Structural Biology Commons^™

Understanding The Role Of Toxs As A Bile Sensing Component Of The Toxrs Virulence Regulatory System In Vibrio Spp., Minje Kim

Dartmouth College Ph.D Dissertations

Pathogenic Vibrio bacteria, such as V. cholerae and V. parahaemolyticus, colonize in the human small intestine to cause severe gastrointestinal disease. During the infection, these bacteria encounter bile salts, antimicrobial cholesterol metabolites secreted into the intestine. Pathogenic Vibrio species have evolved to utilize bile salts as signals to regulate virulence. The signaling depends in part on ToxRS, a conserved co-component transmembrane transcription regulator. ToxRS consists of the transcription factor ToxR and its membrane-tethered binding partner ToxS. ToxS is required for ToxR stability and full transcriptional activity. Although bile salts are known to influence ToxRS-dependent virulence gene expression, the molecular …

Biochemical And Structural Insights Into The Yersinia Effector Yopm And Its Negative Regulation Of The Pyrin Inflammasome, Bethany Wairimu Mwaura

Dartmouth College Ph.D Dissertations

Bacteria utilize sophisticated secretion systems to inject effectors into host cells in order to facilitate their survival and replication in the host. Some pathogenic species of Gram-negative bacteria use a conserved contact-dependent T3SS to inject a wide array of effectors. While the effectors diverge in their structures, functions and cell-localization, the T3SS is well conserved. Several effectors discussed in this thesis target key host inflammasome responses. The focus of this work is how the Yersinia effector YopM inhibits the pyrin inflammasome. During Yersinia infection, two effectors, YopE and YopT inadvertently activate the pyrin inflammasome while targeting RhoA to avoid phagocytosis. …

Computational Modelling And Design Of Antibodies: Benefits From Analysis Of Their Unique Structural Motifs, Katherine M. Mccoy

Dartmouth College Ph.D Dissertations

The complexes that antibodies make with their binding partners, or antigens, are especially valuable to be able to predict and modify due to their unique role in the immune system. Yet, they present significant challenges to computational methods of both modelling and design. Antibodies are unlike most other proteins in that they are composed of a scaffold region, which is a highly conserved structure that is largely the same between antibodies of the same class, and Complementary Determining Regions (CDRs), which are comprised of hypervariable loops that largely determine their binding motifs. Additionally, antibodies and their antigens do not co-evolve …

Understanding The Non-Canonical Regulation Of Srebp In Aspergillus Fumigatus, Muhammad Abubakar Khan

Dartmouth College Ph.D Dissertations

Aspergillus fumigatus is an opportunistic fungal pathogen causing invasive pulmonary aspergillosis (IPA), with high mortality rates in immunocompromised individuals. Adaptation to the hypoxic microenvironment of IPA is crucial for fungal virulence. The transcription factor SrbA, a Sterol Regulatory Element-Binding Protein (SREBP) homolog, plays a key role in this hypoxic response and regulates genes involved in hypoxic growth, sterol biosynthesis, and azole resistance, making it an attractive therapeutic target.

However, SrbA activation in A. fumigatus lacks critical components of the canonical SREBP pathway, such as SCAP, Site-1 protease (S1P), and Site-2 protease (S2P). Instead, the rhomboid protease RbdB, signal peptide peptidase …

Structure-Based Targeting Of The Nemo:Ikk Interaction For Canonical Nf-Κb Inhibition, Amy Kennedy

Dartmouth College Ph.D Dissertations

The NF-κB pathway is important for cell survival and proliferation, inflammation, and innate immunity, and its dysregulation is a common theme in many cancers, autoimmune disorders, and other disease states. The protein-protein interaction between the scaffolding protein NEMO and the kinase IKK in the NF-κB pathway represents a compelling target for selective NF-κB inhibition because it occurs only in the canonical branch of the NF-κB pathway. Disruption of the NEMO:IKK interaction has been established for decades in the literature as a safe and effective way to selectively inhibit overactivation of the canonical branch of the NF-κB pathway. The benchmark in …

Structural Files For The Etr1 Ethylene-Receptor Dimer Based On Computational Modeling, Beenish J. Azhar, Safdar Abbas, Sitwat Aman, Maria V. Yamburenko, Wei Chen, Lena Muller, Buket Uzun, David A. Jewell, Jian Dong, Samina N. Shakeel, Georg Groth, Brad M. Binder, Gevorg Grigoryan, G. Eric Schaller

Dartmouth Scholarship

Structural models for the ETR1 homodimer were generated with AlphaFold-Multimer. Coppers were modeled under two potential coordinations involving Cys65 and His69 of the ETR1 homodimer, one in which the two coppers are bound independently and do not share an interaction with each other, and another where they are closely bonded.

See the following publication for details: Azhar, B.J., Abbas, S., Aman, S., Yamburenko, M.V., Chen, W., Müller, L., Uzun, B., Jewell, D.A., Dong, J., Shakeel, S.N., Groth, G., Binder, B.M., Grigoryan, G., Schaller, G.E. (2023) Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proc. Natl. Acad. …

Molecular Mechanisms Of Wild-Type And Mutant Prion Formation, Daniel J. Walsh

Dartmouth College Ph.D Dissertations

Prion diseases are a class of infectious neurodegenerative disorders which affect humans and many other mammalian species. The causative agent is a unique pathogen known as a prion or PrPSc, a misfolded form of a host-encoded glycoprotein which replicates by templated conformational change. Distinct strains of prions with unique phenotypic and pathologic presentations appear to be encoded by subtle conformational changes within the misfolded protein. While the general manner of prion transmission is known, our detailed understanding of these mechanisms remains incomplete, limiting efforts for the discovery or design of therapeutic treatments for these fatal diseases. In vitro synthesis of …

Mitochondrial Division: Synergizing In Mitochondrial Divisome, Ao Liu

Dartmouth College Ph.D Dissertations

Mitochondria are the energy factories of the cell. The dynamic nature of cells demands routine changes in mitochondrial morphology by fusion and division. The dynamin GTPase Drp1 is a central mitochondrial division protein, driving constriction of the outer mitochondrial membrane via oligomerization. At least four regulatory factors control Drp1 activity on the outer mitochondrial membrane (OMM): 1) receptor proteins (Mff, MiD49, MiD51, and Fis1); 2) actin filaments; 3) the mitochondrial phospholipid cardiolipin (CL); and 4) Drp1 post-translational modifications, of which two phosphorylation sites (S579 and S600) are the most well studied. However, the molecular mechanism of how these factors work …

Bayesian Reconstruction Of P(R) Directly From Two-Dimensional Detector Images Via A Markov Chain Monte Carlo Method, Sudeshna Paul, Alan M. Friedman, Chris Bailey-Kellogg, Bruce Craig

Dartmouth Scholarship

The interatomic distance distribution, P(r), is a valuable tool for evaluating the structure of a molecule in solution and represents the maximum structural information that can be derived from solution scattering data without further assumptions. Most current instrumentation for scattering experiments (typically CCD detectors) generates a finely pixelated two-dimensional image. In contin­uation of the standard practice with earlier one-dimensional detectors, these images are typically reduced to a one-dimensional profile of scattering inten­sities, I(q), by circular averaging of the two-dimensional image. Indirect Fourier transformation methods are then used to reconstruct P(r) from …

A Kinesin Motor In A Force-Producing Conformation, Elisabeth Heuston, C. Eric Bronner, F Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states.

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Dartmouth Scholarship

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …