Biochemistry, Biophysics, and Structural Biology Commons^™

Bisthioether Stapled Peptides Targeting Polycomb Repressive Complex 2 Gene Repression, Gan Zhang

Dissertations, Theses, and Capstone Projects

Interactions between proteins play a key role in nearly all cellular process, and therefore, disruption of such interactions may lead to many different types of cellular dysfunctions. Hence, pathologic protein-protein interactions (PPIs) constitute highly attractive drug targets and hold great potential for developing novel therapeutic agents for the treatment of incurable human diseases. Unfortunately, the identification of PPI inhibitors is an extremely challenging task, since traditionally used small molecule ligands are mostly unable to cover and anchor on the extensive flat surfaces that define those binary protein complexes. In contrast, large biomolecules such as proteins or peptides are ideal fits …

Ck2 Negatively Regulates 5-Ht4 Receptor Signaling In The Prefrontal Cortex And Mediates Depression-Like Behaviors, Julia Castello Saval

Dissertations, Theses, and Capstone Projects

The serotonergic system has been the major candidate in the pathophysiology of mood related disorders such as anxiety and major depressive disorder (MDD). Unfortunately, current antidepressant drugs are ineffective in 50% of the population and require chronic administration for a period of 3-6 weeks before the onset of therapeutic response. 5-HT4 receptor (5-HT₄R) agonists have emerged as potential candidates for fast antidepressant action, since an antidepressant response can be achieved after 3 days of pharmacological administration in rodents.

This dissertation aims to investigate the role of casein kinase 2 (CK2) as a regulator of 5-HT₄R expression …

Analysis Of Oxygen-18 Labeled Phosphate To Study Positional Isotope Experiments Using Lc-Qtof-Ms, Sujatha Chilakala, Iteen Cheng, Ireen Lee, Yan Xu

Chemistry Faculty Publications

A method is proposed in this paper for the determination of oxygen-18 labeled phosphate so that positional isotope experiments using sensitive and rapid liquid chromatography–QTOF–mass spectrometry (LC-QTOF-MS) experiments can be carried out. The positional isotope exchange technique is a useful tool in understanding the mechanisms and kinetics of many enzyme-catalyzed reactions. Detection of the positions and concentration of these exchanged isotopes is the key. Gas chromatography–mass spectrometry (GC-MS) and nuclear magnetic resonance imaging are commonly used analytical techniques for measurement of ¹⁸O/¹⁶O, ³¹P and ¹⁵N isotope enrichment. Since these techniques either require a time-consuming derivatization …

Lncegfl7os Regulates Human Angiogenesis By Interacting With Max At The Egfl7/Mir-126 Locus, Quinbo Zhou, Chastain Anderson, Zhan-Peng Huang, Jakub Hanus, Wensheng Zhang, Yu Han

Faculty and Staff Publications

In an effort to identify human endothelial cell (EC)-enriched lncRNAs,~500 lncRNAswere shown to be highly restricted in primary human ECs. Among them,lncEGFL7OS, located inthe opposite strand of theEGFL7/miR-126gene, is regulated by ETS factors through abidirectional promoter in ECs. It is enriched in highly vascularized human tissues, and upregulatedin the hearts of dilated cardiomyopathy patients. LncEGFL7OS silencing impairs angiogenesis asshown by EC/fibroblast co-culture, in vitro/in vivo and ex vivo human choroid sproutingangiogenesis assays, while lncEGFL7OS overexpression has the opposite function. Mechanistically,lncEGFL7OS is required for MAPK and AKT pathway activation by regulating EGFL7/miR-126expression. MAX protein was identified as a lncEGFL7OS-interacting protein that …

Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana

Dissertations, Theses, and Capstone Projects

Medicinal plants are one of the biggest sources of natural products with therapeutic importance. There are currently over 28,000 plants with putative medicinal values. Plant-derived compounds have been explored extensively for various biological activities ranging from anti-cancer, immune-boosting to anti-inflammatory and anti-oxidant. Some of the most important therapeutic agents are of plant-origin, such as paclitaxel from Pacific yew (Taxus brevifolia) and artemisinin from qinghao su (a Chinese medicinal herb; a.k.a. Artemisia annua) to name a few.

The study presented in this thesis started out as classical pharmacognosy research, which focused on the identification of immunostimulatory factors in …

Structural Studies On Calcium/Calmodulin-Dependent Activation Of Eukaryotic Elongation Factor 2 Kinase, Kwangwoon Lee

Dissertations, Theses, and Capstone Projects

Eukaryotic elongation factor 2 kinase (eEF-2K) is a key modulator of the rate of protein synthesis. Activated by calcium-loaded calmodulin (Ca²⁺-CaM), eEF-2K phosphorylates its only known physiological substrate, eEF-2, on a specific threonine residue (Thr-56). Phosphorylated eEF-2 has reduced affinity for the ribosome, and results in a significant decrease in the rate of translation elongation. Modulation of the rate of translation elongation plays a crucial role in proteostasis – adequate regulation of protein synthesis, protein folding, and protein degradation that greatly influences cellular growth and survival. Binding of Ca²⁺-CaM triggers activation of eEF-2K and remains intact …

The Effect Of Dynamic Kinetic Selection On An Evolving Ribozyme Population, Patrick David Poletti

Dissertations and Theses

Dynamic Kinetic Selection (DKS) suggests that kinetic, rather than thermodynamic, stability will dictate the composition of a replicating population of biomolecules. Here, the results obtained from a series of five related reactions involving gradually increasing percentages of randomly-mutated substrate fragments to generate variants of full-length Azoarcus group I intron through an autocatalytic self-assembly reaction involving a series of recombination events, showed DKS as a driving factor in dictating the population composition of full-length product assembled from substrates that had fewer positions available to randomization.

In trying to elucidate a plausible scheme for the origins of complex biomolecules on the prebiotic …

A Rational Approach For Creating Peptides Mimicking Antibody Binding, Sameer Sachdeva, Hyun Joo, Jerry Tsai, Bhaskara Jasti, Xiaoling Li

School of Pharmacy Faculty Articles

This study reports a novel method to design peptides that mimic antibody binding. Using the Knob-Socket model for protein-protein interaction, the interaction surface between Cetuximab and EGFR was mapped. EGFR binding peptides were designed based on geometry and the probability of the mapped knob-sockets pairs. Designed peptides were synthesized and then characterized for binding specificity, affinity, cytotoxicity of drug-peptide conjugate and inhibition of phosphorylation. In cell culture studies, designed peptides specifically bind and internalize to EGFR overexpressing cells with three to four-fold higher uptake compared to control cells that do not overexpress EGFR. The designed peptide, Pep11, bound to EGFR …

Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão

Chemistry and Biochemistry Faculty Publications

Salicylate hydroxylase (NahG) is a flavin-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of salicylate into catechol in the naphthalene degradation pathway in Pseudomonas putida G7. We explored the mechanism of action of this enzyme in detail using a combination of structural and biophysical methods. NahG shares many structural and mechanistic features with other versatile flavin-dependent monooxygenases, with potential biocatalytic applications. The crystal structure at 2.0 Å resolution for the apo form of NahG adds a new snapshot preceding the FAD binding in flavin-dependent monooxygenases. The k_cat/K_m for the salicylate reaction catalyzed by the holo form is …

Immunization Of Alpacas (Lama Pacos) With Protein Antigens And Production Of Antigen-Specific Single Domain Antibodies, K. Martin Chow, Sidney W. Whiteheart, Jeffrey R. Smiley, Savita Sharma, Kathy Boaz, Meggie J. Coleman, Alvina Maynard, Louis B. Hersh, Craig W. Vander Kooi

Molecular and Cellular Biochemistry Faculty Publications

In this manuscript, a method for the immunization of alpaca and the use of molecular biology methods to produce antigen-specific single domain antibodies is described and demonstrated. Camelids, such as alpacas and llamas, have become a valuable resource for biomedical research since they produce a novel type of heavy chain-only antibody which can be used to produce single domain antibodies. Because the immune system is highly flexible, single domain antibodies can be made to many different protein antigens, and even different conformations of the antigen, with a very high degree of specificity. These features, among others, make single domain antibodies …

Speciated And Total Emission Factors Of Particulate Organics From Burning Western Us Wildland Fuels And Their Dependence On Combustion Efficiency, Coty N. Jen, Lindsay E. Hatch, Vanessa Selimovic, Robert J. Yokelson, Robert Weber, Arantza E. Fernandez, Nathan M. Kreisberg, Kelley C. Barsanti, Allen H. Goldstein

Chemistry and Biochemistry Faculty Publications

Western US wildlands experience frequent and large-scale wildfires which are predicted to increase in the future. As a result, wildfire smoke emissions are expected to play an increasing role in atmospheric chemistry while negatively impacting regional air quality and human health. Understanding the impacts of smoke on the environment is informed by identifying and quantifying the chemical compounds that are emitted during wildfires and by providing empirical relationships that describe how the amount and composition of the emissions change based upon different fire conditions and fuels. This study examined particulate organic compounds emitted from burning common western US wildland fuels …

Itch Nuclear Translocation And H1.2 Polyubiquitination Negatively Regulate The Dna Damage Response, Lufen Chang, Lei Shen, Hu Zhou, Jing Gao, Hangyi Pan, Li Zheng, Brian Armstrong, Yang Peng, Guang Peng, Binhua P. Zhou, Steven T. Rosen, Binghui Shen

Molecular and Cellular Biochemistry Faculty Publications

The downregulation of the DNA damage response (DDR) enables aggressive tumors to achieve uncontrolled proliferation against replication stress, but the mechanisms underlying this process in tumors are relatively complex. Here, we demonstrate a mechanism through which a distinct E3 ubiquitin ligase, ITCH, modulates DDR machinery in triple-negative breast cancer (TNBC). We found that expression of a nuclear form of ITCH was significantly increased in human TNBC cell lines and tumor specimens. Phosphorylation of ITCH at Ser257 by AKT led to the nuclear localization of ITCH and ubiquitination of H1.2. The ITCH-mediated polyubiquitination of H1.2 suppressed RNF8/RNF168-dependent formation of 53BP1 foci, …

Chemistry & Biochemistry Guest Lecture Series, Desmond Murray

Andrews Agenda: Campus News

No abstract provided.

Putative Cellular And Molecular Roles Of Zika Virus In Fetal And Pediatric Neuropathologies, Rajendra Ghardbaran, Rajendra Ghardbaran, Latchman Somenarain

Publications and Research

Although the World Health Organization declared an end to the recent Zika virus (ZIKV) outbreak and its association with adverse fetal and pediatric outcome, on November 18, 2016, the virus still remains a severe public health threat. Laboratory experiments thus far supported the suspicions that ZIKV is a teratogenic agent. Evidence indicated that ZIKV infection cripples the host cells' innate immune responses, allowing productive replication and potential dissemination of the virus. In addition, studies suggest potential transplacental passage of the virus and subsequent selective targeting of neural progenitor cells (NPCs). Depletion of NPCs by ZIKV is associated with restricted brain …

Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When an N-base approaches the tetrel atom of TF4(T = Si, Ge, Sn) the latter moleculedeforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situateitself at either an axial or equatorial position, leading to two different equilibrium geometries.The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol,which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform thetetrahedral monomer into the equatorial structure is much higher than the equivalent deformationenergy in the axial dimer. When these two opposite trends are combined, it is the axial …

Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard

Yale Day of Data

In the biological sciences, image analysis software are used to detect, segment or classify a variety of features encountered in living matter. However, the algorithms that accomplish these tasks are often designed for a specific dataset, making them hardly portable to accomplish the same tasks on images of different biological structures. Recently, convolutional neural networks have been used to perform complex image analysis on a multitude of datasets. While applications of these networks abound in the technology industry and computer science, use cases are not as common in the academic sciences. Motivated by the generalizability of neural networks, we aim …

A Three State Model Can Explain The Dynamics Of Class Iv Drosophila Dendritic Tips, Sabyasachi Sutradhar

Yale Day of Data

No abstract provided.

Deletion Of Mgr2p Affects The Gating Behavior Of The Tim23 Complex, Oygul Mirzalieva, Shinhye Jeon, Kevin Damri, Ruth Hartke, Layla Drwesh, Keren Demishtein-Zohary, Abdussalam Azem, Cory D. Dunn, Pablo M. Peixoto

Publications and Research

The TIM23 complex is a hub for translocation of preproteins into or across the mitochondrial inner membrane. This dual sorting mechanism is currently being investigated, and in yeast appears to be regulated by a recently discovered subunit, the Mgr2 protein. Deletion of Mgr2p has been found to delay protein translocation into the matrix and accumulation in the inner membrane. This result and other findings suggested that Mgr2p controls the lateral release of inner membrane proteins harboring a stop-transfer signal that follows an N-terminal amino acid signal. However, the mechanism of lateral release is unknown. Here, we used patch clamp electrophysiology …

Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao

Chemistry and Biochemistry Faculty Publications

Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB₃O₆ crystal-based optical parametric amplifier, which generates a …

Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity, Ryan R. Kerney, Jasper S. Leavitt, Elizabeth M. Hill, Huanjia Zhang, Eunsoo Kim, John Burns

Biology Faculty Publications

A unique symbiosis occurs between embryos of the spotted salamander (Ambystoma maculatum) and a green alga (Oophila amblystomatis). Unlike most vertebrate host-symbiont relationships, which are ectosymbiotic, A. maculatum exhibits both an ecto- and an endo-symbiosis, where some of the green algal cells living inside egg capsules enter embryonic tissues as well as individual salamander cells. Past research has consistently categorized this symbiosis as a mutualism, making this the first example of a “beneficial” microbe entering vertebrate cells. Another closely related species of salamander, Ambystoma gracile, also harbors beneficial Oophila algae in its egg capsules. However, our …

Antisense Oligonucleotides Targeting Angiotensinogen: Insights From Animal Studies, Chia-Hua Wu, Ya Wang, Murong Ma, Adam E. Mullick, Rosanne M. Crooke, Mark J. Graham, Alan Daugherty, Hong S. Lu

Saha Cardiovascular Research Center Faculty Publications

Angiotensinogen (AGT) is the unique substrate of all angiotensin peptides. We review the recent preclinical research of AGT antisense oligonucleotides (ASOs), a rapidly evolving therapeutic approach. The scope of the research findings not only opens doors for potentially new therapeutics of hypertension and many other diseases, but also provides insights into understanding critical physiological and pathophysiological roles mediated by AGT.

Fabrication Of Miniaturized Paper-Based Microfluidic Devices (Micropads), E. Brandon Strong, Spencer A. Schultz, Andres Martinez, Nathaniel W. Martinez

Chemistry and Biochemistry

Microfluidic paper-based analytical devices (microPADs) are emerging as cost-effective and portable platforms for point-of-care assays. A fundamental limitation of microPAD fabrication is the imprecise nature of most methods for patterning paper. The present work demonstrates that paper patterned via wax printing can be miniaturized by treating it with periodate to produce higher-resolution, high-fidelity microPADs. The optimal miniaturization parameters were determined by immersing microPADs in various concentrations of aqueous sodium periodate (NaIO₄) for varying lengths of time. This treatment miniaturized microPADs by up to 80% in surface area, depending on the concentration of periodate and length of the reaction …

Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl⁻ was thus compared to that of HCOO⁻, HSO₄⁻, and H₂PO₄⁻ with a wide variety of bidentate receptors. A pair …

Radiation Dose Estimation By Completely Automated Interpretation Of The Dicentric Chromosome Assay, Peter Rogan, Yanxin Li, Ben Shirley, Ruth Wilkins, Farrah Norton, Joan Knoll

Biochemistry Publications

Accuracy of the automated dicentric chromosome (DC) assay relies on metaphase image selection. This study validates a software framework to find the best image selection models that mitigate inter-sample variability. Evaluation methods to determine model quality include the Poisson goodness-of-fit of DC distributions for each sample, residuals after calibration curve fitting and leave-one-out dose estimation errors. The process iteratively searches a pool of selection model candidates by modifying statistical and filter cut-offs to rank the best candidates according to their respective evaluation scores. Evaluation scores minimize the sum of squared errors relative to the actual radiation dose of the calibration …

A Bird's-Eye View Of The Multiple Biochemical Mechanisms That Propel Pathology Of Alzheimer's Disease: Recent Advances And Mechanistic Perspectives On How To Halt The Disease Progression Targeting Multiple Pathways., Caleb Vegh, Kyle Stokes, Dennis Ma, Darcy Wear, Jerome Cohen, Sidhartha D. Ray, Siyaram Pandey

Touro College of Pharmacy (New York) Publications and Research

Neurons consume the highest amount of oxygen, depend on oxidative metabolism for energy, and survive for the lifetime of an individual. Therefore, neurons are vulnerable to death caused by oxidative-stress, accumulation of damaged and dysfunctional proteins and organelles. There is an exponential increase in the number of patients diagnosed with neurodegenerative diseases such as Alzheimer’s (AD) as the number of elderly increases exponentially. Development of AD pathology is a complex phenomenon characterized by neuronal death, accumulation of extracellular amyloid-β plaques and neurofibrillary tangles, and most importantly loss of memory and cognition. These pathologies are most likely caused by mechanisms including …

Regulation Of Respiration And Apoptosis By Cytochrome C Threonine 58 Phosphorylation, Junmei Wan, Hasini A. Kalpage, Asmita Vaishnav, Jenney Liu, Icksoo Lee, Gargi Mahapatra, Alice A. Turner, Matthew P. Zurek, Qinqin Ji, Carlos T. Moraes, Maurice-Andre Recanati, Lawrence I. Grossman, Arthur R. Salomon, Brian Fp Edwards, Maik HüTtemann

Biochemistry and Molecular Biology Faculty Publications

Cytochrome c (cytc) is a multifunctional protein, acting as an electron carrier in the electron transport chain (ETC), where it shuttles electrons from bc1 complex to cytochrome c oxidase (COX), and as a trigger of type II apoptosis when released from the mitochondria. We previously showed that cytc is regulated in a highly tissue-specific manner: Cytc isolated from heart, liver, and kidney is phosphorylated on Y97, Y48, and T28, respectively. Here, we have analyzed the effect of a new Cytc phosphorylation site, threonine 58, which we mapped in rat kidney Cytc by mass spectrometry. We generated and overexpressed wild-type, phosphomimetic …

Ultrastructural Analysis Of The Digestive Gland Secretory And Absorptive Processes In Nepenthes Glandulifera, Shannon Manuel

Biochemistry, Cellular and Molecular Biology Honors Papers

Nepenthes glandulifera is a carnivorous pitcher plant native to tropical environments, of which the majority live on the islands in the Malay Archipelago where sunlight and water are abundant. The pitcher trap style contains a modified pitfall trap that attracts insects and other small invertebrates through various attractive mechanisms. These plants also contain digestive glands that secrete digestive fluid to break down prey into nutrients for the plant. The digestive fluid, with remarkably unique properties, has been analyzed in relation to multiple areas of study including the development of an enzyme-supplementation strategy for the treatment of celiac disease and the …

Insights Into The Ribosomal, Extra-Ribosomal And Developmental Role Of Rp L13a In Mammalian Model, Ravinder Kour

ETD Archive

Ribosomal protein L13a plays an extra-ribosomal function in translational silencing of GAIT (IFN-gamma-activated inhibitor of translation) element bearing mRNAs encoding inflammatory proteins but the underlying molecular mechanism of translational silencing and ribosomal incorporation of L13a remains poorly understood. Also, our laboratory showed that L13a acts as a physiological defense against uncontrolled inflammation in macrophage-specific knockout (KO) mice. However, the consequence of a total knockout of L13a in mammals remains unexplored. Therefore, our current study is focused on (i) identifying the amino acid residue(s) of L13a essential for incorporation and translational silencing of target mRNAs and (ii) studying the consequences of …

Identifying C-Mannosylatedproteins In Raw264.7 Cells Via In Vitro Hsc70 Co-Immunoprecipitation Strategies, Nicholas Ryan Kegley

Theses, Dissertations and Capstones

C-mannosylation is a specific type of glycosylation in which α-mannose is covalently bound to the C2 atom of a tryptophan via a carbon-carbon bond. Presently, it is known to occur on proteins that contain the W-x-x-W-x-x-W/C motif found within the Thrombospondin Type-1 Repeat (TSR), with ‘x’ denoting any amino acid. C-mannosylation has been implicated in a number of cellular functions, including protein secretion and type I cytokine receptor function. Previous research has shown that exogenous C-mannosylated peptides derived from TSR-containing proteins upregulate the production of the pro-inflammatory cytokine Tumor Necrosis Factor alpha (TNF-α) in RAW264.7 macrophage cells. This upregulation is …

Characterizing The Effects Of Environmental Stressors On The Photosynthetic Capacity Of Chlorella Vulgaris, Amanda Louise Smythers

Theses, Dissertations and Capstones

Chlorella vulgaris is a unicellular green algae grown throughout the world. Due to its multiple trophic modes as well as its ability to maintain high rates of growth under adverse conditions, it has been of global interest for use in ecological contamination studies, biofuel feedstock optimization, and studies of photosynthetic electron transfer. Using a wide-range of methods for physiological and photosynthetic characterization, the studies within seek to further extend the usefulness of C. vulgaris in a variety of environmentally important studies. Once the protocols were optimized specifically for this alga, they could be applied in both ecologically relevant and biodiesel …