTRAX-18 X-ray generators. The Oxford cryosystem was used when collecting data at low temperature. The data were processed using DENZO and SCALEPACK of HKL suite of programs. The structure factors from the processed data were calculated using TRUCATE of CCP4 suite of programs. The molecular replacement program AMoRe was used for structure solutions. Structure refinements were carried out using the CNS software package and REFMAC of CCP4. Model building was done using the molecular graphics program FRODO. INSIGHT II, ALIGN, CONTACT and PROCHECK of CCP4 were used for the analysis and validation of the refined structure. Dynamic light scattering experiments were carried out using a Dyanpro Molecular Sizing Instrument, and the collected data were analyzed using Dynamic V6 software. Until recently, it has been possible to grow crystals of peanut lectin only when complexed with sugar ligands. It has now been possible to grow them at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of the peptides as well as lactose. Low pH crystal forms of the lectin−lactose complex similar to those obtained at neutral pH could also been grown. Thus, crystals of peanut lectin grown in different environmental conditions, at two pHs with and without sugars bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison among different structures shows that the lectin molecule is sturdy and the effect of changes in pH, ligand-binding and environment on it is small. The region involving the curved front β-sheet and loops around the second hydrophobic core is comparatively rigid. The back β-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible. So is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing rare structural features. Small, consistent movements occur in the combining site on sugar-binding, although the site is essentially preformed. Crystal structures of peanut lectin complexed with Galβ1-3Gal, methyl-T-antigen, Galβ1-6GalNAc, Galα1-3Gal and Galα1-6Glc and that of a crystal grown in the presence of Galα1-3Galβ1-4Gal have been determined using data collected at 100 K. Use of water bridges as a strategy for generating carbohydrate specificity was earlier deduced from the complexes of the lectin with lactose (Galβ1-4Glc) and T-antigen (Galβ1- 3GalNAc). This has been confirmed through the analysis of the complexes with Galβ1-3Gal and methyl-T-antigen (Galβ1-3GalNAc-α-OMe). A detailed analysis of lectin−sugar interactions in the complexes shows that they are more extensive when β-anomer is involved in the linkage. As expected, the second sugar residue is ill defined when the linkage is 1-6. There are more than two-dozen water molecules, which occur in the hydration shells of all structures determined at resolutions better than 2.5 Å. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin−sugar interactions are also substantially conserved. The lectin molecule is robust and does not appear to be affected by change in temperature. Multivalency is believed to be important in the activity of lectins, although definitive structural studies on it have been few and far between. A study has been carried out on the complexation of tetravalent peanut lectin with a synthetic compound containing two terminal lactose moieties, using a combination of crystallography, dynamic light scattering and modelling. Light scattering indicates the formation of an apparent dimeric species and also larger aggregates of the tetrameric lectin in the presence of the bivalent ligand. The crystals of presumably crosslinked lectin molecules could be obtained. They diffract very poorly, but the X-ray data from them are good enough to define the positions of the lectin molecules. Extensive modelling on possible crosslinking modes of protein molecules by the ligand indicated that systematic crosslinking could lead to crystalline arrays. The studies also provided a rationale for the crosslinking in the observed crystal structure. The results obtained provide further insights into the general problem of multivalency in lectins. They indicate that crosslinking involving multivalent lectins and multivalent carbohydrates is likely to lead to an ensemble of a finite number of distinct periodic arrays rather than a unique array. PNA is among the most thoroughly studied lectins. Its structure demonstrated that open structures without point group symmetry cannot be ruled out for oligomeric proteins. It also contributed to the identification of legume lectins as a family of proteins in which small alterations in essentially the same tertiary structure lead to large changes in the quaternary association. Among other things, studies on PNA−sugar complexes led to the identification of water bridges as a strategy for generating carbohydrate specificity in addition to providing detailed information on PNA−sugar interactions. The work reported here significantly added to the information on this important lectin provided by earlier studies. On the basis of a detailed examination of structures of crystals grown under different environmental conditions, the relatively rigid and flexible regions of the molecule could be delineated. The picture that emerges is that of a robust protein with a substantially preformed combining site. The work also added to the information on the dependence of protein−sugar interactions on the different glycosidic linkages in disaccharides. The investigations reported here also provided further insights into the multivalency of peanut lectin.

Starch is a water-insoluble glucose biopolymer used as an energy cache in plants and is synthesized and degraded in a diurnal cycle. Reversible phosphorylation of starch granules regulates the solubility and, consequentially, the bioavailability of starch glucans to degradative enzymes. Glucan phosphatases release phosphate from starch glucans and their activity is essential to the proper diurnal metabolism of starch. Previously, the structural basis of glucan phosphatase activity was entirely unknown. The work in this dissertation outlines the structural mechanism of activity of two plant glucan phosphatases called Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). The crystal structures of SEX4 and LSF2 were determined with and without phosphoglucan ligands bound, revealing the basis of their interaction with an endogenous substrate. The data show that SEX4 and LSF2 interact with starch glucans via distinctive mechanisms. SEX4 binds glucan chains via an aromatic-rich pocket spanning its Carbohydrate Binding Module (CBM) and catalytic Dual Specificity Phosphatase (DSP) domains. Conversely, LSF2 lacks a CBM and, instead, binds glucans at two non-catalytic surface-binding sites that are located distally from its active site. In addition, it was previously reported that SEX4 and LSF2 act upon distinct phospho-glucan substrates: SEX4 preferentially dephosphorylates the C6-position of starch glucans and LSF2 exclusively dephosphorylates the C3- position. The data herein reveal that SEX4 and LSF2 contain differences in their active site topology that serve to position the glucan chain in opposite orientations, therefore accounting for the differences in substrate specificity. Using these insights, SEX4 was engineered with reversed substrate specificity, i.e. preferential C3-specific activity. Previous work has established the interaction between phosphatases and protein, lipid, and nucleic acids; however, the current study represents the first insights into phosphatase interaction with carbohydrate substrates. In addition, the insights gained provide a model that will be used in future studies with the mammalian glucan phosphatase laforin, which is linked to neurodegeneration and the fatal epileptic disorder Laforaʼs Disease.

Endotoxin recognition by the innate immune receptor CD14 is a critical part of the innate immune system’s early detection and activation of the inflammatory response during microbial invasion. The differential recognition and high affinity binding of endotoxins from gram-negative and gram-positive bacteria is performed by the innate immune receptor CD14. Upon endotoxin binding, CD14 transfers the specific endotoxins to a Toll-like receptor signaling complex, which is responsible for initiating the intracellular signaling cascade. In the presence of overwhelming infection, the effects of CD14 lead to the over-activation of the inflammatory response, which results in the life threatening condition known as sepsis. Preparation of a 15N isotopically labeled truncated version of soluble CD14, using Pichia pastoris, allowed direct structural observation of the binding interaction between CD14 and two endotoxin ligands, lipopolysaccharide (LPS) and lipoteichoic acid (LTA), from gram-negative and gram-positive bacteria, respectively using solution NMR spectroscopy. These studies revealed that CD14 uses both a common set of residues, and endotoxin specific subsets of residues, to bind LPS and LTA. To further investigate the structural features of each endotoxin recognized by CD14, 13C 15N isotopically labeled Kdo2–Lipid A, a fully active chemically defined gram-negative endotoxin, and LTA lipid anchor, the minimal unit of LTA, were produced. This allowed detailed NMR spectral mapping of these agonist ligands bound to sCD14 which identified, for the first time, structural regions and features in each that are strongly affected during complex formation with sCD14. Additionally, the presence of differential dynamic behavior was seen in both CD14 and the ligands upon complexation. This behavior suggests a likely role for dynamics in the mechanism of pattern recognition by CD14, which uses the dynamic ability of specific residue combinations to differentially affect endotoxin binding. Using NMR, the dynamic behavior of CD14 was further investigated using temperature and pH-dependence studies of isotopically labeled CD14. These studies clearly demonstrated the presence of multiple conformations for several residues, and may provide a possible explanation for the broad specificity of ligand binding by CD14. In addition, the spin-labeling of isotopically labeled lipid A enabled the collection of intermolecular distances on CD14 bound lipid A.

<div>X-ray crystallography is a foundation of the modern structural biology. Thus, refinement of crystallographic structures remains an important and actively pursued area of research. We have built a software solution for refinement of crystallographic protein structures using X-ray diffraction data in conjunction with state-of-the-art MD modeling setup. This solution was implemented on the platform of Amber 16 biomolecular simulation package, making use of graphical processing unit (GPU) computing. The proposed refinement protocol consists of a short MD simulation, which represents an entire crystal unit cell containing multiple protein molecules and interstitial solvent. The simulation is guided by crystallographic restraints based on experimental structure factors, as well as conventional force-field terms. We assessed the performance of this new protocol against various refinement procedures based on the Phenix engine, which represents the current industry standard. The evaluation was conducted on a set of 84 protein structures with different realizations of initial models; the main criterion of success was free R-factor, R_free. Initially, we performed the re-refinement of the models deposited in the PDB bank. We found that in 58% of all cases our protocol achieved better R_free than Phenix. As a next step, we conducted the refinement on three different sets of lower-quality models that were manufactured specifically to test the competing algorithms (average C^α RMSD from the target structures 0.75, 0.89, and 1.02 Å). In these tests, our protocol outperformed the refinement procedures available in Phenix in up to 89% of all cases. Aside from R-factors, we also compared geometric qualities of the models as measured by MolProbity scores. It was found that our protocol led to consistently better geometries in all of the refinement comparisons.</div><div>Recently, a number of attempts have been made to fully utilize the information encoded in protein diffraction data, including diffuse scattering, which is dependent on molecular dynamics in the crystal. To understand the nature of this dependence, we have chosen three different crystalline forms of ubiquitin. By post-processing the MD data, we separated the effects from different types of motion on the diffuse scattering profiles. This analysis failed to identify any features of the diffuse scattering profiles that could be uniquely linked to certain specific motional modes (e.g. small-amplitude rocking motion of protein molecules in the crystal lattice). However, we were able to confirm the previous experimental observations, made in the combined X-ray diffraction and NMR study, suggesting that the amount of motion in the specific crystal is reflected in the amplitude of diffuse scattering.</div>

<p>Phospholipase Cs (PLCs) are a family of enzymes that hydrolyze membrane lipid phosphatidylinositol-4,5-bisphosphate (PIP2) to generate inositol triphosphate (IP3) and diacylglycerol (DAG). These second messengers activate a variety of intracellular responses, including inflammation, vascular smooth muscle contraction, and cardiac hypertrophy. While much is known about how Gaq-mediated activation of PLCb occurs, the same cannot be said for Gbg-mediated activation. Residues within the PLCb-Gbg binding interface were previously identified in interior regions of the protein, suggesting the PH domain must undergo a conformational change to allow for Gbg-mediated activation. However, the role of PH domain conformational dynamics in Gbg-mediated activation of PLCb has yet to be determined. In this work, I discuss efforts to characterize conformational dynamics of the PLCb PH domain and its role in interactions of the enzyme with liposomes and Gbg. First, I generated a disulfide crosslink between the PH domain and EF hands1/2 of PLCb3, purified under oxidizing or reducing conditions, and conducted biochemical and structural tests to determine any differences in structure and/or function of the protein as compared to wild-type. Results of these studies provided the first direct structural evidence of PLCb PH domain dynamics in solution. Then, I discuss the rationale behind the generation of a surface cysteine-less PLCb for use in solvatochromic fluorescence assays in the presence and absence of liposomes and Gbg. Initial results of these studies suggest the PLCb PH domain favors a buried conformation alone and in the presence of Gbg or liposomes, and likely exists at an equilibrium between open and closed states.</p>

Fabry disease is an X-linked lysosomal storage disease that results from a deficiency in the enzyme α-galactosidase (α-GAL). α-GAL hydrolyzes α-galactosides, and patients with Fabry disease suffer from an accumulation of these undegraded substrates. Human α-GAL naturally occurs as a homodimer, as determined through SEC and crystallographic analysis. This means its quaternary structure consists of two identical α-GAL subunits that are associated together into a single unit. Other species, such as rice, produce a monomeric form of α-GAL, consisting of only a single subunit. If α-GAL is functional as both a homodimer and monomer, then how does homodimerization affect the activity of human α-GAL? This can be answered through two model systems. First, a monomeric form of human α-GAL can be produced, testing the activity of human α-GAL in a monomeric state. A variant of α-GAL was engineered (called α-GALF273G/W277G) that appeared promising. Secondly, another system can be produced capable of stabilizing one active site of the dimer and testing the other active site for activity. Another lysosomal enzyme, α-N-acetylgalactosaminidase (α-NAGAL), shares 46% amino acid sequence identity and share 11 of 13 active site residues. Previously, an α-GAL variant (called α-GALE203S/L206A) was produced, that maintained the antigenicity of α-GAL, but had acquired the enzymatic specificity of α-N-acetylgalactosaminidase (α-NAGAL). A heterodimeric form of α-GAL can be produced combining one subunit of α-GAL with the engineered variant. The engineered site can be stabilized, while the wild-type site can be tested for activity. SEC analysis suggests α-GALF273G/W277G is a monomer, and its kinetic properties are reported. Evidence shows monomeric α-GAL could be useful as an improved enzyme replacement therapy. Western blotting and activity assays suggest the presence of the α-GAL/ α-GALE203S/L206A heterodimer.

<p>The cancer stem cell hypothesis claims that only a small subpopulation of cells within a tumor is responsible for tumor growth, recurrence after treatment and metastasis. These cells have been termed tumor-initiating cells or cancer stem cells and are functionally defined by their capacity to elicit the growth of tumors in immune-compromised animals that recapitulate the cellularity of the tumor from which they were isolated. Several reports demonstrate that tumor-initiating cells are resistant to most current treatments. Hence, novel therapies for breast cancer should be developed that specifically target these tumorigenic cells. The Notch signaling pathway is hyperactive in human breast cancer as well as in mouse mammary tumor-initiating cells. In this study, I have found that inhibitors of the pathway target breast tumor-initiating cells from various breast cancer subtypes and may provide a novel therapy for breast cancer. MRK-003, a gamma-secretase inhibitor that blocks Notch signaling, inhibited the self-renewal of breast tumor-initiating cells <em>in vitro</em> and reduced tumor growth in xenograft models. MRK-003 inhibited proliferation of tumor cells within xenografts and induced their apoptosis and differentiation towards the myoepithelial lineage. Expression of the Notch pathway antagonists led to similar outcome in human breast tumor cell lines. Notably, tumors in MRK-003 treated mice were devoid of tumor initiating cells, suggesting that inhibitors of Notch signaling may lead to durable cancer cures. These findings suggest that GSIs target breast tumor-initiating cells and may prove to be effective novel anti breast cancer drugs. <strong> </strong></p> <p><strong> </strong></p> / Doctor of Philosophy (PhD)

<p>Aggregation of the<strong> </strong>Alzheimer’s Aβ peptide in the brain and blood plasma is controlled by endogenous Aβ binding proteins. The structural basis for the interaction between the Aβ peptide and the Aβ binding proteins is critical not only to understand how Aβ amyloids are controlled in vivo, but also to guide the design of novel Aβ-self association inhibitors. However, the current knowledge of the structures of the Aβ/Aβ binding protein complexes is still sparse. This thesis focuses mainly on the interaction of the Aβ peptide with Human Serum Albumin (HSA). It is known that HSA binds ~90% of the Aβ in human plasma and prevents the Aβ self-association into amyloid fibrils. However, the mechanism of Aβ self-association inhibition by albumin was not understood prior to our work. We have shown that albumin preferentially binds toxic Aβ oligomers and fibrils inhibiting their growth into larger Aβ assemblies through a “monomer competitor” mechanism. Using a combination of NMR, domain deletion mutants, dynamic light scattering and ultrafiltration we have investigated the stoichiomery and affinity of the Aβ oligomer: HSA complexes. Our results indicate that all three domains of HSA bind Aβ oligomers and fibrils with an affinity in the 1-100 nM range. Such binding site degeneracy explains how albumin minimizes competition by other ligands such as fatty acids and drugs. Moreover we have used the soluble and NMR suitable domain 3 of albumin to dissect further the determinants of the Aβ oligomer binding to albumin at subdomain and peptide resolution. We show that both subdomains of the HSA domain 3 (<em>i.e</em>. 3A and 3B) bind the Aβ oligomers. In addition, we identified a peptide sequence within subdomain 3B that displays significant potency in the inhibition of Aβ self-association.</p> / Doctor of Philosophy (PhD)

<p>Sol-gel derived silica provides a bio-compatible material for the solid-phase entrapment of viable cells. A selection of <em>E. coli</em> cells containing unique promoter-linked GFP expression vectors were applied to fluorescence microwell plate assays, plate counting and various microscopy methods to assess changes in the entrapped bacteria and compatibility towards compound screening. Materials screening showed that a fastgelation sol-gel composition from sodium silicate precursor and PBS buffer provided a consistently greater fluorescence signal than non-entrapped cells. It is shown for the first time that entrapped cells are capable of dividing within pockets of the silica gel, and can di vide at a comparable rate to free cells. The entrapment of cells within a silica matrix does not induce the basal expression level of promoters tested here. Silica entrapment provides improved storage capabilities over non-entrapped cells in solution. A set of 12 related GFP-linked promoters were induced in solution and within silica when screened by two DNA gyrase inhibitors, providing similar expression profiles but greater signal-tonoise ratios in silica. The sol-gel derived material is amenable in an array format, and is a prospective material for the fabrication of sol-gel cell microarrays.</p> / Master of Science (MSc)