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A hallmark of Alzheimer's disease (AD) is the accumulation of insoluble senile plaques in the brain.[1] The major component of the insoluble plaques is the amyloid-β peptide (Aβ) that is produced through cleavage of the amyloid-β precursor protein (APP).[2] It is well understood that once the monomeric Aβ is generated, it has the potential to aggregate into soluble oligomers and further into insoluble fibrils. Recently it has been proposed that early oligomers are the main toxic species in the aggregation cascade.[3] However, it has been shown that the formation of toxic early oligomers is inhibited by several endogenous plasma proteins, including albumin and transferrin (Tf). In this investigation we are focusing on the mechanism of inhibition of the Aβ early oligomerization by Tf. Specifically, we have targeted the early stages of Aβ aggregation using a deletion mutant of the Aβ peptide, i.e. the Aβ12-28 fragment, which selectively stabilizes the early Aβ oligomers. Self-association of this peptide was controlled by adding-NaCl to filtered monomeric Aβ samples and the effect of Tf inhibition on these aggregates was probed by 1H relaxation NMR experiments.[4-7] Our data shows that Tf directly targets intermediary Aβ oligomers via a coating mechanism. 1. Kirkitadze, M.D., Condron, M.M. and Teplow, D.B, JMB 2001 312;1103-1119. 2. Stefan F. Lichtenthaler and Christian Haass, JCI 2004 113(10);1384-1387. 3. Necula M., Kayed R., Milton, S. and Glabe C.G, JBC 2007 282(14);10311-10324. 4. Klement K., Wieligmann K., Meinhardt J., Hortschansky P., Richter W., and Fändrich M., JMB 2007 373;1321-1333. 5. Huang H, Milojevic J, Melacini G. J Phys Chem B. 2008 112(18):5795-802. 6. Milojevic J, Esposito V, Das R, Melacini G. JACS. 2007 129(14):4282-90. 7. Milojevic J, Esposito V, Das R, Melacini G. J Phys Chem B. 2006 110(41):20664-70. / Thesis / Master of Science (MSc)

Understanding transport of water molecules and salt ions from a molecular level up to macroscopic length scales is critical to the design of novel materials for many applications, including separations membranes for fuel cell and desalination applications, as well as rechargeable battery technology. This work aims to investigate and develop new models correlating the dynamics and structure of polymeric materials, to the transport of small molecules within them, using a variety of Nuclear Magnetic Resonance (NMR) techniques. We present three studies through which we utilize two chemically similar membranes: hydroxyethyl acrylate-co-ethyl acrylate (HEA-co-EA) and hydroxymethyl methacrylate-co-methyl methacrylate (HEMA-co-MMA), which greatly differ in glass transition temperature, in order to understand the fundamental relationships from polymer chain dynamics and small molecule diffusion. From observations of the micron scale diffusion of these materials we find that the more dynamic, rubbery HEA-co-EA exhibits lower water to salt selectivity than HEMA-co-MMA, and that this difference arises from nanoscale morphology of the materials. From this, we propose a new model for hydrophilic pathways inside polymeric materials consisting of nanometer scale interconnected pathways are interrupted by micron scale arrangements of so-called "dead ends". We also for the first time show the separation of material tortuosity into two regimes, ranging from the nanometer-bulk and micron-bulk length scales. We further separate the contributions of structure from chemical interactions in the chemically similar desalination materials by investigating the local activation energy of diffusion in both materials, as well as aqueous solutions of the hydrophilic monomers analogous to the internal membrane environment. We find that the effects of local geometric confinement are very similar between the two materials, however the intermolecular interactions between water and the hydrophilic monomers, with respect to water transport, are significantly different between the two hydrophilic species. Geometric confinement accounts for a 5 ± 1 kJ/mol increase in diffusive activation energy from solution to membrane for both chemistries, and a 4 ± 1 kJ/mol difference in activation energy is seen between the two chemistries in both solution and membrane form. We propose that the entropic contributions to transport, are strongly impacted by the rigid environment of the HEMA material, and is related to the increased water-salt selectivity, as well as the increasing selectivity with increased ionic size observed compared to the HEA system. Using Dynamic NMR spectroscopy, we further investigate the differences seen in water-monomer intermolecular proton exchange by NMR. We utilize an iterative least-squares solving method to fit our exchange lineshape to a model of an uncoupled, two-site exchange lineshape in order to obtain rate and equilibrium population data from -50 to 70 °C. We find that, similar to the diffusive activation energy, the HEA-water system shows reduced enthalpy and entropy of the transition state compared to HEMA-water, such that there is faster exchange between HEMA and water at all temperatures measured, in addition to more biased populations in the HEA-water system. / Doctor of Philosophy / Understanding transport of water molecules and salt ions from a molecular level up to macroscopic length scales is critical to the design of novel materials for many applications, including separations membranes for fuel cell and desalination applications, as well as rechargeable battery technology. This work aims to investigate and develop new models correlating the dynamics and structure of polymeric materials, to the transport of small molecules within them, using a variety of Nuclear Magnetic Resonance (NMR) techniques. We will present three studies in which we seek to further understand the relationships between a material's physical and chemical properties, with the behavior of small molecules like water absorbed within the material. NMR spectroscopy, while not the standard method for characterizing desalination membranes, allows us to specifically probe direct effects on molecular motion of polymer structure from the microscopic level to the bulk, a feat not easily achieved by any other single technique. The first study presented within focuses on the differences in micrometer scale structure in two near identical sets of materials; differing only in that one is rubbery with flexible polymer chains, and the other is rigid with relatively immobile polymer chains. The second study takes these two materials and investigates them through a different lens, probing the molecular scale differences in water motions imparted by the flexible versus rigid polymer chains. The third and final study looks into the fundamental differences seen in how the two chemistries used to create the polymers in the first two studies interact with water molecules through a different NMR technique. These three studies together represent a series of methods and techniques that can be applied to many other classes of polymer materials, such as those destined for use in fuel cells and rechargeable batteries, in order to better understand the fundamental forces at work in those systems to aid in the design of the next generation's materials.

Yes / Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base-paired DNA duplexes and a Hoogsteen base-paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA-like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′-S-phosphorothiolate (3′-SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. 1H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′-SP modifications is more compact. The 3′-SP modification was previously shown to stabilise G-quadruplex and i-motif structures and therefore is now proposed as a generic solution to stabilising multi-stranded DNA structures.

No / Polysaccharides interact with cells in ways that can be conducive to wound healing. We have recently reported that konjac glucomannan (KGM) which is comprised of D-mannose and D-glucose linked by beta-1,4 glycosidic chains, stimulates fibroblast proliferation. The aim of this study was to produce a range of crosslinked KGMs and bicomponent KGM containing hydrogels and to examine their potential for wound healing. Two types of KGM hydrogel were synthesized, biodegradable from crosslinked KGM and non-biodegradable by forming semi-IPNs and graft-conetworks with a second synthetic component, poly(N-vinyl pyrrolidinone-co-poly(ethyleneglycol) diacrylate) (P(NVP-co-PEGDA)), which was produced by UV initiated radical polymerization. Crosslinked KGM was formed by bimolecular termination of macro-radicals formed by oxidation with Ce(IV). Semi-IPNs were formed by copolymerization of NVP and PEGDA in the presence of KGM and in the graft-conetworks the KGM was also crosslinked using the Ce(IV) procedure. The hydrogels had different swelling properties and differences could be observed in their chemical structure using C-13 solid state NMR, DSC and FTIR. Both forms were cytocompatible but only the graft-conetworks had the ability to stimulate fibroblast metabolic activity and to stimulate the migration of both fibroblasts and keratinocytes. In conclusion a form of KGM hydrogel has been produced that could benefit wound healing.

Yes / Diffusion ordered 1H-NMR spectroscopy (DOSY) is a useful, non-destructive technique for analysing polymer hydrodynamic size and intrinsic/solution viscosity. However, to date there has been no investigation of DOSY under variable temperature conditions that allow trends in polymer conformation to be determined. Poly(2-ethyl-2-oxazoline) (P(EtOx)) is a hydrophilic polymer that has the potential to replace poly(ethylene glycol) (PEG) in biomedical applications. Applying DOSY to a series of narrow-distribution P(EtOx) revealed that the apparent hydrodynamic radii scaled with molecular weight as expected. By altering the temperature of the solution the trends in Flory-type exponents were determined, enabling the determination of the power laws related to the coil-globule conformation of linear polymers directly from NMR data. These measurements were complicated by the onset of convection currents at higher temperatures, which impose a limit to the effective measurement range of ca. 10–35 °C. It was revealed that P(EtOx) had a more expanded random coil conformation than PEG, and it trended towards θ conditions at the lower critical solution temperature. In comparison, PEG was approximately in θ-conditions at room-temperature. This shows the use, and limitations of DOSY in polymer conformation analysis, and applies it to P(EtOx), a polymer which has not been analysed in this manner before. / University of Ghent (Grant Number: RM1602-1695)

Pantothenate synthetase (PS), which catalyzes the last step in the pantothenate (vitamin B5) biosynthesis, is a dimeric enzyme present in bacteria, fungi and plants. The enzymatic properties of PS from Escherichia Coli, Mycobacterium tuberculosi, Fusarium Oxysporum, Lotus japonicus, Oryza sativum, Brassica napus and Arabidopsis thaliana have been characterized. The chemical reaction and the proposed mechanism of reaction are identical for PS, irrespective of the source. However, from an enzyme mechanistic point of view, plant PS’s are dissimilar to their bacterial counterparts, in that they exhibit “allosteric behavior”, a property that has not been observed in the bacterial enzyme. The behavior is quite remarkable when one takes into consideration the fact that plant PS’s share a high degree of sequence identity (~ 40%) with the bacterial enzymes. Even more intriguing is the structural mechanism proposed to explain the observed differences in structure between the PS’s from E.Coli and M.tb, which share a 42% sequence identity. Till date there is no structural information available on the plant PS’s and of the substrate bound conformation of E.coli PS. This thesis aims to provide an understanding on some aspects of the structure – function relationship of this physiologically important enzyme. Specifically, the solution properties of E. coli PS have been examined using high-resolution multinuclear, multidimensional NMR methods. Given the large size of the full-length protein (~ 63 KDa), the structurally distinct N and C-terminal domains were cloned and expressed as individual proteins and their properties investigated. Towards this end, the tertiary fold of the 40 kDa dimeric amino-terminal domain of E. coli pantothenate synthetase has been determined using multidimensional multinuclear nuclear magnetic resonance (NMR) methods (PDB entry 2k6c). Sequence specific resonance assignments for backbone HN, 15N, 13Cα, 13C', sidechain 13Cβ and aliphatic 13CH3 (of isoleucine, leucine and valine residues) were obtained using perdeuterated ILV-methyl protonated samples (BMRB entry 6940). Secondary structure of nPS was determined from 13C secondary chemical shifts and from short and medium range NOEs. Global fold of the 40 kDa homo-dimeric nPS has been determined using a total of 1012 NOEs, 696 dihedral angles, 260 RDCs, 155 hydrogen bonds, radius of gyration potential, non-crystallographic symmetry potential and database derived potential based upon the Ramachandran map. The calculated structures, which show that the N-terminal domain forms a homo-dimer in solution, is of high stereochemical quality as judged by the Ramachandran statistics (70% of the residues have backbone dihedral angles in the allowed region, 25.5% in the additionally allowed region, 4.0% in generously allowed region, and only 0.5% in disallowed region). Dynamics of nPS, which has rotational correlation time τc of 17.3 ns, was investigated by 15N relaxometry measurements. Results of these studies indicate that the E. coli protein exhibits dynamic nature at the dimer interface. These structural and dynamic features of the protein were found to be of interest when correlated with NMR based substrate binding studies. Interaction of homo-dimeric amino-terminal domain (nPS) of E. coli pantothenate synthetase (PS; encoded by the gene panC; E.C. 6.3.2.1) with the substrates pantoate, β-alanine, ATP and the product pantothenate has been studied using isotopically edited solution NMR methods. Addition of pantoate prior to ATP has led to the interesting observation that pantoate binds each monomer of nPS at two sites. ATP displaces a molecule of pantoate from the ATP binding site. β-alanine and pantothenate do not bind the protein under the condition studied. Binding of pantoate and ATP also manifests as changes in residual dipolar couplings (RDCs) of backbone 1H-15N pairs in nPS when compared to the free form of the protein. Structures of homo-dimeric nPS bound to two molecules of pantoate (PDB entry 2k6e) as well as to pantoate + ATP (PDB entry 2k6f) were calculated by inclusion of hydrogen bonds between the ligands and backbone 1H-15N pairs of nPS in addition to other NMR derived restraints. The ligand bound structures have been compared to the similar forms of the M. tb PS. Structure of each monomer of nPS bound to pantoate and ATP shows the substrates in a favorable orientation for the intermediate pantoyl adenylate to form. Moreover, at all stages of substrate binding the symmetry of the dimer was preserved. A single set of resonances was observed for all protein-ligand complexes implying symmetric binding with full-occupancy of the ligands bound to the protein. In an effort to understand the structural basis of the observed enzymatic properties of plant PS’s, a structural model of the Arabidopsis PS was constructed. The results of these structural and substrate binding studies strongly suggest that 1 Substrate binding to PS occurs only at the active site. 2 There are no additional substrate binding sites which could potentially participate as regulatory sites. 3 Pantoate does not bind at the dimer interface to induce the observed homotropic effects. 4 The structural results presented on the substrate bound forms of nPS have direct implication for the development of novel antibacterial and herbicidal agents. Recently a great deal of interest has been evinced on the effects of molecular crowding on protein folding / unfolding pathways. Nuclear magnetic resonance is the only method by which high resolution structural information can be obtained on partially denatured states of a protein under equilibrium condition. Recent methodological advances have enabled the determination of high resolution structures using information embedded in the residual dipolar couplings. Molecular crowding using confinement may thus reveal important details about chaperone mediated protein folding. We have attempted to develop a protocol to study the effects of molecular confinement by sequestering proteins in poly-acrylamide gels and then subjecting these protein molecules to denaturation and then characterize these states by nuclear magnetic resonance. The preliminary results of these studies are described here.

Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative, non-invasive and non-destructive technique useful in biological studies. By manipulating the magnetization of nuclei with non-zero spin, NMR gives insights into atomic level details. Application of NMR as a tool for discovering structure, understanding dynamics of bio-molecules such as proteins, metabolites, DNA, RNA and their interactions constitutes the field of bio-molecular NMR. In this thesis, new methods for rapid data analysis of NMR spectrum of proteins and metabolites are proposed. The first computational method, PROMEB (Pattern Recognition Based Assignment in Metabolomics) is useful for the identification and assignments of metabolites. This is an important step in metabolomics and is necessary for the discovery of new biomarkers. In NMR spectroscopy based studies, the conventional approach involves a database search, wherein chemical shifts are assigned to specific metabolites by use of a tolerance limit. This is inefficient because deviation in chemical shifts associated with pH or temperature variations, as well as missing peaks, impairs a robust comparison with the database. These drawbacks are overcome in PROMEB, which is a method based on matching the pattern of peaks of a metabolite in 2D [13C, 1H] HSQC NMR spectrum, rather than conventionally used absolute tolerance thresholds. A high success rate is obtained even in the presence of large chemical shift deviations such as 0.5 ppm in 1H and 3 ppm in 13C and missing peaks (up to 50%), compared to nearly no assignments obtained under these conditions with existing methods that employ a direct database search approach. The pattern recognition approach thus helps in identification and assignment of metabolites in-dependent of the pH, temperature, and ionic strength used, thereby obviating the need for spectral calibration with internal or external standards. Another computational method, ChemSMP(Chemical Shifts to Metabolic Path-ways), is described which facilitates the identification of metabolic pathways from a single two dimensional (2D) NMR spectrum. Typically in other approaches, this is done after relevant metabolites are identified to allow their mapping onto specific metabolic pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a uniqueness score and a coverage score. Benchmarks show that ChemSMP has a positive prediction rate of > 90% in the presence of decluttered data and can sustain the same at 60 − 70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of metabolic pathways. The third method developed is a new approach for rapid resonance assignments in proteins based on amino acid selective unlabeling. The method involves choosing a set of multiple amino acid types for selective unlabeling and identifying specific tripeptides surrounding the labeled residues from specific 2D NMR spectra in a combinatorial manner. The methodology directly yields sequence specific resonance assignments, without requiring a contiguously assigned stretch of amino acid residues to be linked, and is applicable to deuterated proteins. The fourth method involves a simple approach to rapidly identify amino acid types in proteins from a 2D NMR spectrum. The method is based on the fact that 13Cβ chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the 13C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their 13Cβ chemical shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The 13C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not re-quire the preparation of any additional samples, involves the analysis of 2D [15N,1H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. Finally, the practical application of these methods for laboratory research is presented. PROMEB and ChemSMP is used to study cancer cell metabolism in previously unexplored oncogenic cell line. PROMEB helped in assigning a differential metabolite present at high concentration in cancer cell line compared to control non-cancerous cell line. ChemSMP revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells which were previously reported in literature. The two methods developed for rapid protein resonance assignments can be used in applications such as identifying active-site residues involved in ligand binding, phosphorylation, or protein-protein interactions. The phase modulated experiments will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process. Both the methodology was applied to two proteins: Ubiquitin (8 kDa) and L-IGFBP2 an intrinsically disordered protein (12 kDa), for demonstrating rapid resonance assignment using only set of 2D NMR experiments.

The overall goal of my work was to develop and apply new chemical methods for the study of epigenetic DNA and protein modifications. In Chapter 3 the development of Suzuki-Miyaura cross coupling (SMcc) for the post-synthetic modification of DNA is described. DNA modification by SMcc is efficient (4-6h) and proceeds under mild conditions (37°C, pH 8.5). The incorporation of various groups useful for biological investigations is demonstrated using this methodology. Using a photocrosslinker, introduced into the DNA by SMcc capture experiments are performed to identify potential binding partners of modified DNA. In Chapter 4 a dehydroalanine (Dha) based chemical protein modification method is described that enables the introduction of posttranslational modification (PTM) mimics into histones. The PTM mimics introduced by this method are tested using western- and dot-blot and binding and enzymatic assays, confirming they function as mimics of the natural modifications. Chapter 5 describes the use of a generated PTM mimics to elucidate the function of O-linked β-Nacetylglucosamine (GlcNAc) of histones in transcriptional regulation. It is shown that GlcNAcylation of Thr-101 on histone H2A can destabilize nucleosome by modulating the H2A/B dimer – H3/H4 tetramer interface. N- and C-terminal histone tails play an important role in transcriptional regulation. In Chapter 6, nuclear magnetic resonance is used to investigate the structure of the histone H3 N-terminal tail in a nucleosome. The H3 tail, while intrinsically disordered, gains some α-helical character and adopts a compact conformation in a nucleosome context. This H3 tail structure is shown to be modulated by Ser-10 phosphorylation. The effect of a new covalent DNA modification, 5- hydroxymethylcytosine (5hmC), on transcription factor binding is investigated in Chapter 7. 5hmC influences HIF1α/β, USF and MAX binding to their native recognition sequence, implying involvement of this modification in epigenetic regulation.

Nuclear Magnetic Resonance (NMR) and computational methods increasingly play a predominant and indispensable role in modern chemical research. The insights into the local nuclear environment that NMR can provide is unique information which allows the structural characterization of novel materials, as well as the understanding and explanation of their relevant properties on an atomic scale. Computational methods, on the other hand, can be used to support experimental findings, providing a rigorous theoretical basis. Furthermore, when more complex chemical systems are considered, calculations can prove to be invaluable for the interpretation of experimental data and often allow an otherwise impossible spectral assignment. This thesis presents a series of studies in which NMR spectroscopy, in combination with computational methods, is utilized to investigate a variety of chemical systems both in solution and the solid state. An overview of the thesis and experimental and computational details are given in Chapter 1. In Chapter 2, the quantum mechanical basis necessary for the description of the NMR phenomenon is presented. Chapter 3 explores the main experimental techniques employed routinely for the acquisition of NMR spectra in both solution and the solid state. Chapter 4 describes the main features of density functional theory (DFT) and its implementation in computational methods for the calculation of relevant NMR parameters. Chapter 5 reports an experimental solution-phase NMR study and a parallel computational investigation of the poly(CTFE-co-EVE) fluoropolymer. In Chapter 6, the combination of [superscript(14/15)]N solution-phase NMR techniques and DFT methods for the study of alkylammonium cationic templates used in the synthesis of microporous materials is presented. The characterization of a boroxoaromatic compound in the solid state and the study of its reactivity are described in Chapter 7. In Chapter 8, two experimental NMR methods for the study of the anisotropic chemical shift interaction in the solid state are compared and used to characterize a range of materials. Cross-polarization and nutation of quadrupolar nuclei are computationally investigated under both static and spinning conditions in Chapter 9. A general conclusion and a summary are given in Chapter 10.