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GSBS Dissertations and Theses

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Articles 1 - 30 of 132

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Identification Of Deubiquitinating Enzymes That Control The Cell Cycle In Saccharomyces Cerevisiae, Claudine E. Mapa Nov 2018

Identification Of Deubiquitinating Enzymes That Control The Cell Cycle In Saccharomyces Cerevisiae, Claudine E. Mapa

GSBS Dissertations and Theses

A large fraction of the proteome displays cell cycle-dependent expression, which is important for cells to accurately grow and divide. Cyclical protein expression requires protein degradation via the ubiquitin proteasome system (UPS), and several ubiquitin ligases (E3) have established roles in this regulation. Less is understood about the roles of deubiquitinating enzymes (DUB), which antagonize E3 activity. A few DUBs have been shown to interact with and deubiquitinate cell cycle-regulatory E3s and their protein substrates, suggesting DUBs play key roles in cell cycle control. However, in vitro studies and characterization of individual DUB deletion strains in yeast suggest that these ...


Studies In Antigen Presentation And Antigen Recognition At Different Interfaces Of The Adaptive Immune System, Maria P. Negroni Jul 2018

Studies In Antigen Presentation And Antigen Recognition At Different Interfaces Of The Adaptive Immune System, Maria P. Negroni

GSBS Dissertations and Theses

Antigen presentation and recognition are key processes of the immune system necessary to initiate the adaptive immune response. Longstanding goals of these fields have been to understand the molecular mechanism of MHC II-peptide binding, the way in which dysregulation of this process can lead to disease, and determining how γδTCRs recognize their ligands. To examine some of these outstanding questions, I designed photocleavable peptides that could bind HLA-DR1 and could be used to facilitate peptide exchange. I also performed studies to understand whether peptide exchange on HLA-DR1 can be affected by glycation modifications, which occur in hyperglycemic conditions such as ...


Maelstrom Represses Canonical Rna Polymerase Ii Transcription In Drosophila Dual-Strand Pirna Clusters, Timothy H. Chang Apr 2018

Maelstrom Represses Canonical Rna Polymerase Ii Transcription In Drosophila Dual-Strand Pirna Clusters, Timothy H. Chang

GSBS Dissertations and Theses

Transposons constitute much of the animal genome. While many transposons are ancient and inactivated, numerous others are intact and must be actively repressed. Uncontrolled transposons can cause genomic instability through DNA damage or mutations and must be carefully silenced in the germline or risk sterility or mutations that are passed on to offspring.

In Drosophila melanogaster, 23–30 nt long piRNAs direct transposon silencing by serving as guides for Aubergine, Argonaute3, and Piwi, the three fly PIWI proteins. piRNAs derive from piRNA clusters—large heterochromatic DNA loci comprising transposons and transposon fragments. piRNAs are loaded into PIWI proteins via the ...


Targeting Drug Resistance In Hcv Ns3/4a Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew Apr 2018

Targeting Drug Resistance In Hcv Ns3/4a Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew

GSBS Dissertations and Theses

The Hepatitis C virus (HCV) NS3/4A protease inhibitors (PIs) have become a mainstay of newer all-oral combination therapies. Despite improvements in potency of this inhibitor class, drug resistance remains a problem with the rapid emergence of resistance-associated substitutions (RASs). In this thesis I elucidate the molecular mechanisms of drug resistance for PIs against a resistant variant and apply insights toward the design of inhibitors with improved resistance profiles using structural, biochemical and computational techniques. Newer generation PIs retain high potency against most single substitutions in the protease active site by stacking on the catalytic triad. I investigated the molecular ...


Role Of Trip6 And Angiomotins In The Regulation Of The Hippo Signaling Pathway, Shubham Dutta Mar 2018

Role Of Trip6 And Angiomotins In The Regulation Of The Hippo Signaling Pathway, Shubham Dutta

GSBS Dissertations and Theses

Mechanical tension is an important regulator of cell proliferation, differentiation, migration and cell death. It is involved in the control of tissue architecture and wound repair and its improper sensing can contribute to cancer. The Hippo tumor suppressor pathway was recently shown to be involved in regulating cell proliferation in response to mechanical tension. The core of the pathway consists of the kinases MST1/2 and LATS1/2, which regulate the target of the pathway, the transcription co-activator YAP/ TAZ (hereafter referred to as YAP). When the Hippo pathway is inactive, YAP remains in the nucleus and promotes cell proliferation ...


Understanding Human Erythrocyte Glucose Transporter (Glut1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd Feb 2018

Understanding Human Erythrocyte Glucose Transporter (Glut1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd

GSBS Dissertations and Theses

GLUT1-mediated, facilitated sugar transport is proposed to be an example of transport by a carrier that alternately presents exofacial (e2) and endofacial (e1) substrate binding sites, commonly referred to as the alternating access carrier model. This hypothesis is incompatible with observations of co-existent exo- and endofacial ligand binding sites, transport allostery, and e1 ligand (e.g. cytochalasin B) induced GLUT1 sugar occlusion. The fixed-site carrier model proposes co-existent, interacting e2 and e1 ligand binding sites but involves sugar translocation by geminate exchange through internal cavities. Demonstrations of membrane-resident dimeric and tetrameric GLUT1 and of e2, e1 and occluded GLUT conformations ...


Transcriptome-Wide Analysis Of Roles For Transfer Rna Modifications In Translational Regulation, Hsin-Jung Chou Dec 2017

Transcriptome-Wide Analysis Of Roles For Transfer Rna Modifications In Translational Regulation, Hsin-Jung Chou

GSBS Dissertations and Theses

Covalent nucleotide modifications in RNAs affect numerous biological processes, and novel functions are continually being revealed even for well-known modifications. Among all RNA species, transfer RNAs (tRNAs) are highly enriched with diverse modifications, which are known to play roles in decoding and tRNA stability, charging, and cellular trafficking. However, studies of tRNA modifications have been limited in a small scale and performed by groups with different methodologies. To systematically compare the functions of a large set of noncoding RNA modifications in translational regulation, I carried out ribosome profiling in 57 budding yeast mutants lacking nonessential genes involved in tRNA modifications ...


Adapting The Empiric Approach To Investigate Evolutionary Constraints In Influenza A Virus Surface Proteins, Aneth S. Canale Dec 2017

Adapting The Empiric Approach To Investigate Evolutionary Constraints In Influenza A Virus Surface Proteins, Aneth S. Canale

GSBS Dissertations and Theses

Controlling influenza A virus (IAV) infections remains a challenge largely due to the high replication and mutation rates of the virus. IAV is a negative-sense RNA virus with two main surface proteins — hemagglutinin (HA) and neuraminidase (NA). HA recognizes and binds sialic acid on host cell receptors to initiate virus entry. NA also recognizes sialic acid on host cell receptors but functions by cleaving sialic acid interactions to release progeny virus. Because both HA and NA interact with sialic acid on the host cell surface with opposing effects, their balance is essential for optimal viral infectivity. However, the evolutionary constraints ...


Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli Dec 2017

Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli

GSBS Dissertations and Theses

The translation of mRNA into functional proteins is essential for all life. In eukaryotes, aberrant RNAs containing sequence features that stall or severely slow down ribosomes are subject to translation-dependent quality control. Targets include mRNAs encoding a strong secondary structure (No-Go Decay; NGD) or stretches of positively-charged amino acids (Peptide-dependent Translation Arrest/Ribosome Quality Control; PDTA/RQC), mRNAs lacking an in-frame stop codon (Non-Stop Decay; NSD), or defective 18S rRNAs (18S Nonfunctional rRNA Decay; 18S NRD). Previous work from our lab showed that the S. cerevisiae NGD factors DOM34 and HBS1, and PDTA/RQC factor ASC1, all participate in the ...


Understanding Multiple Independent Functions Of The Tip60 Acetyltransferase In Embryonic Development, Diwash Acharya Dec 2017

Understanding Multiple Independent Functions Of The Tip60 Acetyltransferase In Embryonic Development, Diwash Acharya

GSBS Dissertations and Theses

Chromatin is a dynamic structure, and chromatin remodeling enzymes regulate chromatin structure to control gene expression and proper lineage specification. Tip60-p400 is a multi-subunit chromatin remodeling complex containing two biochemical activities: the Tip60 subunit is a lysine acetyltransferase (KAT) that targets histones and non-histone proteins, and p400 catalyzes ATP-dependent incorporation of histone variant H2AZ into chromatin. Both of these chromatin modifications have been widely studied with respect to gene expression, DNA damage repair, and apoptosis. Ablation of these catalytic subunits causes defects in normal embryonic development, ESC self-renewal, and gene expression. My goal has been to understand the multiple independent ...


Development Of Chimeric Cas9 Nucleases For Accurate And Flexible Genome Editing, Mehmet F. Bolukbasi Nov 2017

Development Of Chimeric Cas9 Nucleases For Accurate And Flexible Genome Editing, Mehmet F. Bolukbasi

GSBS Dissertations and Theses

There has been tremendous amount of effort focused on the development and improvement of genome editing applications over the decades. Particularly, the development of programmable nucleases has revolutionized genome editing with regards to their improvements in mutagenesis efficacy and targeting feasibility. Programmable nucleases are competent for a variety of genome editing applications. There is growing interest in employing the programmable nucleases in therapeutic genome editing applications, such as correcting mutations in genetic disorders.

Type II CRISPR-Cas9 bacterial adaptive immunity systems have recently been engineered as RNA-guided programmable nucleases. Native CRISPR-Cas9 nucleases have two stages of sequence-specific target DNA recognition prior ...


Exploring The Role Of Large Clusters Of Branched Aliphatic Residues On The Folding Free Energy Landscape Of (Βα)8 Tim Barrel Proteins, Kevin T. Halloran Nov 2017

Exploring The Role Of Large Clusters Of Branched Aliphatic Residues On The Folding Free Energy Landscape Of (Βα)8 Tim Barrel Proteins, Kevin T. Halloran

GSBS Dissertations and Theses

(βα)8 TIM barrel proteins are one of the most common structural motifs found in biology. They have a complex folding free energy landscape that includes an initial off-pathway intermediate as well as two on-pathway intermediates. The formation of these intermediates is hypothesized to be driven by large clusters of the branched chain amino acids, isoleucine, leucine, and valine (ILV).

All-atom MD simulations and circular dichroism experiments on polar mutants of the hydrophobic clusters of α-Trp synthase, a TIM barrel protein, revealed the importance of dehydrating the clusters on intermediate states. Custom, single-piece microfluidic chips were interfaced with small angle ...


The Complex Role Of Sequence And Structure In The Stability And Function Of The Tim Barrel Proteins, Yvonne H. Chan Nov 2017

The Complex Role Of Sequence And Structure In The Stability And Function Of The Tim Barrel Proteins, Yvonne H. Chan

GSBS Dissertations and Theses

Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy for elucidating the complex interrelationship in the context of a protein fold.

Fitness effects of point mutations in ...


Regulation Of The Fgf/Erk Signaling Pathway: Roles In Zebrafish Gametogenesis And Embryogenesis, Jennifer M. Maurer Oct 2017

Regulation Of The Fgf/Erk Signaling Pathway: Roles In Zebrafish Gametogenesis And Embryogenesis, Jennifer M. Maurer

GSBS Dissertations and Theses

Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation. Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are ...


Single-Molecule Studies Of Replication Kinetics In Response To Dna Damage, Divya Ramalingam Iyer May 2017

Single-Molecule Studies Of Replication Kinetics In Response To Dna Damage, Divya Ramalingam Iyer

GSBS Dissertations and Theses

In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions ...


Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh May 2017

Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh

GSBS Dissertations and Theses

Chromatin packages eukaryotic genomes via a hierarchical series of folding steps, encrypting multiple layers of epigenetic information, which are capable of regulating nuclear transactions in response to complex signals in environment. Besides the 1-dimensinal chromatin landscape such as nucleosome positioning and histone modifications, little is known about the secondary chromatin structures and their functional consequences related to transcriptional regulation and DNA replication. The family of chromosomal conformation capture (3C) assays has revolutionized our understanding of large-scale chromosome folding with the ability to measure relative interaction probability between genomic loci in vivo. However, the suboptimal resolution of the typical 3C techniques ...


Regulation Of The Drosophila Initiator Caspase Dronc Through Ubiquitylation, Hatem E. Kamber Kaya Jan 2017

Regulation Of The Drosophila Initiator Caspase Dronc Through Ubiquitylation, Hatem E. Kamber Kaya

GSBS Dissertations and Theses

Apoptosis is a programmed cell death mechanism that is evolutionary conserved from worms to humans. Apoptosis is mediated by initiator and effector caspases. The initiator caspases carry long pro-domains for their interaction with scaffolding proteins to form a cell-death platform, which is essential for their activation. Activated initiator caspases then cleave effector caspases that execute cell death through cleaving downstream targets. In addition to their apoptotic function, caspases also participate in events where caspase activity is not required for cell killing, but for regulating other functions, so-called non-apoptotic functions of caspases. The Drosophila initiator caspase Dronc, the ortholog of mammalian ...


Novel Mechanisms Regulating Dopamine Transporter Endocytic Trafficking: Ack1-Controlled Endocytosis And Retromer-Mediated Recycling, Sijia Wu Jan 2017

Novel Mechanisms Regulating Dopamine Transporter Endocytic Trafficking: Ack1-Controlled Endocytosis And Retromer-Mediated Recycling, Sijia Wu

GSBS Dissertations and Theses

Dopamine transporters (DAT) facilitate high-affinity presynaptic dopamine (DA) reuptake in the central nervous system, and are required to constrain extracellular DA levels and maintain presynaptic DAergic tone. DAT is the primary target for addictive and therapeutic psychostimulants, which require DAT binding to elicit reward. DAT availability at presynaptic terminals ensures its proper function, and is dynamically regulated by endocytic trafficking. My thesis research focused on two fundamental questions: 1) what are the molecular mechanisms that control DAT endocytosis? and 2) what are the mechanism(s) that govern DAT’s post-endocytic fate? Using pharmacological and genetic approaches, I discovered that a ...


Role Of Energy Metabolism In The Thermogenic Gene Program, Minwoo Nam Jan 2017

Role Of Energy Metabolism In The Thermogenic Gene Program, Minwoo Nam

GSBS Dissertations and Theses

In murine and human brown adipose tissue (BAT), mitochondria are powerful generators of heat. Emerging evidence has suggested that the actions of mitochondria extend beyond this conventional biochemical role. In mouse BAT and cultured brown adipocytes, impaired mitochondrial respiratory capacity is accompanied by attenuated expression of Ucp1, a key thermogenic gene, implying a mitochondrial retrograde signaling. However, few have investigated this association in the context of mitochondria-nucleus communication.

Using mice with adipose-specific ablation of LRPPRC, a regulator of respiratory capacity, we show that respiration-dependent retrograde signaling from mitochondria to nucleus contributes to transcriptional and metabolic reprogramming of BAT. Impaired respiratory ...


The Structural Basis For The Interdependence Of Drug Resistance In The Hiv-1 Protease, Debra A. Ragland Dec 2016

The Structural Basis For The Interdependence Of Drug Resistance In The Hiv-1 Protease, Debra A. Ragland

GSBS Dissertations and Theses

The human immunodeficiency virus type 1 (HIV-1) protease (PR) is a critical drug target as it is responsible for virion maturation. Mutations within the active site (1°) of the PR directly interfere with inhibitor binding while mutations distal to the active site (2°) to restore enzymatic fitness. Increasing mutation number is not directly proportional to the severity of resistance, suggesting that resistance is not simply additive but that it is interdependent. The interdependency of both primary and secondary mutations to drive protease inhibitor (PI) resistance is grossly understudied.

To structurally and dynamically characterize the direct role of secondary mutations in ...


Mtorc2 Promotes Lipid Storage And Suppresses Thermogenesis In Brown Adipose Tissue In Part Through Akt-Independent Regulation Of Foxo1: A Dissertation, Chien-Min Hung Oct 2016

Mtorc2 Promotes Lipid Storage And Suppresses Thermogenesis In Brown Adipose Tissue In Part Through Akt-Independent Regulation Of Foxo1: A Dissertation, Chien-Min Hung

GSBS Dissertations and Theses

Recent studies suggest adipose tissue plays a critical role in regulating whole body energy homeostasis in both animals and humans. In particular, activating brown adipose tissue (BAT) activity is now appreciated as a potential therapeutic strategy against obesity and metabolic disease. However, the signaling circuits that coordinate nutrient uptake and BAT function are poorly understood. Here, I investigated the role of the nutrient-sensing mTOR signaling pathway in BAT by conditionally deleting Rictor, which encodes an essential component of mTOR Complex 2 (mTORC2) either in brown adipocyte precursors or mature brown adipocytes. In general, inhibiting BAT mTORC2 reduces glucose uptake and ...


Viral Proteases As Drug Targets And The Mechanisms Of Drug Resistance: A Dissertation, Kuan-Hung Lin Sep 2016

Viral Proteases As Drug Targets And The Mechanisms Of Drug Resistance: A Dissertation, Kuan-Hung Lin

GSBS Dissertations and Theses

Viral proteases have been shown to be effective targets of anti-viral therapies for human immunodeficiency virus (HIV) and hepatitis C virus (HCV). However, under the pressure of therapy including protease inhibitors, the virus evolves to select drug resistance mutations both in the protease and substrates. In my thesis study, I aimed to understand the mechanisms of how this protease−substrate co-evolution contributes to drug resistance. Currently, there are no approved drugs against dengue virus (DENV); I investigated substrate recognition by DENV protease and designed cyclic peptides as inhibitors targeting the prime site of dengue protease.

First, I used X-ray crystallography ...


Overcoming Toxicity From Transgene Overexpression Through Vector Design In Aav Gene Therapy For Gm2 Gangliosidoses, Diane L. Golebiowski Sep 2016

Overcoming Toxicity From Transgene Overexpression Through Vector Design In Aav Gene Therapy For Gm2 Gangliosidoses, Diane L. Golebiowski

GSBS Dissertations and Theses

GM2 gangliosidoses are a family of lysosomal storage disorders that include both Tay-Sachs and Sandhoff diseases. These disorders result from deficiencies in the lysosomal enzyme β-N-acetylhexosaminidase (HexA). Impairment of HexA leads to accumulation of its substrate, GM2 ganglioside, in cells resulting in cellular dysfunction and death. There is currently no treatment for GM2 gangliosidoses. Patients primarily present with neurological dysfunction and degeneration. Here we developed a central nervous system gene therapy through direct injection that leads to long-term survival in the Sandhoff disease mouse model. We deliver an equal mixture of AAVrh8 vectors that encode for the two subunits (α ...


Functions Of Argonaute Proteins In Self Versus Non-Self Recognition In The C. Elegans Germline: A Dissertation, Meetu Seth Aug 2016

Functions Of Argonaute Proteins In Self Versus Non-Self Recognition In The C. Elegans Germline: A Dissertation, Meetu Seth

GSBS Dissertations and Theses

Organisms employ sophisticated mechanisms to silence foreign nucleic acid, such as viruses and transposons. Evidence exists for pathways that sense copy number, unpaired DNA, or aberrant RNA (e.g., dsRNA), but the mechanisms that distinguish “self” from “non-self” are not well understood. Our studies on transgene silencing in C. elegans have uncovered an RNA surveillance system in which the PIWI protein, PRG-1, uses a vast repertoire of piRNAs to recognize foreign transcripts and to initiate epigenetic silencing. Partial base pairing by piRNAs is sufficient to guide PRG-1 targeting. PRG-1 in turn recruits RdRP to synthesize perfectly matching antisense siRNAs (22G-RNAs ...


Investigation Of Rna Binding Protein Pumilio As A Genetic Modifier Of Mutant Chmp2b In Frontotemporal Dementia (Ftd): A Masters Thesis, Xing Du Aug 2016

Investigation Of Rna Binding Protein Pumilio As A Genetic Modifier Of Mutant Chmp2b In Frontotemporal Dementia (Ftd): A Masters Thesis, Xing Du

GSBS Dissertations and Theses

Frontotemporal dementia (FTD) is the second most common early-onset dementia. A rare mutation in CHMP2B gene was found to be associated with FTD linked to chromosome 3. Previous studies have shown that mutant CHMP2B could lead to impaired autophagy pathway and altered RNA metabolism. However, it is still unknown what genes mediate the crosstalk between different pathways affected by mutant CHMP2B. Genetic screens designed to identify genes interacting with mutant CHMP2B represents a key approach in solving the puzzle. Expression of mutant CHMP2B (CHMP2Bintron5) in Drosophila eyes leads to a neurodegenerative phenotype including melanin deposition and disrupted internal structure of ...


The Role Of Mdm2 Phosphorylation In P53 Responses To Dna Damage And Tumor Suppression: A Dissertation, Michael I. Carr Jul 2016

The Role Of Mdm2 Phosphorylation In P53 Responses To Dna Damage And Tumor Suppression: A Dissertation, Michael I. Carr

GSBS Dissertations and Theses

The p53 tumor suppressor protein is upregulated in response to DNA damage and other stress signals. The upregulation of p53 involves freeing it from negative regulation imposed by Mdm2 and MdmX (Mdm4). Accumulating evidence indicates that phosphorylation of Mdm proteins by different stress-activated kinases such as ATM or c-Abl significantly impacts p53 functions. We have previously shown that ATM phosphorylation of Mdm2 Ser394 is required for robust p53 stabilization and activation following DNA damage.

This dissertation describes in vivo examination of the mechanism by which Mdm2 Ser394 phosphorylation impacts p53 activities and its contribution to suppression of oncogene and DNA ...


Structural Mechanisms Of The Sliding Clamp And Sliding Clamp Loader: Insights Into Disease And Function: A Dissertation, Caroline M. Duffy Jul 2016

Structural Mechanisms Of The Sliding Clamp And Sliding Clamp Loader: Insights Into Disease And Function: A Dissertation, Caroline M. Duffy

GSBS Dissertations and Theses

Chromosomal replication is an essential process in all life. This dissertation highlights regulatory roles for two critical protein complexes at the heart of the replication fork: 1) the sliding clamp, the major polymerase processivity factor, and 2) the sliding clamp loader, a spiral-shaped AAA+ ATPase, which loads the clamp onto DNA.

The clamp is a promiscuous binding protein that interacts with at least 100 binding partners to orchestrate many processes on DNA, but spatiotemporal regulation of these binding interactions is unknown. Remarkably, a recent disease-causing mutant of the sliding clamp showed specific defects in DNA repair pathways. We aimed to ...


Systematic Experimental Determination Of Functional Constraints On Proteins And Adaptive Potential Of Mutations: A Dissertation, Li Jiang May 2016

Systematic Experimental Determination Of Functional Constraints On Proteins And Adaptive Potential Of Mutations: A Dissertation, Li Jiang

GSBS Dissertations and Theses

Sequence-function relationship is a fundamental question for many branches of modern biomedical research. It connects the primary sequence of proteins to the function of proteins and fitness of organisms, holding answers for critical questions such as functional consequences of mutations identified in whole genome sequencing and adaptive potential of fast evolving pathogenic viruses and microbes. Many different approaches have been developed to delineate the genotype-phenotype map for different proteins, but are generally limited by their throughput or precision. To systematically quantify the fitness of large numbers of mutations, I modified a novel high throughput mutational scanning approach (EMPIRIC) to investigate ...


Characterizing The Disorder In Tristetraprolin And Its Contribution To Post-Transcriptional Gene Regulation: A Dissertation, Laura M. Deveau May 2016

Characterizing The Disorder In Tristetraprolin And Its Contribution To Post-Transcriptional Gene Regulation: A Dissertation, Laura M. Deveau

GSBS Dissertations and Theses

RNA-binding proteins (RBPs) are important for a wide variety of biological processes involved in gene regulation. However, the structural and dynamic contributions to their biological activity are poorly understood. The tristetraprolin (TTP) family of RBPs, including TTP, TIS11b and TIS11d, regulate the stability of mRNA transcripts encoding for key cancer-related proteins, such as tumor necrosis factor- and vascular endothelial growth factor. Biophysical studies have shown that the RNA binding domain, consisting of two CCCH zinc fingers (ZFs), is folded in the absence of RNA in TIS11d and TIS11b. In TTP, however, only ZF1 adopts a stable fold, while RNA is ...


The Identification And Targeting Of Partially-Folded Conformations On The Folding Free-Energy Landscapes Of Als-Linked Proteins For Therapeutic Intervention: A Dissertation, Brian C. Mackness Apr 2016

The Identification And Targeting Of Partially-Folded Conformations On The Folding Free-Energy Landscapes Of Als-Linked Proteins For Therapeutic Intervention: A Dissertation, Brian C. Mackness

GSBS Dissertations and Theses

The hallmark feature of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), is the accumulation of cytoplasmic inclusions of key disease-linked proteins. Two of these proteins, TDP-43 and SOD1, represent a significant proportion of sporadic and familial ALS cases, respectively. The population of potentially aggregation-prone partially-folded states on the folding free-energy landscape may serve as a common mechanism for ALS pathogenesis. A detailed biophysical understanding of the folding and misfolding energy landscapes of TDP-43 and SOD1 can provide critical insights into the design of novel therapeutics to delay onset and progression in ALS.

Equilibrium unfolding studies on the RNA recognition ...