Biochemistry, Biophysics, and Structural Biology Commons^™

Botanical Inventory Highlights And Management Considerations For Covenant Park, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the spring and summer of 2021, Calvin University students and faculty conducted a botanical inventory and assessment of the natural areas in Covenant Park, located at 3724 Shaffer Avenue SE, Kentwood, MI 49512. Given that the property was recently acquired by the City of Kentwood Parks & Recreation, the purpose of this inventory is to inform Kentwood Parks and Recreation staff about the site’s floristic quality, diversity, and ecological significance. The specific objectives of this study are to 1) provide a comprehensive inventory of the species of plants occurring on the property, 2) identify particular areas that would benefit …

Clpxp Degradation System In Escherichia Coli, A Study Of Its Energy Sources And Its Applications In Managing The Expression Levels Of Targeted Membrane And Soluble Proteins, Thilini Abeywansha

Theses and Dissertations--Chemistry

ClpXP is an Escherichia coli protease that carries out energy-dependent intracellular proteolysis. In recent years, this system has been widely studied due to its importance as protein regulatory machinery and a virulence factor. Protein substrates of ClpXP contain degrons with a specific protein sequence. SsrA tag is one of the five degrons known to designate proteins for ClpXP degradation. SsrA is an 11 amino acid peptide added to the C-terminus of nascent polypeptide chains translated from aberrant messenger RNAs lacking stop codons via a process called trans-translation.

ClpXP was known to targets only cytosolic proteins with degrons until recently, …

Investigation Of Multidrug Efflux Transporter Acrb In Escherichia Coli: Assembly, Degradation And Dynamics, Prasangi Irosha Rajapaksha

Theses and Dissertations--Chemistry

The Resistant Nodulation Division (RND) super family member, tripartite AcrA-AcrB-TolC efflux pump, is a major contributor in conferring multidrug-resistance in Escherichia coli. The structure of the pump complex, and drug translocation by functional rotation mechanism have been widely studied. Despite of all these data, the dynamics of the assembly process of the pump and AcrB during functional rotation in the process of drug efflux remains poorly understood. My thesis focuses on understanding the pump assembly process, dynamics of AcrB in functional rotation mechanism, and also investigate the mechanism of degradation of AcrB facilitated by a C-terminal ssrA tag.

In the …

Characterization Of Potential Anti-Infective Agents By Targeting Burkholderia Pseudomallei And Escherichia Coli Ispf, Dakota Lane Grote

Graduate Research Theses & Dissertations

With the likelihood of contracting an antibiotic resistant infection increasing, the need for novel anti-infective agents is critical. The development of novel anti-infective agents benefits from the identification of new target pathways necessary for the survival of the pathogen. One such target is the methylerythritol phosphate (MEP) pathway, responsible for the synthesis of the isoprenoid precursors isopentyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) in bacteria and other pathogenic organisms. The MEP pathway is an attractive target because it is specific to a wide range of pathogenic organisms, while humans have a separate pathway, the mevalonate (MVA) pathway, for the biosynthesis …

Development Of Fluorescence Microscopy Approaches To Study Subcellular Protein Transport And Enzymatic Activity, Anchal Singh

Masters Theses

Understanding the subcellular localization of proteins and their activity is important in understanding their normal function in eukaryotic cells. Fluorescence cellular imaging techniques can selectively and sensitively visualize subcellular biochemistry. Using this approach, two different methods were employed in this thesis. The first focused on studying protein import into peroxisome and the other on monitoring the activity of an endoplasmic reticulum (ER)-localized enzyme, human carboxylesterase 1 (CES1).

Peroxisomes are mainly known as the center for long chain fatty acid b-oxidation as well as the production and detoxification of hydrogen peroxide. Proteins which are needed in the peroxisomes are encoded in …

Xylan-Derived Carbon Nutrient Acquisition By Caulobacter Crescentus, Rhoda Ekuama Inkoom

Masters Theses

Bacterial decomposition of xylan and uptake of xylan-derived carbon compounds require a combination of enzymes, proteins, and complex molecular mechanisms. Bacteria have evolved molecular mechanisms for its utilization depending on its environment and source of xylan. Caulobacter crescentus, a Gram-negative bacterium which lives in an aquatic oligotrophic environment, exhibits asymmetric division which is an adaptive feature for its nutrient poor habitat. Although aromatic hydrocarbon and cellulose-derived mono-, di- and oligosaccharide utilization has been reported in literature, its xylan-derived carbon compound utilization is yet to be characterized. In this study, C. crescentus utilizes xylan-derived monomers arabinose, xylose and acetate as …

Developing Synthetic Strategies For Multifaceted Applications Of Stable Gold-Based Complexes, Randall Tyler Mertens

Theses and Dissertations--Chemistry

Development of stable gold-based complexes has been a rapidly advancing field due to the popularity of gold complexes, particularly for use in biomedical research and catalytic transformations. Given that auranofin, a gold(I) complex with FDA approval for the treatment of rheumatoid arthritis is used in the clinic, the development of stable gold-based molecules of clinical relevance is urgently needed. Herein are reported, synthetic strategies used for the development of new classes of gold(I) and gold(III) complexes for advancement in mitochondrial modulation for use as chemotherapeutics as well as application to gold catalysis due to the unique geometry of complexes presented …

Computational Insights On Medicinal Chemistry Targeting Cyp450s, Alexander D. Fenton

Theses and Dissertations--Chemistry

Modern-day medicinal chemistry has provided researchers with a wide variety of tools to not only gather greater insight from their data, but also to generate data in new ways. One such tool is the construction of computational protein models from crystallographic datasets, and their subsequent use to understand the structure-activity relationships of protein-ligand complexes. These models can be utilized for their predictive power to inform the synthesis of, and improvement of, lead compounds. It is the goal of this work to employ such models to the CYP450 enzyme system such that potent and selective inhibitors can be designed, evaluated biologically, …

Flavin Modification And Redox Tuning In The Bifurcating Electron Transfer Flavoprotein From Rhodopseudomonas Palustris: Two Arginines With Different Roles, Nishya Mohamed-Raseek

Theses and Dissertations--Chemistry

Electron bifurcation is considered as a third fundamental mode of energy conservation mechanism in addition to two well-known mechanisms, substrate level phosphorylation and Oxidative phosphorylation, in electron bifurcation endergonic and exergonic redox reactions are coupled. The newly discovered flavin based electron bifurcation in electron transfer flavoproteins (ETFs) helps to reduce low potential ferredoxin, which provides electrons to drive biologically demanding reactions such as atmospheric dinitrogen fixation in diazotroph and methane production in methanogens.

Current research demonstrates the capacity for electron bifurcation in the Rhodopseudomonas palustris ETF (RpalETF) system. RpalETF contains two chemically identical but functionally different FADs: …

Understanding The Role Of Charge On Particle Transport Within Semidilute And Concentrated Biopolymer Solutions And Tau Protein Condensates, Kanthi Nuti

Theses and Dissertations--Chemistry

Biological polymer networks such as mucus, extracellular matrix, nuclear pore complex, and bacterial biofilms, play a critical role in governing the transport of nutrients, biomolecules and particles within cells and tissues. The interactions between particle and polymer chains are responsible for effective selective filtering of particles within these macromolecular networks. This selective filtering is not dictated by steric alone but must use additional interactions such electrostatics, hydrophobic and hydrodynamic effects to control particle transport within biogels. Depending on chemical composition and desired function, biogels use selective filtering to allow some particles to permeate while preventing others from penetrating the biogel. …

Tet1-Mediated Dna Hydroxymethylation Regulates Adult Remyelination In Mice, Sarah Moyon, Rebecca Frawley, Damien Marechal, Dennis Huang, Katy L.H. Marshall-Phelps, Linde Kegel, Boguslawa Sadowski, Yong-Hui Jiang, David A. Lyons, Wiebke Möbius, Patrizia Casaccia

Advanced Science Research Center

The mechanisms regulating myelin repair in the adult central nervous system (CNS) are unclear. Here, we identify DNA hydroxymethylation, catalyzed by the Ten-Eleven- Translocation (TET) enzyme TET1, as necessary for myelin repair in young adults and defective in old mice. Constitutive and inducible oligodendrocyte lineage-specific ablation of Tet1 (but not of Tet2), recapitulate this age-related decline in repair of demyelinated lesions. DNA hydroxymethylation and transcriptomic analyses identify TET1-target in adult oligodendrocytes, as genes regulating neuro-glial communication, including the solute carrier (Slc) gene family. Among them, we show that the expression levels of the Na+/K+/Cl− transporter, SLC12A2, are …

Brain-Specific Lipoprotein Receptors Interact With Astrocyte Derived Apolipoprotein And Mediate Neuron-Glia Lipid Shuttling, Jun Yin, Emma Spillman, Ethan S. Cheng, Jacob Short, Yang Chen, Jingce Lei, Mary Gibbs, Justin S. Rosenthal, Chengyu Sheng, Yuki X. Chen, Kelly Veerasammy, Tenzin Choetso, Rinat Abzalimov, Bei Wang, Chun Han, Ye He, Quan Yuan

Advanced Science Research Center

Lipid shuttling between neurons and glia contributes to the development, function, and stress responses of the nervous system. To understand how a neuron acquires its lipid supply from specific lipoproteins and their receptors, we perform combined genetic, transcriptome, and biochemical analyses in the developing Drosophila larval brain. Here we report, the astrocyte-derived secreted lipocalin Glial Lazarillo (GLaz), a homolog of human Apolipoprotein D (APOD), and its neuronal receptor, the brain-specific short isoforms of Drosophila lipophorin receptor 1 (LpR1-short), cooperatively mediate neuron-glia lipid shuttling and support dendrite morphogenesis. The isoform specificity of LpR1 defines its distribution, binding partners, and ability to …

Elucidation Of The Structure Of Supramolecular Polymorphs In Peptide Nanofibres Using Raman Spectroscopy, Sian Sloan-Dennison, Ayala Lampel, Eileen Raßlenberg, Rein V. Ulijn, Ewen Smith, Karen Faulds, Duncan Graham

Advanced Science Research Center

Peptide fibre formation via molecular self-assembly is a key step in a range of cellular processes and increasingly considered as an approach to produce supramolecular biomaterials. We previously demonstrated the self-assembly of the tripeptide lysine-dityrosine (KYY) as a substrate for the formation of proton-conducting melanin-like materials. Point based Raman scattering is one of several techniques which were used to characterise the secondary structure of the KYY nanofibre but as is often the case with this type of fibre, the spectra are rather complex and in addition there were variations in intensity between samples making interpretation difficult. Using Raman mapping we …

Development Of Linked-Domain Protein Inhibitors Of The E2-Conjugating Enzyme Ube2d, Anneroos E. Nederstigt

University of the Pacific Theses and Dissertations

In most eukaryotic organisms, the ubiquitination pathway is one of the most important and versatile signaling systems in use. It is integral to processes such as protein degradation and homeostasis, DNA repair cell cycle regulation, signaling and regulation, epigenetics, and many more. Ubiquitin (Ub) is a short polypeptide of 8.6 kDa, 76 residues that functions as a reversible post-translation modification (PTM). It furthermore contains 7 different lysine residues (K6, K11, K27, K29, K33, K48, K63), all of which can form isopeptide linkages with one another to link individual Ub moieties to form unique polyUb chains onto substrates. The type of …

Critical Behavior In Evolutionary And Population Dynamics, Stephen Walter Ordway

Doctoral Dissertations

“This study is an exploration of phase transition behavior in evolutionary and population dynamics, and techniques for predicting population changes, across the disciplines of physics, biology, and computer science. Under the looming threat of climate change, it is imperative to understand the dynamics of populations under environmental stress and to identify early warning signals of population decline. These issues are explored here in (1) a computational model of evolutionary dynamics, (2) an experimental system of decaying populations under environmental stress, and (3) a machine learning approach to predict population changes based on environmental factors. Through the lens of critical phase …

Broadening The Capability Of Kinetics Analysis In Biomechanics, Nicholas Nelson

Electronic Theses and Dissertations

Two studies are discussed in this manuscript each preceded by a literature review of the topic. The first review and study explore agility movements and the effect that alternative upper designs in shoes might have on ground reaction force measures of performance. The second review and study evaluate methods of predicting ground reaction forces without the use of a force platform. A method of using effective forces and ways of improving its accuracy are evaluated in depth.

Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne

Articles

Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) …

Structure Based Prediction Of A Novel Gpr120 Antagonist Based On Pharmacophore Screening And Molecular Dynamics Simulations, Ajay Pal Mr, Gemma K. Kinsella, James Curtin

Articles

The G-protein coupled receptor, GPR120, has ubiquitous expression and multifaceted roles in modulating metabolic and anti-inflammatory processes. Recent implications of its role in cancer progression have presented GPR120 as an attractive oncogenic drug target. GPR120 gene knockdown in breast cancer studies revealed a role of GPR120-induced chemoresistance in epirubicin and cisplatin-induced DNA damage in tumour cells. Higher expression and activation levels of GPR120 is also reported to promote tumour angiogenesis and cell migration in colorectal cancer. Some agonists targeting GPR120 have been reported, such as TUG891 and Compound39, but to date development of small-molecule inhibitors of GPR120 is limited. …

Function Of Mllt3 In Liver Metabolism, Grace Ann Hammack

Master's Theses

The chromatin regulator MLLT3 recognizes target genes through the YEATS domain that identifies post-translationally modified histones, with preference for crotonyl and acetyl marks, and recruits different multiprotein effector complexes through its C-terminal domain to target genes. To study the role of MLLT3 in gene regulation, the Zeleznik-Le and Hemenway labs developed Mllt3 whole-body knockout (Mllt3;Rosa26-CreERT2) mice. These mice have a hematopoietic stem cell phenotype and an unexpected obesity and hepatic steatosis phenotype. It was unknown whether these phenotypes were from liver intrinsic effects or influenced by other parts of the body. To study this fatty liver phenotype further, Mllt3;Alb-Cre were …

Beta-Adrenergic Receptor Mediated Transcriptional Dysregulation In Hematopoeitc Stem And Progenitor Cells Leads To Bone Marrow Erythroid Suppresion In Multiple Myeloma Patients - Ex Vivo Investigations, Vimal Ravi Subramaniam

Master's Theses

The sympathetic nervous system (SNS) regulates our body’s involuntary response to stress or harm. Once activated, it releases hormones and neurotransmitters known as catecholamines throughout the body to mediate its recovery. The catecholamines bind to adrenergic receptors located on various cells in a process designated as adrenergic signaling to elicit this response. This process is not always to our benefit. Adverse symptoms such as anemia can result due to adrenergic signaling. Our laboratory previously showed that burn injury triggers adrenergic receptor stimulation resulting in anemia induced by diminished erythropoiesis. The development of anemia in these studies was found to be …

Rapid Induction Of The Unfolded Protein Response And Apoptosis By Estrogen Mimic Ttc-352 For The Treatment Of Endocrine-Resistant Breast Cancer, Balkees Abderrahman, Philipp Y Maximov, Ramona F Curpan, Sean W Fanning, Jay S Hanspal, Ping Fan, Charles E Foulds, Yue Chen, Anna Malovannaya, Antrix Jain, Rui Xiong, Geoffrey L Greene, Debra A Tonetti, Gregory R J Thatcher, V Craig Jordan

Faculty, Staff and Students Publications

Patients with long-term estrogen-deprived breast cancer (BC), after resistance to tamoxifen or aromatase inhibitors develops, can experience tumor regression when treated with estrogens. Estrogen’s anti-tumor effect is attributed to apoptosis via the estrogen receptor (ER). Estrogen treatment can have unpleasant gynecological and non-gynecological adverse events thus the development of safer estrogenic agents remains a clinical priority. Here, we study synthetic selective estrogen mimics (SEMs) BMI-135 and TTC-352, and the naturally-occurring estrogen estetrol (E4), which are proposed as safer estrogenic agents compared to 17β-estradiol (E2), for the treatment of endocrine-resistant BC. TTC-352 and E4 are being evaluated in BC clinical trials. …

Small-Molecule Inhibitor Of Af9/Enl-Dot1l/Af4/Aff4 Interactions Suppresses Malignant Gene Expression And Tumor Grow, Fangrui Wu, Shenyou Nie, Yuan Yao, Tong Huo, Xin Li, Xiaowei Wu, Jidong Zhao, Yi-Lun Lin, Yinjie Zhang, Qianxing Mo, Yongcheng Song

Faculty, Staff and Students Publications

Chromosome translocations involving mixed lineage leukemia (MLL) gene cause acute leukemia with a poor prognosis. MLL is frequently fused with transcription cofactors AF4 (~35%), AF9 (25%) or its paralog ENL (10%). The AHD domain of AF9/ENL binds to AF4, its paralog AFF4, or histone-H3 lysine-79 (H3K79) methyltransferase DOT1L. Formation of AF9/ENL/AF4/AFF4-containing super elongation complexes (SEC) and the catalytic activity of DOT1L are essential for MLL-rearranged leukemia. Protein-protein interactions (PPI) between AF9/ENL and DOT1L/AF4/AFF4 are therefore a potential drug target.

Methods: Compound screening followed by medicinal chemistry was used to find inhibitors of such PPIs, which were examined for their biological …

Lrrtm4 Is A Member Of The Transsynaptic Complex Between Rod Photoreceptors And Bipolar Cells, Melina A Agosto, Theodore G Wensel

Faculty, Staff and Students Publications

Leucine rich repeat transmembrane (LRRTM) proteins are synaptic adhesion molecules with roles in synapse formation and signaling. LRRTM4 transcripts were previously shown to be enriched in rod bipolar cells (BCs), secondary neurons of the retina that form synapses with rod photoreceptors. Using two different antibodies, LRRTM4 was found to reside primarily at rod BC dendritic tips, where it colocalized with the transduction channel protein, TRPM1. LRRTM4 was not detected at dendritic tips of ON-cone BCs. Following somatic knockout of LRRTM4 in BCs by subretinal injection and electroporation of CRISPR/Cas9, LRRTM4 was abolished or reduced in the dendritic tips of transfected …

In Silico And In Vitro Tudies For Identification Of Novel Egfr Tyrosine Kinase Inhibitors, Duangjai Todsaporn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Epidermal growth factor receptor (EGFR) has been identified as a promising target in the treatment of non-small cell lung cancer (NSCLC). Mutations, including L858R/T790M double and L858R/T790M/C797S triple mutations, in the TK domain of EGFR have been linked to the severity of several cancers, especially NSCLC. A combination of comprehensive molecular modeling and in vitro kinase inhibition assay was used to unravel the mutational effects of EGFR on the susceptibility of five commercial drugs (erlotinib, gefitinib, afatinib, dacomitinib, and osimertinib) from each generation of EGFR in comparison with the wild-type EGFR. The binding affinity of five-FDA-approved drugs towards the L858R/T790M …

Neuroprotective Effect Of Passiflora Edulissims Against Amyloid Beta-Induced Neurotoxicity, Shuqin Cao

Chulalongkorn University Theses and Dissertations (Chula ETD)

Alzheimer’s disease (AD) is a common and devastating disease characterized by pathological aggregations of beta-amyloid (Aβ) plaques extracellularly, and Tau tangles intracellularly. While our understandings of the aetiologies of AD have greatly expanded over the decades, there is no drug available to stop disease progression. This study involves two parts. First, we demonstrate the potential of P. edulis pericarp (PP) extract in protecting against Aβ-mediated neurotoxicity in mammalian cells and Caenorhabditis elegans models of AD. We show PP protects against memory deficit, neuronal loss, and promotes longevity in the Aβ model of AD via stimulation of mitophagy, the selective cellular …

Substrate Binding Mechanism Of Glycerophosphodiesterase Towards Pesticides And Improvement Of Stability By Mutational Analysis, Nayana Bhat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Molecular dynamics studies have been providing a great number of atomistic details of biological systems to understand enzymatic activity and underlying reaction mechanisms. Herein, molecular dynamic (MD) simulations were employed to study the binding mechanisms of organophosphate pesticides towards two metallohydrolases, i.e., glycerophosphodiesterase (GpdQ) and methyl parathion hydrolase (MPH). OPH are the class of enzymes which breaks down harmful organophosphates, including the pesticides and warfare agents into less harmful byproducts. Hence, these enzymes are excellent candidates for bioremediation. In the present study, various nonspecific organophosphate pesticides were docked into GpdQ and MPH enzymes to construct the pesticide/protein complex for performing …

Functional Characterization Of Rice Malate Synthase In Arabidopsis Responding To Salt Stress, Supisara Thanabut

Chulalongkorn University Theses and Dissertations (Chula ETD)

Salt stress is one of the major abiotic stresses that seriously limit plant growth and development and can lead to a significant reduction in crop yield, especially rice. Salt stress affects plants via ionic toxicity and osmotic stress. Osmotic stress results in a reduction of water absorption ability. Ionic toxicity causes Na+ toxicity, which disrupts photosynthesis, protein synthesis, and enzyme activity. The previous study of KDML105 rice transcriptome profile and qRT-PCR revealed that rice malate synthase (OsMS) encoding malate synthase, which is one of the key enzymes in glyoxylate cycle was up-regulated under salt stress, so OsMS may involve in …

In Silico And In Vitro Screening Of Newly Designed Compounds Against Coxsackivirus A16 And Enterovirus A71, Amita Sripattaraphan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Outbreaks of hand, foot, and mouth disease (HFMD) occur around the world. It is caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71) that belong to the Enterovirus genus. Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir, one of the drug candidates for HFMD treatment, has been attractive for the development of its analogs with broad biological activities. This drug is an inhibitor for 3C protease of CV-A16 and EV-A71, an enzyme that plays a crucial role in the viral replication process. ). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 …

In Silico And In Vitro Studies On Inclusion Complexation Of Anthraquinone Derivatives With Beta-Cyclodextrin Derivatives, Amy Oo

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this study, we investigated the cytotoxicity of 6 anthraquinones (ventilanone K, emodin, chrysophanol, aurantio-obtusin, 1-O-methyl-2-methyoxychrysophanol, and questin) toward A549 lung cancer cells and emodin (ED) exerted the most potent cytotoxicity with IC50 value of 34.27 ± 1.27 µM. The anti-cancer activity of ED has been well reported but its usage in practical applications has been restricted due to its poor solubility. To address this issue, we performed inclusion complexation of ED with βCD, hydroxypropyl-β-cyclodextrin (HPβCD), 2,6-di-O-methyl-β-cyclodextrin (DMβCD), and sulfobutylether-β-cyclodextrin (SBEβCD) theoretically using molecular dynamics simulations and experimentally using phase solubility study and cytotoxicity screening toward cholangiocarcinoma cell lines (KKU-213A …

Mechanistic Insights Of Mitochondrial Reactive Oxygen Species In Alzheimer's Disease Models, Jakob C. Green

Theses and Dissertations

Alzheimer’s disease (AD) is a neurodegenerative disease that results in impaired cognition, disorientation, confusion, poor judgement, and behavioral changes. The mitochondrial cascade hypothesis (MCH), which postulates that accumulating oxidative stress and mitochondrial dysfunction plays an integral role in the development of the disease, potentially upstream, in conjunction with or independent of Aβ and tau. The literature supports the critical role of mitochondrial dysfunction in the progression and development of AD, but is inconclusive about what precise role, as initiator or delegate, it performs. Regardless, the impact that oxidative stress and mitochondrial dysfunction have on AD deserves further study and investigation. …