2020-21 Alumni

  • Adarsh Balaji

    Adarsh Balaji

    Email: adbalaji@ucsd.edu
    Undergraduate Institution: UCLA
    Program: Chemistry & Biochemistry
    Advisor: Colleen McHugh

    Biophysical characterization of long non-coding RNA and protein complexes

    Long non-coding RNA (lncRNA) refer to a class of RNA molecules that contain more than 200 nucleotides and do not code for protein sequences. LncRNAs are currently extensively studied due to their observed dysregulation in human diseases and oncogenic or tumor-suppression function in cancers. LncRNA function is often dependent on the formation of a stable long non-coding ribonucleoprotein complex (lncRNP) for downstream regulation of target genes or proteins. Unfortunately, current computational modelling approaches for lncRNP identification are unable to provide residue-specific information regarding binding dynamics. In addition, there are very few biophysical studies for lncRNP identification in the current literature.3 Thus, a biophysics-based approach to study the folding, structure and binding of these novel lncRNPs will help address this gap in literature and shed light on the role of lncRNAs in human disease. The MALAT1/TDP43 lncRNP in human K562 cancer cells will be used as the experimental model. A tandem of biophysical techniques will be explored, including density ultracentrifugation, a combination of northern and western blotting, and microscopy for structural studies.

  • Aileen Button

    Aileen Button

    Email: acbutton@ucsd.edu 
    Undergraduate Institution: University of Vermont
    Program: Chemistry & Biochemistry
    Advisor: Colleen McHugh

    Characterization of interactions between Xist long non-coding RNA and transcriptional regulators of gene expression

    Long non-coding RNA (lncRNA) and protein interactions play important roles in cellular function. Increasing numbers of these interactions are being identified by high throughput methods. However, more detailed structural characterization of these complexes is needed to determine the molecular basis of RNA-protein interactions, and to understand how these molecules achieve specificity in the complex cellular environment. Prediction of RNA-protein interactions is complicated by a relative lack of sequence conservation in RNA molecules, and secondary and tertiary RNA structures seem to be conserved and important for function.

    A major challenge in the field is that we still do not understand the rules governing lncRNA-protein interactions. To start addressing this question, we are studying the interaction between Xist (a lncRNA) and SHARP (a transcriptional repressor). This interaction was recently identified by RAP-MS (RNA affinity purification with mass spectrometry) and has been shown to be required for X chromosome inactivation in female mammals, including humans. Interestingly, SHARP also binds another lncRNA, the steroid receptor RNA activator (SRA)5. Furthermore, SHARP contains four RNA recognition motifs (RRMS), which are well-established domains for RNA binding. For these reasons, the Xist-SHARP and SRA-SHARP interactions are an excellent gateway into understanding what makes a lncRNA-protein interaction specific.

  • Quinn Cowan

    Quinn Cowan

    Email: qcowan@ucsd.edu 
    Undergraduate Institution: University of Southern California
    Program: Chemistry & Biochemistry
    Advisor: Alexis Komor

    Multiplexing base editing for the functional investigation of linked-SNVs

    Although sequencing has identified 4.6 million missense variants, only 2% have a defined clinical interpretation in ClinVar and over half remain variants of uncertain significance. These variants often occur in tandem, requiring multiple editing events for functional analysis. Traditional CRISPR/Cas9 genome editing methods rely on DNA double-strand break (DSB) induction and the disfavored homology-directed repair pathway. The simultaneous introduction of multiple DSBs is cytotoxic, yields low efficiencies, and forms unwanted genetic alterations. However, a new class of genome editing tools, base editors, were recently developed that circumvent DSB induction. The two existing base editors employ an inactivated Cas9 and specific deamination chemistries to catalyze the conversion of C•G to T•A base pairs or A•T to G•C base pairs. Engineering a multiplexed base editing system to precisely install multiple point mutations throughout the genome will allow researchers to endogenously characterize of the effects of linked-single nucleotide variants (SNVs). This novel system would be transformative for the study and potential treatment of human genetic diseases.

  • Andrea Dickey

    Andrea Dickey

    Email: adickey@ucsd.edu
    Undergraduate Institution: UC Berkeley
    Program: Biological Sciences
    Advisor: Samara Reck-Peterson

    Investigating the Role of LRRK2 in Regulating the Microtubule Cytoskeleton and Intracellular Transport

    The microtubule cytoskeleton and its motors are responsible for the spatial and temporal distribution of intracellular components, which are vital for cellular development and survival. Non-motor microtubule-associated proteins help to maintain this delicate distribution of intracellular components by stabilizing or destabilizing the cytoskeleton and disrupting or enhancing the motility of motor proteins. Leucine Rich Repeat Kinase 2 (LRRK2) is a large, multi-domain protein that has roles in intracellular trafficking and colocalizes with microtubules. Mutations in LRRK2 are the most common cause of familial Parkinson’s Disease. The Reck-Peterson and Leschziner labs recently showed that microtubule-associated LRRK2 can act as a roadblock for the motor proteins dynein and kinesin in vitro. However, many questions remain as to what impact this microtubule-associated LRRK2 has on intracellular transport and microtubule dynamics. The goal of my work is to understand the mechanisms by which LRRK2 filaments form on microtubules, their impact on microtubule dynamics, and their role in modulating intracellular transport. I am using biochemical and in vitro reconstitution methods combined with single-molecule imaging to dissect the mechanisms of LRRK2’s interaction with the cytoskeleton. I aim to provide molecular-level insights into LRRK2’s functions and how they are perturbed in disease.

  • Nesreen Elathram

    Nesreen Elathram

    Email: nelathra@ucsd.edu
    Undergraduate Institution: UNC Charlotte
    Program: Chemistry & Biochemistry
    Advisor: Galia Debelouchina

    Elucidating the role of histone H4 K20 methylation in chromatin compaction

    Chromatin is a complex of protein and DNA that works together to guard and regulate genetic information in eukaryotic cells. As the fundamental building block of chromatin, the nucleosome comprises 147 bp of DNA wrapped around an octamer of the histone proteins H2A, H2B, H3 and H4. The nucleosome is the active site of many different post translational modifications (PTMs) such as acetylation, methylation and ubiquitylation. These PTMs function in the recruitment of chromatin effector proteins and by directly impacting chromatin’s biophysical properties. I am investigating two post-translational modifications involved in gene silencing. This includes histone H3 lysine 9 methylation which is recognized by a key gene silencing protein called heterochromatin protein 1α (HP1α), and histone H4 lysine 20 trimethylation which is known to compact chromatin.  To understand how these modifications, regulate chromatin structure and dynamics, I am developing advanced solution and solid-state NMR tools that allow us to probe chromatin environments at atomic resolution. My project aims to uncover how small chemical modifications such as methylation can influence gene regulation and nuclear organization on a much larger scale.

  • Ximena Garcia Arceo

    Ximena Garcia Arceo

    Email: xgarciaa@ucsd.edu
    Undergraduate Institution: UC Santa Barbara
    Program: Chemistry & Biochemistry
    Advisor: Brian Zid

    Stochastic Modeling of mRNA Localization to Mitochondria

    Over 99% percent of yeast mitochondria proteins are transcribed in the nucleus and translated in the cytoplasm, yet some key proteins are encoded by the mitochondrial genome. The simultaneous translation and localization of nuclear-encoded mitochondrial mRNAs attunes the cytoplasmic to the mitochondrial translation program but the gene-specific and condition-specific localization behaviors have not been modeled quantitatively. We have created a stochastic model that incorporates molecular binding, translation and morphology to predict the localization patterns of mRNAs, which are known to be sensitive to mitochondrial size. Given the inherent competition between diffusion and biochemical affinity of some mRNA-ribosome complexes for the mitochondrial surface, the model also illuminates the limits as well as the opportunities for differential localization of various classes of mRNAs. Since mitochondria increase in volume as respiratory flux and cellular doubling time increase, our model informs our experimental endeavor to elucidate post-transcriptional regulation of metabolic flux and cellular growth rate.

  • Alexander Hoffnagle

    Alexander Hoffnagle

    Email: ahoffnag@ucsd.edu 
    Undergraduate Institution: University of Pennsylvania
    Program: Chemistry & Biochemistry
    Advisor: Akif Tezcan

    De novo design of dimeric metalloenzymes

    Metalloenzymes fulfill diverse cellular roles and are capable of catalyzing a wide range of chemical reactions. As such, there is considerable interest in engineering metalloenzymes to carry out functions for applications in synthetic chemistry, biotechnology, and more. Recently our lab has developed a new approach to designing a protein metal binding site, dubbed Metal Active Sites by Covalent Tethering, or MASCoT. Unlike other engineering approaches, which largely rely on a preexisting site in the interior of a tertiary or quaternary structure, MASCoT allows for a metal binding site to be created along a protein-protein interface. Crucially, these metal binding sites tend to be coordinatively unsaturated, raising the possibility of using them as active sites in catalysis. My goal is to use rational design and directed evolution to develop these MASCoT-designed metal binding proteins into novel, functional metalloenzymes.

  • An Hsieh

    An Hsieh

    Email: a1hsieh@ucsd.edu 
    Undergraduate Institution: Case Western Reserve University
    Program: Chemistry & Biochemistry
    Advisor: Tatiana Mishanina

    Human mitochondrial transcription and DNA replication

    Transcription of DNA to RNA by RNA polymerase (RNAP) is an underlying foundation of biological processes. However, an important place where transcription occurs that is still not well understood is in human mitochondria. The mitochondrial genome (mtDNA) encodes essential proteins required for oxidative phosphorylation (OXPHOS), the cell’s major source of energy. To keep up with the needed energy production, mitochondria must replicate their genome and divide constantly – a process closely coupled to transcription.  Mutations that compromise OXPHOS and replication can lead to devastating disease. Therefore, my project is to gain a thorough understanding of mitochondrial transcription and its coupling with mtDNA replication and other gene expression processes, particularly when the mitochondrial RNA polymerase (mtRNAP) pauses transcription. I will test a pause site of mtRNAP and determine its potential role in switching from transcription and mtDNA replication.

  • Calvin Lin

    Calvin Lin

    Email: clin@ucsd.edu 
    Undergraduate Institution: UC Santa Barbara
    Program: Chemistry & Biochemistry
    Advisor: Elizabeth Komives

    Structural characterization of ubiquitination in Cullin-RING E3 Ligases

    Our cells have evolved to recycle proteins and use the ubiquitin (Ub) proteasome system as the main mechanism to target specific proteins for degradation. Protein complexes known as E3 ligases initiate this process by tagging proteins with Ubiquitin chains, which are recognized and degraded by proteasomes. Cullin-RING complexes are the largest group of E3 ligases and are involved in neurodegenerative diseases and various cancers. However, a lack of structures of multi-protein Cullin-RING complexes limits comprehensive understanding of the E3-mediated ubiquitination mechanism and rational drug design. My goal is to obtain structures that capture the full complex before and during Ub transfer using cryo-electron microscopy (cryoEM). I will complement my structural studies of Cullin5-RING complex with information about the dynamics between substrate and E3 using crosslinking and hydrogen-deuterium exchange mass spectrometry (HDX-MS).

  • Hoang Nguyen

    Hoang Nguyen

    Email: hon005@ucsd.edu 
    Undergraduate Institution: Arizona State University
    Program: Chemistry & Biochemistry
    Advisor: Mark Herzik

    Structural and biophysical insights into mitochondrial preprotein receptor plasticity

    Mitochondria are the central hub of eukaryotic cells and are critically involved in many cellular processes including metabolism, energy production, heme and lipid biosynthesis, and apoptosis. Of the ~1500 proteins that necessary for normal mitochondria function in humans, 99% of those proteins result from nuclear-encoded genes that must be translated in the cytosol as precursor proteins (preproteins) and subsequently imported into mitochondria. Importantly, mitochondrial dysfunction is a hallmark of a wide variety of diseases, including cancer, cardiovascular disease, diabetes, aging, and neurodegeneration, with most of these diseases exhibiting some form of impaired mitochondrial protein import. The translocase of the outer membrane (TOM) complex is the primary preprotein gateway locating to the outer membrane of mitochondria and imports nearly all mitochondrial preproteins. The TOM complex comprises 7 subunits, including two primary preprotein receptors, Tom20 and Tom70, that recognize mitochondrial preproteins possessing either a N-terminal signaling sequence or an internal targeting signal, respectively, for import into mitochondria. Amazingly, these receptors recognize, bind, and deliver ~1300 different preproteins to the TOM complex despite the considerable sequence variation that exists within these targeting signals. Furthermore, Tom70 possesses a single preprotein binding site that must adapt to the vast sequence space necessary for preprotein engagement and import. Although these complexes have been studied biochemically for decades, a myriad of open questions remain due to a lack of structural information. Using a combination of high-resolution single-particle electron cryomicroscopy (cryo-EM), hydrogen-deuterium exchange by mass spectrometry (HDX-MS), molecular dynamics simulations, and biochemical assays, I aim to provide molecular-level insights into Tom70 preprotein engagement and import.

  • Angel Payan

    Angel Payan

    Email: anpayan@ucsd.edu 
    Undergraduate Institution: Rochester Institute of Tech.
    Program: Chemistry & Biochemistry
    Advisor: Mark Herzik

    Utilizing Molecular Dynamics and in silico Electron Microscopy Data to Better Understand Conformational Heterogeneity in cryo-EM

    A molecular-level description of the complex conformational landscape a biological macromolecule must traverse to perform its function is critical to understanding its role in the cellular context. Electron cryomicroscopy (cryo-EM) is an increasingly powerful tool for visualizing these conformationally complex macromolecules in near native environments. Indeed, a single cryo-EM dataset often enables us to view multiple conformations of macromolecules that can then be “in silico” purified using current data processing methodologies to yield multiple conformationally distinct major classes. Unfortunately, however, these processing strategies often yield the most populated, low-energy states of a given protein with local dynamics being lost. The major challenge is distinguishing between these subtle minor conformations in order to gain a better insight into both the local and global dynamic behavior of proteins. Toward this end, I will generate in silico simulated EM data derived from long-scale molecular dynamics simulations of several proteins whose structures have been determined to high-resolution using cryo-EM. Using these data, I will develop methodologies to better quantify local and global conformational heterogeneity that can then be applied to all cryo-EM data. Achieving this will allow for the thorough investigation of these protein ensembles and their roles in protein function, further pushing the boundaries of cryo-EM.

  • Christine Stephen

    Christine Stephen

    Email: c6stephe@ucsd.edu 
    Undergraduate Institution: UC Santa Barbara
    Program: Chemistry & Biochemistry
    Advisor: Tatiana Mishanina

    Structural and Mechanistic Study of a pH-Responsive Riboswitch

    Riboswitches are 5’-untranslated regions (UTRs) of mRNA that control the fate of their respective transcript in response to a ligand-binding event.  However, this ligand-based model of riboswitch function has been challenged with the discovery of a “pH-responsive element” (PRE) riboswitch at the alx gene locus in E. coli.  At neutral pH, the PRE folds into a translationally inactive structure with an occluded ribosome binding sequence; however, at alkaline pH, the PRE adopts a translationally active structure. PRE folding is kinetically controlled: RNA polymerase (RNAP) pausing – a temporary inhibition of nucleotide addition during transcript elongation – is enhanced by alkaline pH at two specific sites on the alx gene, promoting folding of the PRE into the active structure.  Although it is known that transcriptional pausing mediates these distinct structural outcomes, the mechanistic basis for this pH-responsive pause behavior remains unknown. With the support from the training grant, I will investigate the molecular mechanisms underlying this novel, pH-responsive riboswitch, by utilizing a combination of structural approaches and biochemical assays. Ultimately, elucidating the mechanism of PRE folding and its control by RNAP pausing will drive design of pH-responsive sensors for microbial engineering, which has diagnostic and therapeutic applications.

  • Ryan Weeks

    Ryan Weeks

    Email: rweeks@ucsd.edu  
    Undergraduate Institution: North Carolina State University
    Program: Chemistry & Biochemistry
    Advisor: Jin Zhang

    Direct detection of intracellular Ras protein

    Ras is a key signaling protein that controls numerous cellular outcomes such as growth and differentiation.  Activated downstream of epidermal growth factors, and upstream of the Raf-MEK-ERK axis, this protein plays a key role in controlling growth in cells.  As such, activating mutations of Ras are frequent in many cancers.  Currently I am developing and characterizing a genetically encoded biosensor that interacts with activated Ras and reports on its activation directly.  Biosensors to date, such as the Ras-Raichu sensor, contain full-length Ras protein within the design, and technically report on the activity of upstream regulators.  With direct detection, endogenous levels of Ras may be sensed, and direct detection of Ras inhibition by small molecule drugs can theoretically be tracked live within the cell.

2019-20 Alumni

  • Bryce Ackermann

    Bryce Ackermann

    Email: beackerm@ucsd.edu 
    Undergraduate Institution: University of California: Davis
    Program: Chemistry & Biochemistry
    Advisor: Galia Debelouchina

    Interrogating genome packaging

    The human genome is compacted into cell nuclei in the form of chromatin, a giant polymer of protein and DNA that spatially organizes to allow for timely execution of nuclear processes. On a crude level, chromatin separates into transcriptionally hindered and transcriptionally active regions dependent on local chemical modifications and chromatin interacting proteins that lead to differential compaction densities. The effects can be visualized at the nuclear level but difficult to study in molecular detail. Therefore, our lab will focus on advancing methodology for structural biology in cells. We will develop chemical biology and nuclear magnetic resonance spectroscopy tools to investigate the structure and dynamics of differentially packaged chromatin in human cells.

  • Joshua Corpuz

    Joshua Corpuz

    Email: jccorpuz@ucsd.edu 
    Undergraduate Institution: UC San Diego
    Program: Chemistry & Biochemistry
    Advisor: Michael Burkart

    Understanding PCP-mediated protein-protein interactions in NRPS systems.

    49% of FDA approved anticancer drugs are natural products or derivatives of natural products. Natural products also have a variety of bioactivities in humans and other organisms, including antibiotic, antiviral, and antifungal activities. A major family of enzymes that synthesize these natural products are nonribosomal peptide synthetases (NRPS). Since they are prevalent in natural product synthesis, NRPSs have become targets for protein engineering to create novel pharmaceutical drugs and novel biosynthetic pathways of the drugs.

    NRPS are modular enzymes that act like an assembly line to create peptide products.One of the core domains in the NRPS is the peptidyl carrier protein (PCP); its role is to transport the growing peptide chain between multiple domains in a specific order. The molecular mechanism by which the PCP recognizes the different domains is not well understood. My project helps advance our understanding of PCP-mediated protein-protein interactions through biochemical and structural analysis of the PCP and partner proteins. With increased understanding of the interactions, we can better engineer NRPS systems to create novel pathways and pharmaceutical drugs.

  • Mounir Fizari

    Mounir Fizari

    Email: mfizari@ucsd.edu 
    Undergraduate Institution: Univ. of Illinois Urbana-Champaign
    Program: Physics
    Advisor: Doug Smith

    Single molecule studies of bacteriophage phi29 DNA packaging

    A critical step in the lifecycle of many bacteriophages and some eukaryotic viruses is the packaging of the viral genome into a prohead by an ATP-powered molecular motor. The bending rigidity and electrostatic self-repulsion of the DNA and the entropic penalty of confinement make this process energetically unfavorable. In bacteriophage phi29, previous studies have found evidence that the nonequilibrium dynamics of the confined DNA affect packaging by providing a resistive load on the motor and triggering an allosteric feedback mechanism. Using optical tweezers to monitor the force exerted and rate of DNA packaged by individual phi29 complexes, I will vary the prevalence of nonequilibrium conformations by reducing the rate of packaging, nicking the genome to reduce the DNA’s bending rigidity, and using a larger mutant phi29 prohead to probe the relationship between nonequilibrium conformations and packaging kinetics.

  • Sonjiala Hotchkiss

    Sonjiala Hotchkiss

    Email: sonjiala@ucsd.edu 
    Undergraduate Institution: Univ. of New Orleans
    Program: Chemistry & Biochemistry
    Advisor: Gourisankar Ghosh

    My proposed research will focus on characterizing and elucidating how the binding of small molecule inhibitors of human IKK2/b affect its protein dynamics and therefore its function. IKK2 is a catalytic subunit of the heterotrimer IkB Kinase (IKK). The two additional subunits are IKK1/a, also a catalytic subunit, and NF-kB essential modulator (NEMO/IKKg), a regulatory subunit. IKK is an essential kinase in the activation pathway of the nuclear factor kB (NF-kB) family of transcription factors. This family consists of five proteins that can combine to form homo- or hetero-dimers: p65/RelA, p50, p52, c-Rel, and RelB. The NF-kB dimers remain inactive in most cells which can be activated by a large number of stimuli including cytokines, pathogens and radiation though a cascade of reactions that mostly starts at the cell surface. NF-kB activation occurs along two pathways, the canonical pathway and the noncanonical pathway. As an enzyme in the canonical pathway, IKK2 is activated by phosphorylation of its activation loop serines, S177 and S181.

  • Dominic McGrosso

    Dominic McGrosso

    Email: dmcgross@ucsd.edu 
    Undergraduate Institution: CSU San Marcos
    Program: Biomedical Sciences
    Advisor: Geoffrey Chang

    My current research in the lab of Dr. Geoffrey Chang utilizes directed evolution techniques to generate and characterize small molecule binders to investigate the physical properties and biomolecular structure of small molecule pollutants and their binders. Small molecules, especially pollutants such as polycyclic aromatic hydrocarbons, polybrominated diethyl ethers, and triclosan, have been found in many environments including those essential for humans, like water used for drinking, ocean fisheries, and farmland. Many of these molecules have been demonstrated to have negative effects on human health and environmental robustness. There are multiple methods used to detect small molecule pollutants in use today, including mass spectrometry and other various chromatographic and spectrophotometric methods, however each of these methods have inherent weaknesses that preclude them from direct field applications.

  • Elizabeth Porto

    Elizabeth Porto

    Email: eporto@ucsd.edu 
    Undergraduate Institution: Univ. of Missouri - Kansas City
    Program: Chemistry & Biochemistry
    Advisor: Alexis Komor

    Expanding the Scope of DNA Base Editing

    The use of the clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) system has become the standard method for genome editing. The system relies on the ability of Cas9 to introduce a double strand break (DSB) at a desired DNA sequence, followed by precise repair from a donor template through homology-directed repair (HDR). However, DSB-reliant genome editing results in stochastic mixtures of unwanted genome modifications, making it less reliable for commercial use. Base editing is an alternative technique that enables the direct, irreversible conversion of a single target DNA base in a precise, programmable manner without introducing a DSB or requiring a donor template. This methodology is currently limited in its scope by only facilitating C•G to T•A or A•T to G•C base pair conversions. My project is focused on engineering new DSB-free genome editing tools that expand the types of DNA base pair transformations researchers can cleanly and efficiently introduce into the genome of living cells. This project will advance basic scientific understanding of genome editing enzymes as well as accelerate novel organism engineering efforts, with the potential to be used commercially in improving therapeutic efforts.

  • Douglas Zhang

    Douglas Zhang

    Email: doz023@ucsd.edu 
    Undergraduate Institution: UCLA
    Program: Chemistry and Biochemistry
    Advisor: Thomas Hermann

    Functionalization of Nucleic Acid Nano-Structures

    Nucleic acids have traditionally been recognized for their role in carrying genetic information, however, their ability to self-assemble into a variety of shapes based on simple Watson-Crick base-pairing rules makes nucleic acids an ideal material for nanotechnology. Combining the structures of RNA as architectural joints with DNA as functional modules, the Hermann lab has created a variety of nucleic acid nano-architectures. We are now focused on expanding the types of nano-structures that can be formed as well as the functionalization of these nano-structures for the purposes of protein-protein interaction studies, biosensors, and catalysis.

2018-19 Alumni

  • Joshua Arriola

    Joshua Arriola

    Email: jtarriol@ucsd.edu
    Undergraduate Institution: UC Santa Barbara
    Program: Chemistry & Biochemistry
    Advisor: Ulrich Muller

    Prebiotic peptides and their interaction with catalytic RNA

    The Muller lab is interested in studying the role catalytic RNA may have played in the early stage of life. The goal of my research project is to determine how peptides aided in the emergence of catalytic RNA.  An in vitro selection in the presence of peptides composed of different prebiotically plausible amino acids will be used to identify any catalytic RNA that require such peptides in order to function. Prebiotically plausible amino acids may differ from natural amino acids in the biophysical characteristics of their interactions with RNA. We are interested in characterizing and quantifying the biophysics of these RNA – peptide interactions as well as determining which residues, if any, are important for catalytic function.

  • Cyrus DeRozieres

    Cyrus DeRozieres

    Email: cderozie@ucsd.edu 
    Undergraduate Institution: UC San Diego
    Program: Chemistry & Biochemistry
    Advisor: Simpson Joseph

    The role of the influenza viral protein NS1 in translation initiation

    Influenza is a seasonal respiratory illness that causes thousands of deaths and billions of dollars in medical expenses and lost earnings every year in the United States alone. It is caused by an RNA virus that is capable of hijacking host cell machinery in order to direct its focus on viral protein production. It accomplishes this with few proteins that perform a wide variety of roles. Non-structural protein 1 (NS1) is a critical protein involved in influenza pathology. NS1 is known to down-regulate the host immune response and increase the rate of translation of its own viral RNAs among other roles. The goal of my research is to investigate how NS1 up-regulates viral protein synthesis by characterizing the protein-protein and protein-RNA interactions involved. Using biochemical and biophysical techniques, I aim to elucidate the mechanism by which NS1 brings translation factors and viral RNAs together. My work will serve to increase our knowledge of this debilitating virus in the hopes of developing new and effective targets for treatment.

  • John Gillies

    John Gillies

    Email: jgillies@ucsd.edu
    Undergraduate Institution: University of Oregon
    Program: Biological Sciences
    Advisor: Samara Reck-Peterson

    Investigation of the biophysical mechanisms governing dynein cargo-specificity

    The microtubule cytoskeleton and its associated motors are responsible for the organization of cellular components necessary for development, cell division, and neuronal function. Cytoplasmic dynein-1 (dynein) is the only minus-end-directed transporter in the cytoplasm, yet is responsible for the transport of dozens of different cargos. This raises a fundamental question: how does dynein achieve cargospecificity? “Activator” proteins, which both activate dynein motility and link dynein to its cargos, play a role in governing cargo specificity. The Reck-Peterson lab recently identified the dynein transport machinery interactome using proteomic methods. My project is centered around two classes of proteins identified using these discovery methods. 1) Candidate non-canonical activators, those that can interact with the dynein transport machinery, but not activate motility. 2) Candidate novel regulatory proteins that may influence which activators are bound to the dynein machinery. I am using biochemical reconstitution and single-molecule motility assays to address these fundamental components of dynein regulation.

  • Riley Peacock

    Riley Peacock

    Email: rpeacock@ucsd.edu
    Undergraduate Institution: Gonzaga University
    Program: Chemistry & Biochemistry
    Advisor: Elizabeth Komives

    Probing the Allosteric Networks of Thrombin

    The clotting cascade is initiated in response to blood vessel trauma, resulting in the downstream activation of the serine protease thrombin. Activated thrombin selectively binds and cleaves various procoagulative substrates, thereby activating them and allowing for the formation of a blood clot. The cofactor thrombomodulin (TM) is found within the cell membrane of the endothelial layer of the blood vessel, and once TM binds to thrombin, thrombin switches its substrate specificity away from procoagulative substrates in favor of the enzyme protein C. Activated PC (APC) initiates the anticoagulative response, resulting in a decrease in the activation of new thrombin molecules. Though the events leading to the switching of thrombin’s substrate specificity have been studied extensively, we are still unsure as to what change occurs within thrombin when TM binds that causes this switch in target preference. Crystallographic evidence suggests that there in not an appreciable difference in conformation between apo-thrombin and TM-bound thrombin, but accelerated molecular dynamics simulations have identified differences between the micro- to millisecond backbone motions of the two species. My work consists of using experimental techniques, such as hydrogen-deuterium exchange and nuclear magnetic resonance, to provide an experimental measure of how the dynamic motions of thrombin are altered by the presence of TM.

  • Kira Podolsky

    Kira Podolsky

    Email: kpodolsky@ucsd.edu
    Undergraduate Institution: Western Washington University
    Program: Biomedical Sciences
    Advisor: Neal Devaraj

    Artificial cells as a model for biological processes

    Liposomes are an essential tool in cellular biology and medicine providing insights into the basic biology of cellular processes, drug delivery, and origin of life. Mimicking “normal” membranes through liposomal modeling research provides fundamental insights into these areas. Other labs have explored simulating basic cellular membrane processes such as membrane division, fusion, and cell growth using synthesized vesicles. My research is focused on creating liposomes that mimic cellular phospholipid bilayers to serve as a model for cell structure and function and to apply these models to biologically relevant systems.

  • Clara Posner

    Clara Posner

    Email: cposner@eng.ucsd.edu 
    Undergraduate Institution: UCLA
    Program: Bioengineering
    Advisor: Jin Zhang

    Elucidating enzyme activity architecture using FLINC biosensor

    Zhang lab focuses on probing the spatiotemporal organization and local activity of various enzymes using genetically encoded biosensors and fluorescence imaging technologies. Our group recently created a new generalizable class of biosensors called Fluorescence fLuctuation Increase by Nonlocal Contact (FLINC) biosensors to directly visualize dynamic biochemical activities on the molecular length-scale in live cells. My project focuses on further enhancing the FLINC class of biosensors by improving the spatial resolution and creating additional protein kinase FLINC sensors.

  • Hannah Rutledge

    Hannah Rutledge

    Email: hrutledge@ucsd.edu
    Undergraduate Institution: Rice University
    Program: Chemistry & Biochemistry
    Advisor: Akif Tezcan

    Determining the conformational gating mechanism in nitrogenase

    Reduced forms of nitrogen are required for life and are necessary for the synthesis of many biological molecules. Nitrogenase is the only known enzyme capable of reducing dinitrogen to ammonia. Nitrogenase contains many metal clusters which are involved in electron transfer, but many aspects of the mechanism remain unknown. The goal of my research is to determine the role of ATP hydrolysis in conformational changes associated with electron transfer between the metal clusters in nitrogenase. To achieve this goal, I am using protein crystallography, characterizing nitrogenase mutants, and searching nitrogeanse sequences for covarying amino acid residues.

  • Bryce Timm

    Bryce Timm

    Email: btimm@ucsd.edu
    Undergraduate Institution: Hamilton College
    Program: Chemistry & Biochemistry
    Advisor: Kamil Godula

    Molecular Origins of Human Extracellular Sulfatase Specificity

    Human endosulfatases (HSulfs), active in the extracellular matrix, cleave sulfate groups from glycosaminoglycan (GAG) polysaccharides with high specificity for the targeted GAG structure, influencing growth factor and cytokine binding. Our project seeks to investigate the molecular interactions underpinning HSulf activity and selectivity. With no crystal structure available, we hope to use synthetic chemistry to delineate and visualize form and function via customizable affinity probes. Once built, the substrate mimic will serve as a tool, used in conjunction with enzymatic modifications and biophysical techniques, to provide structural information regarding the enzyme and the relationship with its targets.

  • Hetika Vora

    Hetika Vora

    Email: hvora@ucsd.edu
    Undergraduate Institution: University of California, Irvine
    Program: Biomedical Sciences
    Advisor: Neal Devaraj

    Targeted Depalmitoylation of N-Ras for Suppression of Oncogenic Signaling Pathways

    Protein S-palmitoylation is a reversible post-translational modification that is present on proteins involved in numerous biophysical processes. Recently, S-palmitoylation has been shown to play an integral role in cancer signaling pathways. Of particular interest is the oncogenic protein N-Ras, which is known to be mutated in many types of cancers. N-Ras is palmitoylated by DHHC palmitoyltransferase, which enables it to transport from the Golgi to the plasma membrane. This association allows the oncogenic N-Ras protein to control a range of signal transduction pathways necessary for cell growth. A potential mechanism to inhibit oncogenic N-Ras activity is to depalmitoylate N-Ras with compounds capable of cleaving endogenous S-palmitoyl modifications. Our group has synthesized a class of molecules capable of chemoselective reactions with long chain thioesters, which could be utilized for in vivo depalmitoylation of N-Ras. We will use live-cell imaging and western blotting to study the molecular biophysics of N-Ras protein interactions with the cell membrane as well as downstream oncogenic signaling pathways affected by the protein modifications. By developing chemical tools capable of in situ protein depalmitoylation, we can better study the effects of post-translational lipidation on the membrane localization and biophysical activity of endogenous N-Ras.

2017-18 Alumni

  • Evan Kobori

    Evan Kobori

    Email: ekobori@ucsd.edu
    Undergraduate Institution: UC Berkeley
    Program: Chemistry & Biochemistry
    Advisor: Susan Taylor

    Structural Studies of PKA

    cAMP dependent protein kinase (PKA) is a ubiquitous kinase in mammalian cells that regulates many biological processes and is associated with a variety of diseases and disorders.  Physiologically, PKA exists as a tetrameric holoenzyme consisting of two regulatory (R) subunits and two catalytic (C) subunits.  There are four structurally and functionally non-redundant R isoforms, and the goal of my research is to utilize cryoEM to obtain the structure of the RIβ holoenzyme in a more native state.  This information can further show structural differences between the holoenzymes of the other R isoforms.  Additionally, I am using x-ray crystallography to elucidate the interactions responsible for localizing PKA to the cell membrane and other subcellular environments.

  • Adam Maloney

    Adam Maloney

    Email: amaloney@ucsd.edu
    Undergraduate Institution: Elon University
    Program: Chemistry & Biochemistry
    Advisor: Simpson Joseph

    An in vitro model of eukaryotic translation for studies of Fragile X syndrome

    Fragile X syndrome is a common neurological disease that stems from a single genetic defect. This defect produces a nonfunctioning version of the protein FMRP, which is involved in regulation of protein translation in the brain. My research is focused on developing an in vitro model of translation that can be used in biophysical studies of FMRP interacting with the ribosome. By investigating the mechanism through which FMRP inhibits translation we hope to gain an understanding of how translation is fundamentally regulated.

  • Kevin Sweeney

    Kevin Sweeney

    Email: kjsweene@ucsd.edu
    Undergraduate Institution: University of California, Santa Cruz
    Program: Chemistry & Biochemistry
    Advisor: Ulrich Müller

    RNA World Ribozymes Recruiting Peptides as Cofactors

    Due to early origin of life experiments by Stanley Miller and others, we can say that amino acids and short peptides are likely to have existed in the prebiotic world. This would mean that they may have aided in the development of an RNA world. Supporting this idea is the fact that many larger ribozymes use proteins as cofactors today, including the ancient and ubiquitous ribosome. We aim to use a robust, established in vitro selection procedure to identify RNAs that triphosphorylate their 5’-ends using peptide cofactors and then characterize the RNAs and the nature of their interactions with peptides.

2016-17 Alumni

  • DeeAnn Asamoto

    DeeAnn Asamoto

    Email: dasamoto@ucsd.edu
    Undergraduate Institution: California State University, Long Beach
    Program: Chemistry & Biochemistry
    Advisor: Judy Kim

    Membrane proteins play integral parts in the key processes of life. They act as regulators of communication between the cell and its surrounding environment. Using outer membrane protein A (OmpA) as a model β-barrel protein, I will use fluorescence spectroscopy, including Förster Resonance Energy Transfer (FRET), UV Resonance Raman (UVRR), and bimolecular quenching experiments in order to gain insight into its functions and assembly mechanisms in preformed nanodiscs. Nanodiscs are water-soluble nanoscale phospholipid bilayers that serve as excellent biological membrane mimics which self-assembles integral membrane proteins for biophysical or structural investigation and are well suited for controlled in vitro experiments.

  • Jeff Mindrebo

    Jeff Mindrebo

    Email: jmindrebo@ucsd.edu
    Undergraduate Institution: University of Houston
    Program: Chemistry & Biochemistry
    Advisor: Joseph Noel/Michael Burkart

    Primary metabolism describes essential metabolic processes for the viability of an organism, while secondary metabolism provides an organism with advantages that enable further proliferation and survival. Due to the sessile nature of plants, evolutionary flexibility of secondary metabolic enzymes have afforded them the ability to develop a large repertoire of small molecules to aid in their survival and evolution. Vitis vinifera (grapevine) is found on nearly every continent and produces an abundance of secondary metabolites; making it an ideal system for studying how plants evolve new enzymes with unique chemistry in order to have greater fitness in their environments.

  • Sarah Ur

    Sarah Ur

    Email: s1ur@ucsd.edu
    Undergraduate Institution: Cal Poly San Luis Obispo
    Program: Biomedical Sciences
    Advisor: Kevin Corbett

    The MutS Homologs (MSH) have been identified in all organisms from E. coli to humans, and function in the initial recognition of mismatched base pairs in the conserved mismatch repair pathway. In contrast to MSH2-MSH6 and MSH2-MSH3, the MSH4-MSH5 complex does not participate in mitotic mismatch repair, but plays a critical role in meiotic recombination and the segregation of homologous chromosomes during gamete/spore formation. My aim is to reveal how MSH4 and MSH5 interact with chromosomes and components of recombination machinery. By researching the MSH4-MSH5 complex and its downstream partners, we will be able to make a leap in understanding the physical basis of crossover formation.

2015 Alumni

  •  Anastassia Gomez

    Anastassia Gomez

    Email: abgomez@ucsd.edu
    Undergraduate Institution: UC Santa Cruz
    Program: Chemistry & Biochemistry
    Advisor: Nav Toor
    Viroids are non-coding infectious RNAs, typically between 250 and 400 nucleotides long, that infect plants. Viroids do not encode for proteins and yet can cause devastating plant diseases which affect food crops like peach, apple, avocado and many others. My goal is to determine the structure of a viroid and explore the relationship between its tertiary architecture and its infectivity in plants. A combination of x-ray crystallography, biochemistry and in vivo plant studies will be used to determine the mechanism(s) of pathogenesis by viroids and to determine the identity of protein partners of the viroid RNA in vivo.