Indiana University-Purdue University Indianapolis (IUPUI) / Symmetry plays a significant role in protein structural assembly and function. This is especially true for large homo-oligomeric protein complexes due to stability and finite control of function. But, symmetry in proteins are not perfect due to unknown reasons and leads to pseudosymmetry. This study focuses on symmetry analysis of homo-oligomers, specifically homo-dimers, homo-trimers and homo-tetramers. We defined Off Symmetry (OS) to measure the overall symmetry of the protein and Structural Index (SI) to quantify the structural difference and Assembly Index (AI) to quantify the assembly difference between the subunits. In most of the symmetrical homo-trimer and homo-tetramer proteins, Assembly Index contributes more to Off Symmetry and in the case of homo-dimer, Structural index contributes more than the Assembly Index. The main chain atom Carbon-Alpha (CA) is more symmetrical than the first side chain atom Carbon-Beta (CB), suggesting protein mobility may contribute to the pseudosymmetry. In addition, Pearson coefficient correlation between their Off-Symmetry and their respective atoms B-Factor (temperature factor) are calculated. We found that the individual residues of a protein in all the subunits are correlated to their average B-Factor of these residues. The correlation with BFactor is stronger in Structure Index than Assembly Index. All these results suggest that protein dynamics play an important role and therefore a larger off-symmetry may indicate a more mobile and flexible protein complex.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

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Protein misfolding and the accumulation of insoluble aggregates is a hallmark of several neurodegenerative disorders, including Alzheimer’s (AD) and Parkinson’s disease (PD). In AD and PD patients, extracellular protein deposits consisting of amyloid beta (Aβ) and intraneuronal inclusions composed of alpha synuclein (αS) are observed, respectively. Notably, the spatiotemporal patterning of soluble protein oligomers of αS and Aβ closely follow disease progression, giving support to an emerging role of soluble oligomers in PD and AD pathogenesis. However, the structural features underlying the toxicity of Aβ and αS oligomers remain elusive. This doctoral dissertation aims at elucidating the structural determinants of oligomer toxicity by focusing on the development and application of multidisciplinary approaches based primarily on solution NMR in combination with electron microscopy, multi-angle light scattering, fluorescence microscopy, wide-angle x-ray diffraction and cellular biophysics. Using this interdisciplinary approach, in chapters 2 and 3, we identify at atomic resolution the key structural elements that facilitate the colocalization, interaction and subsequent insertion of soluble Aβ oligomers into membranes, which ultimately result in the loss of membrane integrity. Notably, we show that small molecules, such as green tea catechins, remodel these structural features and effectively perturb the interactions with membranes. In chapter 4, we extend these analyses to αS and identify how the chaperone, Human Serum Albumin (HSA), remodels toxic αS oligomers into non-toxic species and breaks the catalytic cycle that generates new toxic oligomers. Lastly, in chapter 5, we describe a novel solution NMR approach to map at atomic resolution the sites of early self-association, with minimal bias from monomer dynamics, an effect that frequently dominates residue-dependent variations in solution NMR measurements. Overall, given that Aβ and αS are archetypical amyloidogenic proteins, we anticipate that the structure – toxicity relationships established herein, and the related experimental approaches may be transferrable to other amyloidogenic systems. / Dissertation / Doctor of Philosophy (PhD)

A series of reactive phenylethynyl endcapped imide oligomers has been prepared in either fully cyclized or amic acid precursor form. Soluble oligomers have been synthesized with controlled molecular weights ranging from 2- to 12 Kg/mol. Molecular weight characterization was performed using SEC (size exclusion chromatography) and 13C-NMR, revealing good agreement between the theoretical and experimental (Mn) values. Crosslinked polyimides were obtained by solution or melt processing the oligomers into films and gradually heating in a programmed temperature manner up to the appropriate reaction temperature for the phenylethynyl groups, which is approximately 350-400°C. Thermal analysis of the resulting films showed high glass transition temperatures (>300°C) and excellent thermal stability, comparable to those found for thermoplastic control polyimides. The crosslinked films also had exceptional solvent resistance as evidenced by a high gel fraction (greater than or equal to 95%) following extraction in common solvents for several days. This was in contrast to the amorphous thermoplastic controls, which quickly dissolved upon immersion in solvents. The monomers used for synthesizing the polyimide oligomers were varied systematically within the series to study the influence of both molecular structure and molecular weight on the physical and film-forming properties. The incorporation of fluorinated monomers, such as 4,4'-(hexafluoroisopropylidene)diphthalic anhydride (6FDA), reduced water absorption and lowered the dielectric constant relative to non-fluorinated polyimides in the series. When flexible ether linkages were incorporated in the repeat unit by using 4,4'-oxydianiline (ODA), relatively more ductile solvent-cast films were obtained from oligomers having Mn values as low as 10 Kg/mol. Additionally, oligomer Mn and the relative rigidity/symmetry of the repeat unit structure greatly influenced the solubility of polyimides in NMP. For example, even 6FDA/p-phenylenediamine based oligomers with Mn values targeted below 10 Kg/mol precipitated from NMP at 180°C during solution imidization. The relationship between solution viscosities of polyimide and poly(amic acid) thermosetting oligomers and wetting/spreading ability to form continuous films during spin casting was elucidated. Employing o-dimethoxybenzene (DMB) as a cosolvent with NMP improved the film-forming ability of the fully imidized 6FDA/ODA oligomer series. This was evidenced by a decrease in viscosity (via suppression of physical-type gel formation) and better overall coverage and clarity of the films. Humidity was found to have a detrimental effect, causing the polyimide oligomers to phase separate to form cloudy or porous films. When moisture was reduced, oligomers having Mn greater than or equal to 6 Kg/mol formed spin cast films of <20 micrometer thickness with good qualitative adhesion to several inorganic substrates. Dielectric constants (epsilon) were estimated for several of the polyimides by measuring the refractive indices (n) of the films and using Maxwell's relationship (epsilon at optical frequencies is equal to n raised to the second power). The apparent dielectric constants were low, ranging from 2.47 to 2.75. The novel combination of low dielectric constant, solvent resistance and isotropic physical properties inherent in the thermosetting polyimide oligomers makes these materials excellent candidates for use as thin film insulating layers in microelectronics packaging applications. / Ph. D.

Neurotoxic aggregates of amyloid beta (Aβ) peptide contribute to the etiology of Alzheimer's disease (AD). Aβ1-42 forms oligomeric structures that undergo further aggregation into protofibrils and fibrils. Oligomeric Aβ1-42 is more toxic than monomers or mature fibrils. In this work, we used two distinct approaches to inhibit Aβ1-42 oligomerization and toxicity. First, seven distinct but overlapping Aβ fragments were used to identify their individual aggregation propensities and their effects on Aβ1-42 oligomerization and cytotoxicity. Studies on suppression of Aβ1-42 cytotoxicity by peptides, including those derived from Aβ1-42, have been conducted before, but peptides encompassing the whole Aβ1-42 sequence have not been systematically analyzed. Aβ1-42 was allowed to aggregate and form oligomeric assemblies in aqueous buffer for 4 h in the absence or presence of 2-fold molar excess of an Aβ fragment. Cytotoxicity analysis then recorded the impact of each fragment on Aβ1-42 cytotoxicity as well as the toxicity of the fragments themselves. An enzyme-linked immunosorbent assay that detects oligomeric Aβwas used to determine the effect of each fragment on Aβ1-42 oligomerization after 4 h of aggregation. Four fragments of Aβ1-42 inhibited the toxicity of oligomeric Aβ1-42 to various degrees, while two others conferred no cellular protection against Aβ1-42 toxicity. Interestingly, one fragment enhanced Aβ1-42 toxicity after 4 h of aggregation. Three of the four fragments that blocked Aβ1-42 toxicity partially disrupted oligomer formation, showing correlation between the inhibition of Aβ1-42 aggregation and the inhibition of cellular toxicity. Second, we examined whether protein disulfide isomerase (PDI), a chaperone mainly found in the endoplasmic reticulum, could reverse the oligomeric state of aggregated Aβ1-42 and thus its toxicity. Previous work has demonstrated that PDI inhibits Aβ1-42 aggregation at sub-stoichiometric concentrations. To assess PDI's effect on Aβ1-42 toxicity, Aβ1-42 was allowed to aggregate for 2 h before the addition of PDI at a 1:10 molar ratio of PDI to Aβ1-42 and then allowed to aggregate for another 2 h. MTS cytotoxicity assays using PC-12 cells showed that adding PDI 2 h after the start of aggregation improves cell survival. Through a differential centrifugation assay followed by Western blot, we qualitatively illustrated that PDI can reverse a 2 h aggregate of Aβ1-42 to the monomeric state. Overall, in this project we have learned that inhibiting the oligomeric assembly of Aβ1-42 directly decreases the effect of Aβ1-42 toxicity. Inhibition of Aβ1-42 toxicity was seen with both fragments derived from Aβ1-42 and PDI, shedding light into two novel approaches as possible therapeutics for AD.

La synthèse d'une nouvelle famille d'oligomères de motifs contraints de dipeptides est décrite dans ce manuscrit. Les monomères utilisés sont des motifs 3(S)-amino-5-carbonylméthyl-2,3-dihydro-1,5-benzothiazépine-4(5H)-one (DBT), acide 2-aminométhyl-phényl-acétique (AMPA) et α-amino γ-lactames. La structure secondaire de ces édifices a été étudiée par spectroscopies RMN, IR, CD et RX. Nous avons montré tout d'abord que les oligomères de DBT sont capables d'adopter des structures stables et définies en ruban. En se basant sur ces structures, nous avons conçu de nouveaux systèmes beaucoup plus versatiles qui permettent de répartir diverses fonctions (basiques, acides, aromatiques) de part et d'autre de l'axe du ruban. Une stratégie de synthèse originale a été développée à cet effet. Elle consiste en la conversion directe de séquences peptidiques, incorporant des méthionines, en oligomères d'α-amino γ-lactames. Ils sont capables, au même titre que ceux de DBT, d'adopter des structures en ruban et de pénétrer dans les cellules. Enfin une étude in vivo chez la souris a montré le fort potentiel anti-tumoral d'un bioconjugué associant des oligomères d'AMPA à un inhibiteur de la Cathepsine D, enzyme lysosomale surexprimée et sécrétée par de nombreuses tumeurs solides. / The synthesis of a new type of constrained dipeptide motif oligomers is described. Monomers used are the (3S)-amino-5-(carboxylmethyl)-2,3-dihydro-1,5-benzothiazepin-4(5H)-one (DBT), the 2-aminomethyl-phenyl-acetic acid (AMPA) and α-amino γ-lactams. The secondary structure of those architectures has been studied by NMR, IR, CD and X-ray spectroscopies. Firstly, we demonstrated that DBT oligomers are able to adopt stable and well defined ribbon like structures. Based on these structures, we designed new systems, far more versatile which are able to distribute various functions (basic, acidic, aromatic) on each side of the ribbon axis. An original strategy has been developed for this purpose. It consists in the direct conversion of peptidic sequences, incorporating methionine, in α-amino γ-lactams oligomers. They are able, as the DBT, to adopt ribbon like structures and to be internalized into cells. Finally, an in vivo study in mice showed the high anti-tumoral potency of a bioconjugate linking AMPA oligomers to an inhibitor of the cathepsin D, a lysosomal enzyme overexpressed and secreted by numerous solid tumors.