Scholars

Current Scholars

Andrea Andress Huacachino
Advisor: Trevor M. Penning
Mechanisms of androgen excess-driven lipotoxicity in polycystic ovary syndrome

Gabrielle Blizard
Advisor: Mark Sellmyer
My project is the development of a PET imaging approach to monitor lipid nanoparticle-delivered mRNA translation in vivo.

Kristen Fiore
Advisor: E. James Petersson
Structural, biophysical, and in vivo effects of thioamides on protein structure and function

Craig Gambogi
Advisor: Ben Black
Understanding the relationship between DNA sequence and centromere formation.

Marshall Lougee
Advisor: E. James Petersson
Crosslinking to identify binding sites and protein interactions of alpha-synuclein

Hoang Anh T. Phan
Advisor: E. James Petersson
Development of thioamide-based peptides as proteolysis probes, imaging agents, and therapeutics.

Diane Rafizadeh
Advisor: David M. Chenoweth
Preparation and application of linked and cyclic collagen mimetic peptides

Dominic Santoleri
Advisor: Paul Titchenell
Evaluating the role of glucokinase in hepatic glucose and lipid metabolism.

Kyle Shaffer
Advisor: E. James Petersson
The synthesis and incorporation of fluorescent unnatural amino acids for studying protein folding and function.

Marie Shimogawa
Advisor: E. James Petersson
Investigating the combinatorial effects of post-translational modifications in alpha-synuclein on its function and pathology

Mary Szurgot
Advisor: Ronen Marmorstein
Molecular characterization of the Chaetomium thermophilum HIRA histone chaperone complex

Graduated Scholars

Atrish Bagchi
Advisor: Kathryn Ferguson and Mark Lemmon
Structural basis for allosteric regulation of receptor tyrosine kinases in the epidermal growth factor receptor family, employing a combination of hydrogen/deuterium exchange and x-ray crystallography coupled to solution biochemical, biophysical, and cellular approaches

Solongo Batjargal
Advisor: James Petersson
Development of strategies to incorporate thioamides, which can be used as fluorescence quenchers, into proteins to study conformational changes.

Taylor Barrett
Advisor: James Petersson
Incorporation of thioamides into peptides to inhibit aggregation and proteolysis

Kiara Berrios
Advisor: Rahul Kohli
Development of DNA deaminase enzymes with efficient and controllable genome-based editing activities

Patrick Blank
Advisor: David Christianson
Exploratory Mutagenesis Studies on the Class 1 Terpenoid Cyclase Epi-isozizaene synthase (EIZS)

Renee Carrington
Advisor: Greg Vanduyne
Biochemical and biophysical analysis is being carried out to characterize the function of the conserved YG box of the spinal muscular atrophy-determining gene, SMN. 

Joel Courter
Advisor: Amos Smith
HIV-1 entry inhibitors and Ultrafast Photochemical Triggers as probes of peptide dynamics are being designed, synthesized and biologically evaluated. 

Valentina Dimitrova
Advisor: Dr. Zhe Lu
Structural and biochemical characterization of fungal transient receptor potential channels.

Sunbin Deng
Advisor: Ronen Marmorstein
Molecular mechanism of protein N-terminal acetylation by yeast and human NatE complexes.

Ian Farrell
Advisor: Barry Cooperman
Time-resolved fluorescent measurements are used to study tRNA movement on the bacterial ribosome. 

Jacque Lynn Faylo
Advisor: David Christianson
Investigating substrate channeling and cooperativity in assembly-line terpene synthases by structural characterization.

Mark Fegley
Advisor: James Petersson
Design of a universal synthetase through the synthesis and design of charged adenosine analogs that are capable of binding to a modified tRNA synthetase enzyme and capable of aminoacylation of tRNA.

Jack Ferrie
Advisor: E. James Petersson
Computational and experimental study of the structure of alpha-synuclein

Brian Frederick
Advisor: Alan Diehl
Identifying a mechanistic explanation for PERK-mediated cell survival and motility in response to ER stress and the tumor microenvironment using biochemistry and molecular cell biology. 

Sam Giannakoulias
Advisor: E. James Petersson
Small molecule interactions with aggregating proteins

Bryan Gibb
Advisor: Greg Vanduyne
Chemical probes, biochemistry, and structural biology are being used to investigate the mechanism of catalysis by Cre recombinase. 

Kyle Harpole
Advisor: Josh Wand
Nuclear Magnetic Resonance methodologies are being used to probe the role of conformational entropy on protein interactions with small molecules. 

Yu-San Houh
Advisor: Kate Ferguson
Biochemical and structural techniques are being employed to determine the molecular basis for substrate recognition by the E3 ubiquitin ligase Pellino.

Andre Isaacs
Advisor: Jeff Winkler
Alkaloid Cyclopamine analogue inhibitors of the Hedgehog signaling pathway are being designed, synthesized, and evaluated in cells.

Martin Iwanicki
Advisor: Sergei Vinogradov
Our work involves developing novel neuronal optical voltage-sensing probes using synthetic proteins. Particularly, we are interested in incorporating natural cofactors, fluorescent proteins, and fluorescent nanoparticles in the designs for the voltage-sensing probes.

Chloe Jones
Advisor: E. James Petersson
The synthesis and incorporation of fluorescent unnatural amino acids for studying protein folding and function.

Alexander Jon Kasznel
Advisor: David M. Chenoweth
Design, Synthesis, Structural Studies, & Applications of Synthetic Collagen Peptides

Michelle Kinder
Advisor: Ellen Puré
Biochemistry and cell biological techniques are being employed to study the role of fatty acid metabolism and hematopoiesis. 

Yi-Chih Lin
Advisor: Zahra Fakhraai
The studies of the amyloid fibrils formed in solution and on surface.

Chun Liu
Advisor: Tobias Baumgart
Inferfacial enzyme catalysis on supported lipid bilayer, studying how enzyme is regulated by the lipid and vice versa.

Patrick Lombardi
Advisor: David Christianson
Chemical and structural approaches are being used to understand the molecular basis for the unique substrate specificity of acetylpolyamine amidhydrolase amongst the Arginase-class I/II deactylase related family of enzymes. 

Kim Malecka
Advisor: Ronen Marmorstein
Small molecule screens for inhibitors of human Papillomavirus E6 protein is being carried out and these inhibitors are being evaluated in vitro and in cells. 

Tomoyasu Mani
Advisor: Sergei Vinogradov
Photophysical and photochemical methods are being employed to design and develop advanced probes for optical imaging. 

Zach March
Advisor: James Shorter
Molecular basis of Hsp104-mediated protein remodeling using directed evolution

Mark Mason
Advisor: Emmanuel Skordalakes
Molecular basis for telomere maintenance

Kristen McKibben
Advisor: Elizabeth Rhoades
Impact of posttranslational modifications on tau function

Samuel Melton
Advisor: David M. Chenoweth
Synthesis and characterization of synthetic collagen mimetic peptides to probe biological interactions

Philipp Mews
Advisor: Shelley Berger
Biochemical and molecular techniques such as SILAC and ChIP-seq are employed to explore how intermediary metabolism and neuronal histone acetylation are linked to mediate learning and memory.

Charlie Y. Mo
Advisor: Rahul Kohli, Ph.D.
Understanding and targeting the LexA repressor-protease, the regulator of bacterial SOS mutagenesis

Jacob Nagy
Advisor: Jeffrey Winkler
The synthesis and study of a novel bipyridyl Troger's Base analog is being pursued as a possible monomeric building block of non-covalent, self-assembled helical mimetics.

Julie Norseen
Advisor: Paul Lieberman
The role of the G-quadruplex RNA binding motif of EBNA1 protein in the mechanism of EBV DNA replication and maintenance during latency is being studied using small-molecule probes.

Cristian Ochoa
Advisor Marisa Kozlowski
Synthesis of Honokiol analogues for anti-bacterial and anti-biofilm activity

Jeremy Osko
Advisor: David Christianson
Analyzing structural insights into the rational design of Histone Deacetylase 6 (HDAC6) selective inhibitors.

Buyan Pan
Advisors: James Petersson/Elizabeth Rhoades
Alpha-Synuclein post-translational modifications on synaptic vesicle trafficking

Nicholas Porter
Advisor: David W. Christianson
Probing the catalytic effects of conserved residues and substrate specificy in HDAC enzymes.

Katie Pulsipher
Advisor: Ivan Dmochowski
Biophysical and materials characterization techniques are being used to better understand the encapsulation of inorganic nanomaterials by thermophilic ferritin.

Teresa Rapp
Advisor: Ivan Dmochowski
Photochemistry of Ruthenium compounds and their applications in oligonucleotide caging, triggers for peptide folding, and crosslinking agents in hydrogels.

Alec Ricciuti
Advisor: S. Walter Englander and James Shorter
Native hydrogen-deuterium exchange mass spectrometry measurements are employed to probe the quaternary structure, local conformational dynamics, and nucleotide binding energetics of Hsp104 to understand the fine details of its disaggregase mechanism

Brittany Riggle
Advisor: Ivan Dmochowski
Our work involves developing targeted cryptophane host molecules for use in biosensing applications and towards the specific goal of identifying cancer cell lines in xenon-129 NMR/MRI.

Ben Roose
Advisor: Ivan Dmochowski
Structural characterization of genetically-encoded and synthetic xenon-129 biosensors

Brittani Ruble
Advisor: Ivan Dmochowski
Synthetic nucleic acid chemistry is being applied to develop probes to turn target genes on and off with light. 

Emily Schutsky
Advisor: Rahul Kohli
Characterization of AID/APOBEC family cytosine deaminases and implications for immunity, epigenetics, and cancer

Garry Seward
Advisor: Ivan Dmochowski
Synthetic chemistry and biochemistry is being applied to develop xenon biosensors for cancer diagnostics.

 Kate Smith
Advisor: Feng Gai
Single-molecule and ensemble fluorescence techniques are being developed and applied to investigate the dynamics and mechanism of protein folding and interaction.

Lee Speight
Advisor: James Petersson
My research currently focuses on the synthesis of acridonylalanine (Acd), a fluorescent amino acid, and derivatives, as well as the use of mutant tRNA aminoacyl synthetases to allow for in vivo incorporation of this fluorophore into proteins.

Liz Sweeny
Advisor: Jim Shorter
Biophysical and chemical methodologies are being used to probe the protein folding and disaggregration properties of the heat shock protein HSP104.

Miklos Szantai-Kai
Advisor: James Petersson
Developing side-chain thioamides as fluorescence quencher probes.

Kate Thorn
Advisor: David Christianson
Synthetic organic chemistry and structural biology is being combined to develop potent and selective Arginase I inhibitors.

Dora Von Trentini
Advisor: Ivan Dmochowski
Investigating the cellular delivery of fluorescently labeled oligonucleotides.

Ryan Walvoord
Advisor: Dr. Marisa C. Kozlowski
Design and implementation of colorimetric probes for the detection and quantification of small molecule hydrogen bond activation.

Tong Wang
Advisor: Rahul Kohli
My project is to develop an enzymatic sequencing method for studying cytosine modifications.

Jun Wang
Advisor: Bill Degrado
Novel influenza A virus M2 proton channel inhibitors are being designed, synthesized, screened and structurally characterized. 

Sarah Welsh
Advisor: Alessandro Gardini
Molecular mechanism of Integrator activity in cell differentiation

Daniel Wu
Advisor: David W. Chenoweth
Design and synthesis of versatile chemically inducible dimerizers (CID) used to spatiotemporally control protein-protein and protein-molecule interactions.

Zhengyi (Neo) Wu
Advisor: Mark Lemmon
Dynamics of full-length EGF receptor probed by hydrogen-deuterium exchange.

Zach Zimmerman
Advisor: Tobias Baumgart
Studying lipid interconversion by enzymes on model plasma membranes.

Mingyang (Elaine) Zhou
Advisor: Ronen Marmorstein
ACSS2 structure/function determination and inhibitor development by cryo-EM.