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Description
Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications.

Atomic Force Microscopy (AFM)

Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications.

Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to functionalize AFM tips. For multiplexed recognition imaging, recognition heads based on a C3 symmetrical three arm linker with azide functionalities at its ends were synthesized and the chemistry to attach them to AFM tips was developed, and these recognition heads were used in detecting multiple proteins simultaneously using AFM.

A bis-Angiopeptide-2 conjugate with this three-arm linker was synthesized and this was conjugated with anti-West Nile virus antibody E16 site specifically to target advanced West Nile virus infection in the Central Nervous System. The bis-Angiopeptide-2 conjugate of the antibody shows higher efficacy compared to a linear linker-Angiopeptide-2 conjugate of the antibody in in vitro studies and currently the efficacy of this antibody conjugate in studied in mice. Surface Plasmon Resonance imaging (SPRi) results indicate that the conjugation does not affect the antigen binding activity of the antibody very significantly.

A Y-shaped bisbiotin ligand was also prepared as a small sized antibody mimic. Compared to a monovalent biotin ligand, the y-Bisbiotin can cooperatively form a significantly more stable complex with streptavidin through intramolecular bivalent interactions, which were demonstrated by gel electrophoresis, SPR and AFM. Continuing on these lines, a four-arm linker was synthesized containing three single chain variable fragments (scFv) linked to the scaffold to form a tripod base, which would allow them to concomitantly interact with a trimeric Glycoprotein (GP) spike that has a “chalice” configuration. Meanwhile, a human IgG1 Fc is to be installed on the top of the tetrahedron, exerting effector functions of a monoclonal antibody.
ContributorsManna, Saikat (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Gould, Ian (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Structural-based drug discovery is becoming the essential tool for drug development withlower cost and higher efficiency compared to the conventional method. Knowledge of the three-dimensional structure of protein targets has the potential to accelerate the process for screening drug candidates. X-ray crystallography has proven to be the most used and indispensable technology in

Structural-based drug discovery is becoming the essential tool for drug development withlower cost and higher efficiency compared to the conventional method. Knowledge of the three-dimensional structure of protein targets has the potential to accelerate the process for screening drug candidates. X-ray crystallography has proven to be the most used and indispensable technology in structural-based drug discovery. The provided comprehensive structural information about the interaction between the disease-related protein target and ligand can guide the chemical modification on the ligand to improve potency and selectivity. X-ray crystallography has been upgraded from traditional synchrotron to the third generation, which enabled the surge of the structural determination of macromolecular. The introduction of X-ray free electron laser further alleviated the uncertain and time-consuming crystal size optimization process and extenuated the radiation damage by “diffraction before destruction”. EV-D68 2A protease was proved to be an important pharmaceutical target for acute flaccid myelitis. This thesis reports the first atomic structure of the EV-D68 2A protease and the structuresof its two mutants, revealing it adopting N-terminal four-stranded sheets and C-terminal six-stranded ß-barrels structure, with a tightly bound zinc atom. These structures will guide the chemical modification on its inhibitor, Telaprevir. Integrin ⍺Mβ2 is an integrin with the α I-domain, related to many immunological functions including cell extravasation, phagocytosis, and immune synapse formation, so studying the molecular ligand-binding mechanism and activation mechanism of ⍺Mβ2 is of importance. This thesis uncovers the preliminary crystallization condition of ⍺Mβ2-I domain in complex with its ligand Pleiotrophin and the initial structural model. The structural model shows consistency with the previous hypothesis that the primary binding sites are metal iondependent adhesion sites on ⍺Mβ2-I domain and the thrombospondin type-1 repeat (TSR) domains of Pleiotrophin. Drug molecules with high potency and selectivity can be designed based on the reported structures of the EV-D68 2A protease and ⍺Mβ2-I domain in the future.
ContributorsLiu, Chang (Author) / Liu, Wei (Thesis advisor) / Stephanopoulos, Nicholas (Committee member) / Chiu, Po-Lin (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Transient protein-protein and protein-molecule interactions fluctuate between associated and dissociated states. They are widespread in nature and mediate most biological processes. These interactions are complex and are strongly influenced by factors such as concentration, structure, and environment. Understanding and utilizing these types of interactions is useful from both a fundamental

Transient protein-protein and protein-molecule interactions fluctuate between associated and dissociated states. They are widespread in nature and mediate most biological processes. These interactions are complex and are strongly influenced by factors such as concentration, structure, and environment. Understanding and utilizing these types of interactions is useful from both a fundamental and design perspective. In this dissertation, transient protein interactions are used as the sensing element of a biosensor for small molecule detection. This is done by using a transcription factor-small molecule pair that mediates the activation of a CRISPR/Cas12a complex. Activation of the Cas12a enzyme results in an amplified readout mechanism that is either fluorescence or paper based. This biosensor can successfully detect 9 different small molecules including antibiotics with a tuneable detection limit ranging from low µM to low nM. By combining protein and nucleic acid-based systems, this biosensor has the potential to report on almost any protein-molecule interaction, linking this to the intrinsic amplification that is possible when working with nucleic acid-based technologies. The second part of this dissertation focuses on understanding protein-molecule interactions at a more fundamental level, and, in so doing, exploring design rules required to generalize sensors like the ones described above. This is done by training a neural network algorithm with binding data from high density peptide micro arrays incubated with specific protein targets. Because the peptide sequences were chosen simply to evenly, though sparsely, represent all sequence space, the resulting network provides a comprehensive sequence/binding relationship for a given target protein. While past work had shown that this works well on the arrays, here I have explored how well the neural networks thus trained, predict sequence-dependent binding in the context of protein-protein and peptide-protein interactions. Amino acid sequences, either free in solution or embedded in protein structure, will display somewhat different binding properties than sequences affixed to the surface of a high-density array. However, the neural network trained on array sequences was able to both identify binding regions in between proteins and predict surface plasmon resonance-based binding propensities for peptides with statistically significant levels of accuracy.
ContributorsSwingle, Kirstie Lynn (Author) / Woodbury, Neal W (Thesis advisor) / Green, Alexander A (Thesis advisor) / Stephanopoulos, Nicholas (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami technology enables the fabrication of nearly arbitrary DNA architectures with nanoscale precision,

Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami technology enables the fabrication of nearly arbitrary DNA architectures with nanoscale precision, which can serve as excellent building blocks for the construction of tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, a general design and assembly method are described for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. A critical design parameter, interhelical distance (D), was identified, which determined the conformation of monomer tiles and the outcome of tessellation. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability. To demonstrate the generality of the design method, 9 tile geometries and 15 unique tile designs were generated. The designed tiles were assembled into single-crystalline lattices ranging from tens to hundreds of square micrometers with micrometer-scale, nearly defect-free areas readily visualized by atomic force microscopy. Two strategies were applied to further increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and co-assembling tiles of various geometries. The designed 6 complex tilings that includes 5 Archimedean tilings and a 12-fold quasicrystal tiling yielded various tiling patterns that great in size and quality, indicating the robustness of the optimized tessellation system. The described design and assembly approach can also be employed to create square DNA origami units for algorithmic self-assembly. As the square units assembled and expanded, they executed the binary function XOR, which generated the Sierpinski triangular pattern according to the predetermined instructions. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
ContributorsTang, Yue (Author) / Yan, Hao (Thesis advisor) / Guo, Jia (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Tissues within the body enable proper function throughout an individual’s life. After severe injury or disease, many tissues do not fully heal without surgical intervention. The current surgical procedures aimed to repair tissues are not sufficient to fully restore functionality. To address these challenges, current research is seeking new tissue

Tissues within the body enable proper function throughout an individual’s life. After severe injury or disease, many tissues do not fully heal without surgical intervention. The current surgical procedures aimed to repair tissues are not sufficient to fully restore functionality. To address these challenges, current research is seeking new tissue engineering approaches to promote tissue regeneration and functional recovery. Of particular interest, biomaterial scaffolds are designed to induce tissue regeneration by mimicking the biophysical and biochemical aspects of native tissue. While many scaffolds have been designed with homogenous properties, many tissues are heterogenous in nature. Thus, fabricating scaffolds that mimic these complex tissue properties is critical for inducing proper healing after injury. Within this dissertation, scaffolds were designed and fabricated to mimic the heterogenous properties of the following tissues: (1) the vocal fold, which is a complex 3D structure with spatially controlled mechanical properties; and (2) musculoskeletal tissue interfaces, which are fibrous tissues with highly organized gradients in structure and chemistry. A tri-layered hydrogel scaffold was fabricated through layer-by-layer stacking to mimic the mechanical structure of the vocal fold. Furthermore, magnetically-assisted electrospinning and thiol-norbornene photochemistry was used to fabricate fibrous scaffolds that mimic the structural and chemical organization of musculoskeletal interfacial tissues. The work presented in this dissertation further advances the tissue engineering field by using innovative techniques to design scaffolds that recapitulate the natural complexity of native tissues.
ContributorsTindell, Raymond Kevin (Author) / Holloway, Julianne (Thesis advisor) / Green, Matthew (Committee member) / Pizziconi, Vincent (Committee member) / Stephanopoulos, Nicholas (Committee member) / Acharya, Abhinav (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Antibodies are the immunoglobulins which are secreted by the B cells after a microbial invasion. They are stable and stays in the serum for a long time which makes them an excellent biomarker for disease diagnosis. Inflammatory bowel disease is a type of autoimmune disease where the immune system mistakenly

Antibodies are the immunoglobulins which are secreted by the B cells after a microbial invasion. They are stable and stays in the serum for a long time which makes them an excellent biomarker for disease diagnosis. Inflammatory bowel disease is a type of autoimmune disease where the immune system mistakenly attacks the commensal bacteria and leads to inflammation. We studied antibody response of 100 Crohn’s disease (CD), 100 ulcerative colitis (UC) and 100 healthy controls against 1,173 bacterial and 397 viral proteins. We found some anti-bacterial antibodies higher in CD compared to controls while some antibodies lower in UC compared to controls. We were able to build biomarker panels with AUCs of 0.81, 0.87, and 0.82 distinguishing CD vs. control, UC vs. control, and CD vs. UC, respectively. Subgroup analysis based on the Montreal classification revealed that penetrating CD behavior (B3), colonic CD location (L2), and extensive UC (E3) exhibited highest antibody reactivity among all patients. We also wanted to study the reason for the presence of autoantibodies in the sera of healthy individuals. A meta-analysis of 9 independent biomarker study was performed to find 77 common autoantibodies shared by healthy individuals. There was no gender bias; however, the number of autoantibodies increased with age, plateauing around adolescence. Molecular mimicry likely contributed to the elicitation of a subset of these common autoantibodies as 21 common autoantigens had 7 or more ungapped amino acid matches with viral proteins. Intrinsic properties of protein like hydrophilicity, basicity, aromaticity, and flexibility were enriched for common autoantigens. Subcellular localization and tissue expression analysis indicated the sequestration of some autoantigens from circulating autoantibodies can explain the absence of autoimmunity in these healthy individuals.
ContributorsShome, Mahasish (Author) / LaBaer, Joshua (Thesis advisor) / Borges, Chad (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Mycobacterial infections, as represented by leprosy and tuberculosis, have persisted as human pathogens for millennia. Their environmental counterparts, nontuberculous mycobacteria (NTM), are commodious infectious agents endowed with extensive innate and acquired antimicrobial resistance. The current drug development process selects for antibiotics with high specificity for definitive targets within bacterial metabolic

Mycobacterial infections, as represented by leprosy and tuberculosis, have persisted as human pathogens for millennia. Their environmental counterparts, nontuberculous mycobacteria (NTM), are commodious infectious agents endowed with extensive innate and acquired antimicrobial resistance. The current drug development process selects for antibiotics with high specificity for definitive targets within bacterial metabolic and replication pathways. Because these compounds demonstrate limited efficacy against mycobacteria, novel antimycobacterial agents with unconventional mechanisms of action were identified. Two highly resistant NTMs, Mycobacterium abscessus (Mabs) a rapid-growing respiratory, skin, and soft tissue pathogen, and Mycobacterium ulcerans (MU), the causative agent of Buruli ulcer, were selected as targets. Compounds that indicated antimicrobial activity against other highly resistant pathogens were selected for initial screening. Antimicrobial peptides (AMPs) have demonstrated activity against a variety of bacterial pathogens, including mycobacterial species. Designed antimicrobial peptides (dAMPs), rationally-designed and synthetic contingents, combine iterative features of natural AMPs to achieve superior antimicrobial activity in resistant pathogens. Initial screening identified two dAMPs, RP554 and RP557, with bactericidal activity against Mabs. Clay-associated ions have previously demonstrated bactericidal activity against MU. Synthetic and customizable aluminosilicates have also demonstrated adsorption of bacterial cells and toxins. On this basis, two aluminosilicate materials, geopolymers (GP) and ion-exchange nanozeolites (IE-nZeos), were screened for antimicrobial activity against MU and its fast-growing relative, Mycobacterium marinum (Mmar). GPs demonstrated adsorption of MU cells and mycolactone, a secreted, lipophilic toxin, whereas Cu-nZeos and Ag-nZeos demonstrated antibacterial activity against MU and Mmar. Cumulatively, these results indicate that an integrative drug selection process may yield a new generation of antimycobacterial agents.
ContributorsDermody, Roslyn June (Author) / Haydel, Shelley E (Thesis advisor) / Bean, Heather (Committee member) / Nickerson, Cheryl (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2022
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Description
The biological lipid bilayer on cells or the cell membrane is a surface teeming with activity. Several membrane proteins decorate the lipid bilayer to carry out various functionalities that help a cell interact with the environment, gather resources and communicate with other cells. This provides a repertoire of biological structures

The biological lipid bilayer on cells or the cell membrane is a surface teeming with activity. Several membrane proteins decorate the lipid bilayer to carry out various functionalities that help a cell interact with the environment, gather resources and communicate with other cells. This provides a repertoire of biological structures and processes that can be mimicked and manipulated. Since its inception in the late 20th century deoxyribonucleic acid (DNA) nanotechnology has been used to create nanoscale objects that can be used for such purposes. Using DNA as the building material provides the user with a programmable and functionalizable tool box to design and demonstrate these ideas. In this dissertation, I describe various DNA nanostructures that can insert or interact with lipid bilayers for cargo transport, diagnostics and therapeutics. First, I describe a reversibly gated DNA nanopore of 20.4nm x 20.4nm cross sectional width. Controlled transport of cargoes of various sizes across a lipid bilayer through a channel formed by the DNA nanopore was demonstrated. This demonstration paves the way for a class of nanopores that can be activated by different stimuli. The membrane insertion capability of the DNA nanopore is further utilized to design a nanopore sensor that can detect oligonucleotides of a specific s equence inside a lipid vesicle. The ease with which the sensor can be modified to i dentify different diagnostic markers for disease detection was shown by designing a sensor that can identify the non small cell lung cancer marker micro ribonucleic acid -21 (miRNA21). Finally, I demonstrate the therapeutic capabilities of DNA devices with a DNA tetrabody that can recruit natural killer cells (NK cells) to target cancer cells. The DNA tetrabody functionalized with cholesterol molecules and Her2 affibody inserts into NK cell membrane leading it to Her2 positive cancer cells. This shows that inthe presence of DNA tetrabody, the NK cell activation gets accelerated.
ContributorsAbraham, Leeza (Author) / Yan, Hao (Thesis advisor) / Liu, Uan (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Exoelectrogenic organisms transfer electrons from their quinone pool to extracellular acceptors over m-scale distances through appendages known as “biological nanowires”. These structures have been described as cytochrome-rich membrane extensions or pili. However, the components and mechanisms of this long-range electron transfer remain largely unknown. This dissertation describes supramolecular assembly of

Exoelectrogenic organisms transfer electrons from their quinone pool to extracellular acceptors over m-scale distances through appendages known as “biological nanowires”. These structures have been described as cytochrome-rich membrane extensions or pili. However, the components and mechanisms of this long-range electron transfer remain largely unknown. This dissertation describes supramolecular assembly of a tetraheme cytochrome into well-defined models of microbial nanowires and uses those structures to explore the mechanisms of ultra-long-range electron transfer. Chiral-induced-spin-selectivity through the cytochrome is also demonstrated. Nanowire extensions in Shewanella oneidensis have been hypothesized to transfer electrons via electron tunneling through proteinaceous structures that reinforce π-π stacking or through electron hopping via redox cofactors found along their lengths. To provide a model to evaluate the possibility of electron hopping along micron-scale distances, the first part of this dissertation describes the construction of a two-component, supramolecular nanostructure comprised of a small tetraheme cytochrome (STC) from Shewanella oneidensis fused to a peptide domain that self-assembles with a β-fibrillizing peptide. Structural and electrical characterization shows that the self-assembled protein fibers have dimensions relevant to understanding ultralong-range electron transfer and conduct electrons along their length via a cytochrome-mediated mechanism of electron transfer. The second part of this dissertations shows that a model three-component fiber construct based on charge complementary peptides and the redox protein can also be assembled. Structural and electrical characterization of the three-component structure also demonstrates desirable dimensions and electron conductivity along the length via a cytochrome-mediated mechanism. In vivo, it has been hypothesized that cytochromes in the outer surface conduit are spin-selective. However, cytochromes in the periplasm of Shewanella oneidensis have not been shown to be spin selective, and the physiological impact of the chiral-induced-spin-selectivity (CISS) effect on microbial electron transport remains unclear. In the third part of this dissertation, investigations via spin polarization and a spin-dependent conduction study show that STC is spin selective, suggesting that spin selectivity may be an important factor in the electron transport efficiency of exoelectrogens. In conclusion, this dissertation enables a better understanding of long-range electron transfer in bacterial nanowires and bioelectronic circuitry and offers suggestions for how to construct enhanced biosensors.
ContributorsNWACHUKWU, JUSTUS NMADUKA (Author) / Jones, Anne K. (Thesis advisor) / Mills, Jeremy (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023
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Description
In the past decade, technological breakthroughs have facilitated structure determination of so many difficult-to-study membrane protein targets. In this thesis research, three techniques were investigated to enable the structural determination of such challenging targets, polychromatic pink-beam serial crystallography with high-viscous sample, lipidic cubic phase (LCP)-based microcrystal electron diffraction (MicroED), and

In the past decade, technological breakthroughs have facilitated structure determination of so many difficult-to-study membrane protein targets. In this thesis research, three techniques were investigated to enable the structural determination of such challenging targets, polychromatic pink-beam serial crystallography with high-viscous sample, lipidic cubic phase (LCP)-based microcrystal electron diffraction (MicroED), and single-particle cryogenic electron microscopy targeting (cryoEM).

Inspired by the successful serial crystallography (SX) experiment at a synchrotron radiation source, it is first-time equipping the high-viscosity injector to X-ray fluxes increased at 100 times by a moderate increased in bandwidth to perform the pink beam SX experiments. The structure of proteinase K (PK) was determined to 1.8 Å resolution with 4 consecutive 100 ps X-ray pink beam pulse exposures. The structure of human A2A adenosine receptor (A2AAR) reached to a 4.2 Å resolution using 24 consecutive X-ray pink beam pulse exposures. It has proven the feasibility to utilize such storage-ring synchrotron sources complemented to serial femtosecond crystallography, presenting new opportunities for microcrystallography and the time-resolved experiments.

As an alternative approach to serial femtosecond crystallography, a novel protocol was developed to combine the lipidic cubic phase crystallization approach and microED strategy and solved the structure from LCP-embedded proteinase K microcrystals with the comparable high resolution to conventional crystallographic method.

It cannot be neglected that only very few portions of membrane proteins were able to be successfully crystallized for structure determination. Single particle cryoEM method allows the structural studies from protein molecules detour away from crystallization. An atomic resolution structure of the β1-AR bound with agonist in complex with Gs protein, with particle size of less than 200 kDa, was determined by cryoEM, reaching to an atomic resolution of 3.8 Å. The complex structure captured a fully active conformation and revealed the important mechanisms of how the agonist bound receptor activated Gs protein.

These technological developments provide more opportunities to the structural biology community to discover mechanisms underlying such complicated machinery network, which would eventually benefit the structure-based drug discovery.
ContributorsZhu, Lan, Ph.D (Author) / Liu, Wei (Thesis advisor) / Mills, Jeremy (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2019