Open Access. Powered by Scholars. Published by Universities.®
Biochemistry, Biophysics, and Structural Biology Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Molecular Biology (110)
- Medicine and Health Sciences (101)
- Cell and Developmental Biology (87)
- Cell Biology (82)
- Laboratory and Basic Science Research (64)
-
- Medical Sciences (62)
- Genetics and Genomics (46)
- Diseases (44)
- Molecular Genetics (41)
- Medical Cell Biology (30)
- Medical Molecular Biology (28)
- Microbiology (19)
- Neoplasms (19)
- Biological Phenomena, Cell Phenomena, and Immunity (18)
- Cancer Biology (18)
- Genetic Processes (17)
- Organisms (16)
- Physiology (13)
- Biochemistry (12)
- Fungi (12)
- Neuroscience and Neurobiology (12)
- Cellular and Molecular Physiology (11)
- Immunology and Infectious Disease (11)
- Molecular and Cellular Neuroscience (11)
- Analytical, Diagnostic and Therapeutic Techniques and Equipment (9)
- Chemicals and Drugs (8)
- Disease Modeling (8)
- Nervous System Diseases (8)
- Keyword
-
- Cyclin C (14)
- Humans (14)
- Saccharomyces cerevisiae (10)
- Animals (9)
- Apoptosis (7)
-
- RNA (7)
- Med13 (6)
- Saccharomyces cerevisiae Proteins (6)
- Yeast (6)
- Autoantibodies (5)
- Biomarkers (5)
- Cell death (5)
- Gene Expression Regulation (5)
- Male (5)
- Mitochondria (5)
- Neurodegenerative Diseases (5)
- Oxidative Stress (5)
- Autophagy (4)
- Biofilms (4)
- Blood-Brain Barrier (4)
- Caenorhabditis elegans (4)
- Cancer (4)
- Cdk8 (4)
- DNA (4)
- Female (4)
- Mice (4)
- Mutation (4)
- Oxidative stress (4)
- Reactive Oxygen Species (4)
- Signal Transduction (4)
- Publication Year
- Publication
- Publication Type
Articles 1 - 30 of 130
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
A Rho5-Cnc1-Dnm1 Signalling Module Coordinates Multi-Organelle Execution Of Regulated Cell Death In Yeast, Justin Bauer
A Rho5-Cnc1-Dnm1 Signalling Module Coordinates Multi-Organelle Execution Of Regulated Cell Death In Yeast, Justin Bauer
Theses and Dissertations
Regulated cell death is a conserved process with major implications for health and disease, yet how yeast cells integrate stress signals to determine survival versus death remains unclear. This thesis investigates Cyclin C (Cnc1), a conserved Mediator kinase module component with both transcriptional and mitochondrial roles. Together with Cdk8 Cnc1 primarily represses stress response genes, while upon stress it translocates to the mitochondria to induce mitochondrial fragmentation with the dynamin-related GTPase Dnm1. Using structure-guided separation-of-function mutants, I demonstrate that Cnc1-dependent death requires its mitochondrial function rather than its transcriptional role, and that its effector Dnm1 acts as a signaling node …
Biophysical Insights Into A Cryptic, Hydrophobic Binding Site On Pcna, Alexis Dispensa
Biophysical Insights Into A Cryptic, Hydrophobic Binding Site On Pcna, Alexis Dispensa
Theses and Dissertations
Proteins are dynamic molecules whose functional landscapes extend beyond static structural representations. Transient cryptic pockets (buried cavities that emerge through protein motion) represent underexplored targets for allosteric regulation and drug discovery. General anesthetics are small, lipophilic, weakly polar molecules that are well suited to partition into such hydrophobic sites. In this work, environment-sensitive fluorescence, photoaffinity labeling, mass spectrometry, mutational analysis, and microsecond molecular dynamics simulations were integrated to discover and characterize a cryptic, highly apolar binding site within the hydrophobic core of human proliferating cell nuclear antigen (PCNA), a central scaffold in DNA replication and repair. Using the solvatochromic fluorescent …
The Role Of Emerin In Myogenic Differentiation, Nicholas Marano
The Role Of Emerin In Myogenic Differentiation, Nicholas Marano
Theses and Dissertations
The nucleus harbors genetic material encapsulated by the nuclear envelope which is composed of an inner and outer nuclear membrane. The establishment and organization of chromatin at the INM is essential for cell fate during the differentiation program. Integral INM proteins are responsible for chromatin organization at the nuclear envelope. Emerin is a highly conserved type II integral INM protein with roles in chromatin organization, cell signaling, and nuclear structure. Mutations in the emerin gene cause Emery Dreifuss Muscular Dystrophy 1 (EDMD1). Emerin is ubiquitously expressed, but loss of emerin function affects specifically skeletal muscle and cardiac tissue. The precise …
Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation., Nicholas Marano, Liza Elif Guner, Rachel S Riley, James M Holaska
Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation., Nicholas Marano, Liza Elif Guner, Rachel S Riley, James M Holaska
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Emery-Dreifuss muscular dystrophy 1 (EDMD1) arises from mutations in EMD. Most EDMD1 patients lack detectable emerin expression. They experience symptoms such as skeletal muscle wasting, joint contractures, and cardiac conduction defects. Currently, physicians rely on treating patient symptoms without addressing the underlying cause-lack of functional emerin protein. Thus, there is a need for therapeutic approaches that restore emerin protein expression to improve patient outcomes. One way would be to deliver emerin mRNA or protein directly to affected tissues to restore tissue homeostasis. Here, we evaluated the utility of lipid nanoparticles (LNPs) to deliver emerin mRNA to diseased cells. LNPs …
From Differentiation To Disease: Cyclin C Directly Coordinates Transcription And Mitochondrial Dynamics, Alicia Campbell
From Differentiation To Disease: Cyclin C Directly Coordinates Transcription And Mitochondrial Dynamics, Alicia Campbell
Theses and Dissertations
Organelle crosstalk is essential for coordinating cellular responses to various external cues, including stress and differentiation. Two key organelles, the nucleus and mitochondria, engage in extensive crosstalk to manage responses to a range of environmental and developmental signals. Complex processes such as stem cell differentiation and neuronal development rely on organelle crosstalk. Both processes integrate changes in gene expression with cytosolic and organellar remodeling. However, it remains unclear how these two complex processes are coordinated to achieve the desired outcome. This project concentrates on cyclin C (CCNC), a component of the Mediator Kinase Module (MKM), and its role in directly …
Ion-Dna Interactions As A Key Determinant Of Uracil Dna Glycosylase Activity., Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser
Ion-Dna Interactions As A Key Determinant Of Uracil Dna Glycosylase Activity., Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Because of their ubiquitous presence, ions interact with numerous macromolecules in the cell and affect critical biological processes. Here, we discuss how cations including Mg2+ alter the enzymatic activity of a DNA glycosylase by tuning its affinity for DNA. The response of uracil DNA glycosylase (UNG2) to Mg2+ ions in solution is biphasic and paradoxical, where low concentrations of the ion stimulate the enzyme, but high concentrations inhibit the enzyme. We analyzed this phenomenon by modeling experimental data with a statistical framework that we empirically derived to understand molecular systems that display biphasic behaviors. Parameters from our statistical …
Exploring The Role Of Lysine Acetylation During Biofilm Formation In Bacillus Subtilis, Jennifer Nguyen, Briana Ericka Reid, Valerie Carabetta
Exploring The Role Of Lysine Acetylation During Biofilm Formation In Bacillus Subtilis, Jennifer Nguyen, Briana Ericka Reid, Valerie Carabetta
Rowan-Virtua Research Day
Biofilms are structured communities of bacterial cells encased in a self-produced extracellular matrix, composed of polysaccharides, extracellular DNA, and proteins. Bacteria in a biofilm pose significant challenges in healthcare due to their resistance to disinfectants and tolerance to antibiotics. In some species, histone-like proteins were found to be important structural components of the biofilm. Nε-Lysine acetylation is a widespread post-translational modification (PTM) in bacteria, which can alter a protein’s function. The histone-like protein HBsu in Bacillus subtilis is acetylated at seven sites in vivo. We hypothesized that the acetylation state of HBsu may alter biofilm structure or the genetic programming, …
Exploring Intracellular Signaling Responses To Ks18, A Potent Mcl-1 Inhibitor, In Multiple Myeloma, Emily Nelson, Omar S Al-Odat, Dhruti A. Brahmbhatt, Tulin Budak-Alpdogan, Subash Jonnalagadda, Manoj Kumar Pandey
Exploring Intracellular Signaling Responses To Ks18, A Potent Mcl-1 Inhibitor, In Multiple Myeloma, Emily Nelson, Omar S Al-Odat, Dhruti A. Brahmbhatt, Tulin Budak-Alpdogan, Subash Jonnalagadda, Manoj Kumar Pandey
Rowan-Virtua Research Day
Multiple myeloma (MM), a cancer of plasma B cells, is a hematological malignancy in which patients inevitably relapse and develop drug resistance. Mcl-1, a member of the anti-apoptotic subgroup of Bcl-2 family proteins, plays a critical role in the progression of multiple myeloma and contributes significantly to drug resistance. Elevated Mcl-1 expression is observed in approximately 52% of MM patients at diagnosis, increasing to 81% at relapse. Given its driving role in disease progression and therapy resistance, Mcl-1 inhibition has emerged as a promising therapeutic target, prompting ongoing research into the development and clinical evaluation of Mcl-1 inhibitors, particularly for …
Direct Synthesis Of Cerium Oxide Nanoparticles In Reducing Sugars: Enhanced Ce3+ Surface Density For Biological Application, Balaashwin Babu, Elayaraja Kolanthai, Craig J. Neal, Samarah V. Harb, Udit Kumar, Yifei Fu, Sudipta Seal
Direct Synthesis Of Cerium Oxide Nanoparticles In Reducing Sugars: Enhanced Ce3+ Surface Density For Biological Application, Balaashwin Babu, Elayaraja Kolanthai, Craig J. Neal, Samarah V. Harb, Udit Kumar, Yifei Fu, Sudipta Seal
Rowan-Virtua Research Day
Cerium oxide nanoparticles (CNPs) are recognized for their ability to scavenge reactive oxygen species (ROS), making them promising candidates for mitigating oxidative damage in biomedical applications. However, many conventional synthesis methods limit the formation of Ce³⁺ states, which are critical for this antioxidant function. Building upon previous findings that glucose can promote Ce³⁺ formation, this study investigates the broader impact of both reducing (glucose, fructose, galactose) and non-reducing (dextran, sucrose, cyclodextrin) natural sugars on CNP synthesis. CNPs were synthesized in the presence of these sugars, and the surface densities of Ce³⁺ were measured. Results showed that reducing sugars significantly increased …
Hypoxia Induced Ribosomal Rna Fragmentation Mediated By Rnase L, Vanessa Kristina Pizutelli, Dimitri G Pestov
Hypoxia Induced Ribosomal Rna Fragmentation Mediated By Rnase L, Vanessa Kristina Pizutelli, Dimitri G Pestov
Rowan-Virtua Research Day
Ischemic injury contributes to a range of global pathologies. Ischemia/Reperfusion Injury (IRI) is a paradoxical phenomenon that involves an initial restriction of blood flow followed by a sudden restoration of perfusion. This type of injury takes place in conditions such as myocardial infarction, acute kidney disease, and ischemic stroke and often leads to cellular death. Additionally, IRI exacerbates post-surgical outcomes and plays a role in graft dysfunction and transplant rejection. Despite efforts to develop therapies targeting known IRI pathways, clinical trials have largely been unsuccessful, underscoring the need for alternative mechanisms and biomarkers associated with IRI-induced apoptosis. Reactive oxygen species …
Cargo Hitchhiking Autophagy - A Hybrid Autophagy Pathway Utilized In Yeast, Katrina F Cooper
Cargo Hitchhiking Autophagy - A Hybrid Autophagy Pathway Utilized In Yeast, Katrina F Cooper
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Macroautophagy is a catabolic process that maintains cellular homeostasis by recycling intracellular material through the use of double-membrane vesicles called autophagosomes. In turn, autophagosomes fuse with vacuoles (in yeast and plants) or lysosomes (in metazoans), where resident hydrolases degrade the cargo. Given the conservation of autophagy,
Inhibition Of Lysine Deacetylase Activity Impacts Formation Of The Vitamin D Receptor Activation Complex, Shannon Dwyer
Inhibition Of Lysine Deacetylase Activity Impacts Formation Of The Vitamin D Receptor Activation Complex, Shannon Dwyer
Theses and Dissertations
The vitamin D endocrine system is responsible for the regulation of many biological processes including bone metabolism, calcium homeostasis, cell proliferation and cell differentiation. Alterations to the vitamin D signaling pathway are associated with several diseases including bone diseases, diabetes, cardiovascular diseases, autoimmune diseases, and cancer. Vitamin D precursors are chemically modified to become the biologically active hormone, calcitriol. Calcitriol binds to the vitamin D receptor (VDR), a member of the nuclear hormone receptor (NHR) superfamily. VDR forms a heterodimer with retinoid X receptor (RXR) and together they bind to promoters containing vitamin D response elements (VDREs) to activate transcription …
Effects Of Cadherin Mediated Contact Normalization On Oncogenic Src Kinase Mediated Gene Expression And Protein Phosphorylation, Rachel E Nicoletto, Cayla J Holdcraft, Ariel C Yin, Edward P Retzbach, Stephanie A Sheehan, Amanda A Greenspan, Christopher M Laugier, Jason Trama, Caifeng Zhao, Haiyan Zheng, Gary S Goldberg
Effects Of Cadherin Mediated Contact Normalization On Oncogenic Src Kinase Mediated Gene Expression And Protein Phosphorylation, Rachel E Nicoletto, Cayla J Holdcraft, Ariel C Yin, Edward P Retzbach, Stephanie A Sheehan, Amanda A Greenspan, Christopher M Laugier, Jason Trama, Caifeng Zhao, Haiyan Zheng, Gary S Goldberg
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called "contact normalization", to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a β-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. β-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to …
Dissecting The Interplay Of Protein Synthesis And Degradation Pathways In Cellular Adaptation To Stress, Brittany Friedson
Dissecting The Interplay Of Protein Synthesis And Degradation Pathways In Cellular Adaptation To Stress, Brittany Friedson
Theses and Dissertations
Adaptation to stress requires cells to reprogram transcription, translation, and proteolytic pathways. Although much is known about the response of each program, it remains unclear how they coordinate following stress. My studies in S. cerevisiae identified the Cdk8 kinase module (CKM) of the Mediator complex as a new player in coordinating these processes. It is well established that the CKM consists of four highly conserved proteins (cyclin C, its cognate kinase Cdk8, and two structural proteins Med12 and Med13) and predominantly represses a subset of stress responsive genes in yeast. We demonstrated for the first time that the CKM also …
Emerin Deficiency Drives Mcf7 Cells To An Invasive Phenotype, Emily Hansen, Christal Rolling, Matthew Wang, James M Holaska
Emerin Deficiency Drives Mcf7 Cells To An Invasive Phenotype, Emily Hansen, Christal Rolling, Matthew Wang, James M Holaska
Rowan-Virtua School of Osteopathic Medicine Departmental Research
During metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer …
A Homogeneous Time-Resolved Fluorescence Screen To Identify Sirt2 Deacetylase And Defatty-Acylase Inhibitors, Jie Yang, Joel Cassel, Brian C Boyle, Daniel Oppong, Young-Hoon Ahn, Brian P Weiser
A Homogeneous Time-Resolved Fluorescence Screen To Identify Sirt2 Deacetylase And Defatty-Acylase Inhibitors, Jie Yang, Joel Cassel, Brian C Boyle, Daniel Oppong, Young-Hoon Ahn, Brian P Weiser
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Human sirtuin-2 (SIRT2) has emerged as an attractive drug target for a variety of diseases. The enzyme is a deacylase that can remove chemically different acyl modifications from protein lysine residues. Here, we developed a high-throughput screen based on a homogeneous time-resolved fluorescence (HTRF) binding assay to identify inhibitors of SIRT2's demyristoylase activity, which is uncommon among many ligands that only affect its deacetylase activity. From a test screen of 9600 compounds, we identified a small molecule that inhibited SIRT2's deacetylase activity (IC50 = 7 μM) as well as its demyristoylase activity (IC50 = 37 μM). The inhibitor was composed …
Discovery Of Oligomeric States And Small Molecules That Affect Deacylase Activities Of Human Sirtuin-2 (Sirt2), Jie Yang
Theses and Dissertations
Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that removes various acyl modifications from lysine residues. SIRT2 is involved in many biological processes, such as transcription, DNA repair, cell proliferation, and metabolism. Due to its diverse functions, SIRT2 is implicated in various disease states, including cancers and neurodegenerative disorders. This dissertation aimed to understand the regulation of SIRT2’s deacylase activities and to discover small molecule modulators of SIRT2. In this work, we found that SIRT2 dimerized in solution, and the dimerization decreased the deacetylase activities without affecting the defatty-acylase activity of this protein. Dimerized SIRT2 dissociates into monomers upon …
Rewiring The Sex-Determination Pathway During The Evolution Of Self-Fertility., Yongquan Shen, Shin-Yi Lin, Jonathan Harbin, Richa Amin, Allison Vassalotti, Joseph Romanowski, Emily Schmidt, Alexis Tierney, Ronald E Ellis
Rewiring The Sex-Determination Pathway During The Evolution Of Self-Fertility., Yongquan Shen, Shin-Yi Lin, Jonathan Harbin, Richa Amin, Allison Vassalotti, Joseph Romanowski, Emily Schmidt, Alexis Tierney, Ronald E Ellis
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Although evolution is driven by changes in how regulatory pathways control development, we know little about the molecular details underlying these transitions. The TRA-2 domain that mediates contact with TRA-1 is conserved in Caenorhabditis. By comparing the interaction of these proteins in two species, we identified a striking change in how sexual development is controlled. Identical mutations in this domain promote oogenesis in Caenorhabditis elegans but promote spermatogenesis in Caenorhabditis briggsae. Furthermore, the effects of these mutations involve the male-promoting gene fem-3 in C. elegans but are independent of fem-3 in C. briggsae. Finally, reciprocal mutations in these genes show …
Maackia Amurensis Seed Lectin (Masl) And Soluble Human Podoplanin (Shpdpn) Sequence Analysis And Effects On Human Oral Squamous Cell Carcinoma (Oscc) Cell Migration And Viability, Ariel C Yin, Cayla J Holdcraft, Eamonn J Brace, Tyler J Hellmig, Sayan Basu, Saumil Parikh, Katarzyna Jachimowska, Evelyne Kalyoussef, Dylan Roden, Soly Baredes, Eugenio M Capitle, David I Suster, Alan J Shienbaum, Caifeng Zhao, Haiyan Zheng, Kevin Balcaen, Simon Devos, Jurgen Haustraete, Mahnaz Fatahzadeh, Gary S Goldberg
Maackia Amurensis Seed Lectin (Masl) And Soluble Human Podoplanin (Shpdpn) Sequence Analysis And Effects On Human Oral Squamous Cell Carcinoma (Oscc) Cell Migration And Viability, Ariel C Yin, Cayla J Holdcraft, Eamonn J Brace, Tyler J Hellmig, Sayan Basu, Saumil Parikh, Katarzyna Jachimowska, Evelyne Kalyoussef, Dylan Roden, Soly Baredes, Eugenio M Capitle, David I Suster, Alan J Shienbaum, Caifeng Zhao, Haiyan Zheng, Kevin Balcaen, Simon Devos, Jurgen Haustraete, Mahnaz Fatahzadeh, Gary S Goldberg
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Maackia amurensis lectins serve as research and botanical agents that bind to sialic residues on proteins. For example, M. amurensis seed lectin (MASL) targets the sialic acid modified podoplanin (PDPN) receptor to suppress arthritic chondrocyte inflammation, and inhibit tumor cell growth and motility. However, M. amurensis lectin nomenclature and composition are not clearly defined. Here, we sought to definitively characterize MASL and its effects on tumor cell behavior. We utilized SDS-PAGE and LC-MS/MS to find that M. amurensis lectins can be divided into two groups. MASL is a member of one group which is composed of subunits that form dimers, …
The Role Of Med13 In Proteaphagy, John Sauer, Brittany Friedson, Katrina Cooper
The Role Of Med13 In Proteaphagy, John Sauer, Brittany Friedson, Katrina Cooper
Rowan-Virtua Research Day
Regulation of proteasomes is important for adaptation to cellular stress. Previous studies have shown that following starvation stress, proteasomes are targeted for destruction by autophagy. However, how cells control proteasomes in response to nitrogen starvation remains unclear. This study delves into the intricate interplay between Med13, proteaphagy, and stress response regulation, aiming to elucidate their roles in cellular survival mechanisms. It focused on the highly conserved Cdk8 kinase module (CKM) of the Mediator complex a that plays a pivotal involvement in cellular signaling and gene regulation under stress conditions. During the investigation, we asked if the degradation of specific proteasome …
Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova
Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA–guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus …
Ksp1 Is An Autophagic Receptor Protein For The Snx4-Assisted Autophagy Of Ssn2/Med13, Sara E Hanley, Stephen D Willis, Steven J Doyle, Randy Strich, Katrina F Cooper
Ksp1 Is An Autophagic Receptor Protein For The Snx4-Assisted Autophagy Of Ssn2/Med13, Sara E Hanley, Stephen D Willis, Steven J Doyle, Randy Strich, Katrina F Cooper
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting …
The Role Of The Cdk8 Kinase Module In Maintaining Proteostasis, Stephen Willis
The Role Of The Cdk8 Kinase Module In Maintaining Proteostasis, Stephen Willis
Theses and Dissertations
The underlying etiology of numerous disease states results from perturbations in the maintenance of cellular proteostasis. Carcinogenesis relies on these perturbations to foster uncontrolled cell growth and eventual metastases, while neurodegenerative diseases are a consequence of such perturbations. Control of these processes occurs at numerous molecular levels, commonly starting with transcription. A key transcriptional complex that is involved is the CDK8 Kinase Module (CKM). The CKM is conserved from yeast to man, forming a tetrameric complex consisting of MED12, MED13, CDK8, and CCNC. The CKM has not only been implicated in a variety of cancers but also in a spectrum …
Elastin-Like Polypeptide As A Model To Study Intrinsically Disordered Proteins, Sadegh Majdi
Elastin-Like Polypeptide As A Model To Study Intrinsically Disordered Proteins, Sadegh Majdi
Theses and Dissertations
The elastin-like polypeptide (ELP) is a well-studied structural protein that is easily amenable to amino acid (AA) sequence modifications and has the potential to yield a wide variety of uses in bioengineering and biomedical applications. One unique property of ELP is the inclusion of intrinsically disordered domains (IDP) within the structure that allow for its diversity of physical properties. While it is generally understood that amino acid sequence dictates protein folding arrangements, the contributions of specific amino acid sequences to the intrinsic disorder of ELP has yet to be fully resolved. Therefore, identifying the contributions of specific amino acid sequences …
Unveiling The Unique Ras Isoform And Domain Specific Regulation Of Braf Kinase, Tarah Trebino
Unveiling The Unique Ras Isoform And Domain Specific Regulation Of Braf Kinase, Tarah Trebino
Theses and Dissertations
BRAF kinase is a key member of the MAPK pathway, important for cell growth and division. Upstream signals promote BRAF activation by interaction with the membrane bound GTPase, RAS, which leads to relief of autoinhibition and dimerization. The N-terminal regulatory domains of BRAF, including the BRAF specific region (BSR), the RAS binding domain (RBD), and the cysteine rich domain (CRD), govern the conformational state of the cytosolic, autoinhibited monomer and drive the RAS-RAF interaction. Active BRAF phosphorylates and activates its substrate MEK, which in turn phosphorylates and activates ERK. Mutations in RAS and BRAF are the cause of many cancers …
Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova
Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …
Fused In Sarcoma Regulates Glutamate Signaling And Oxidative Stress Response, Chiong-Hee Wong, Abu Rahat, Howard C Chang
Fused In Sarcoma Regulates Glutamate Signaling And Oxidative Stress Response, Chiong-Hee Wong, Abu Rahat, Howard C Chang
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Mutations in fused in sarcoma (fust-1) are linked to ALS. However, how these ALS causative mutations alter physiological processes and lead to the onset of ALS remains largely unknown. By obtaining humanized fust-1 ALS mutations via CRISPR-CAS9, we generated a C. elegans ALS model. Homozygous fust-1 ALS mutant and fust-1 deletion animals are viable in C. elegans. This allows us to better characterize the molecular mechanisms of fust-1-dependent responses. We found FUST-1 plays a role in regulating superoxide dismutase, glutamate signaling, and oxidative stress. FUST-1 suppresses SOD-1 and VGLUT/EAT-4 in the nervous system. FUST-1 also regulates synaptic AMPA-type glutamate receptor …
Effects Of Dimerization On The Deacylase Activities Of Human Sirt2., Jie Yang, Nathan I Nicely, Brian P Weiser
Effects Of Dimerization On The Deacylase Activities Of Human Sirt2., Jie Yang, Nathan I Nicely, Brian P Weiser
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that …
Evolutionary Conservation And Times Of Action Of Heterochronic Genes, Maria Ivanova
Evolutionary Conservation And Times Of Action Of Heterochronic Genes, Maria Ivanova
Theses and Dissertations
The heterochronic pathway of C. elegans is the most well-characterized system to date for controlling the sequence and timing of developmental events. However, we still have critical unanswered questions to address. First, little is known about the evolution of the heterochronic pathway, and of developmental timing in general. To determine if the roles of major heterochronic genes are conserved, I made mutants in orthologs of these genes in C. briggsae, using CRISPR/Cas9. My studies revealed a significant drift in the roles of some of the genes, although all of them are still involved in the developmental timing regulation, and several …
Fundamental Study Of Ionic Liquid Physicochemical Effects On Thermal Stability Of Model Biological Macromolecules, Austin Keith Clark
Fundamental Study Of Ionic Liquid Physicochemical Effects On Thermal Stability Of Model Biological Macromolecules, Austin Keith Clark
Theses and Dissertations
Ionic Liquids (ILs) are substances with a unique physical attribute compared to that of solid ionic salts. At room temperature, ILs are molten salts that have a variety of physical effects that can play a role in their impact on other molecules, as solvents or solutes. They can play the role of the solvent in a variety of applications, from biofuels to organic catalysis or as excipients in pharmaceutical formulations. These ILs have a desirable use as solvents due to their ability to be tunable substances. Changing the cation or anion of the IL causes a change in its physical …