Our Team

Stephen D. Fried

Principal Investigator

Stephen is a native of Kansas City. He received two S.B. degrees (2009) from MIT in chemistry and physics and completed his doctoral training at Stanford under the mentorship of Prof. S. G. Boxer in 2014. As a graduate student, Stephen's research focused on understanding the physical principles underpinning enzymes’ catalytic power. From 2014 to 2018, Stephen was a Junior Research Fellow of King’s College and conducted research at the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom.

Stephen joined the Johns Hopkins University Department of Chemistry in 2018 as an assistant professor. He currently holds appointments with the T. C. Jenkins Department of Biophysics and the Department of Biology, and is affiliated with the CMDB, PMB, and CBI training programs.

He has been the recipient of numerous awards, including the NIH Director’s New Innovator award, an NSF CAREER award, a Cottrell scholar, a Camille Dreyfus teacher-scholar award, and a Sloan fellowship.

Outside the lab, Stephen enjoys cooking, lifting, and traveling.

Postdoctoral Fellows

Sreemantee Sen (Chem-3)

Education: PhD, National Centre for Biological Sciences, Tata Institute of Fundamental Research, 2022

Projects: Proteome-wide identification of binding-sites of DnaK chaperone and Understanding the origin of non-refoldability by measuring kinetic stability.

Graduate Students

Divya Yadav (chem-6)

Education: B.S. Chemistry, Hindu College, University of Delhi, 2016; M.S. Chemistry, Indian Institute of Technology, Delhi, 2018

Interests: Running and hiking

Projects: Probing the role of DnaKJ and trigger factor in de novo folding of the E. coli proteome

In Fried lab, my research focuses in developing and applying novel proteomics and mass spec approaches to study the role of Trigger factor and DnaKJ in the folding of E. coli proteome. Sometimes, I also explore crosslinking mass spec to study protein-protein interactions.

Edgar Manriquez-Sandoval (PMB-5)

Education: Biomedical Engineering, B.S.E., Arizona State University, 2016–2020
Biochemistry, B.S., Arizona State University, 2016–2020

Interests: World travel, History, Nature, Food

Projects Understanding the evolution of protein refoldability: My research focuses on understanding the physiochemical properties that give proteins the ability to refold after denaturing events. Using evolution as a lens, I am trying to understand how specific proteins' evolutionary process made them more or less refoldable across multiple Bacterial species.

Haley Moran (CBI-6)

Education: B.A. Chemistry, Biochemistry & Molecular Biology, 2020; M.S. Chemical Biology, Johns Hopkins University, 2022

Interests: Dungeons & Dragons, reading, PC gaming, musicals

Projects: Investigating Extremophilic Proteome Refoldability via LiP-MS
Assessing Protein Structure Protection in Extremotolerant Desiccation Response with LiP-MS

My projects utilize limited proteolysis mass spectrometry to complete proteome-wide assessments of protein structure in response to or in the presence of extreme conditions. In particular, I probe thermophiles, piezophiles, and desiccation-tolerant species.

April Xia (Chem-5)

Education: B.S. Chemistry and Biochemistry, minor in German, University of California, Santa Barbara, 2020

Interests: Photography, video editing

Projects: Unraveling the Complexity of Protein Folding: A Structural Characterization of Misfolded E. coli Phosphoglycerate Kinase

Understanding protein folding and misfolding mechanisms is critical for elucidating cellular processes and pathological conditions. Although a significant fraction of E. coli proteins fail to refold properly after chemical denaturation, their folding pathways and the structures of the misfolded proteins remain unclear. To tackle this, we are developing a systematic approach on E. coli PGK, a well-established model protein, to elucidate the structural characteristics of these misfolded conformations.

Haley Tarbox (CBI)

Education: B.S. Biochemistry, Hofstra University, 2019; M.S. Chemical Biology, Johns Hopkins University, 2021

Interests: Reading, music, kickball

Projects: Using Structural Proteomics to Investigate the Molecular Basis of Cognitive Decline in Aging

My research utilizes limited proteolysis mass spectrometry (LiP-MS), a structural proteomics technique, to investigate how protein structures change proteome-wide between cognitively impaired and unimpaired aged rats. I am also investigating how these structural changes affect protein turnover, and utilizing crosslinking to study protein structures at the synapse.

Neil Wood (Biophysics-4)

Education: B.S. Biological Science with minor in Chemistry, University of Vermont, 2019

Interests: Improv comedy, film, and dance

Projects: Investigating Age-related Changes to Protein Structure in S. cerevisiae

Broadly, I am interested in how aging-related loss of proteostasis translates to changes in protein structure across the proteome. My project has made me interested in understanding age-related changes to the stress granule, a phase-separated condensate formed in response to stress. I am also interested in the effects of aging on co-translational folding of proteins.

Xinzhe Ren (Chem-4)

Education: B.S. Chemistry, University of Massachusetts Amherst, 2021

Interests: Angling, archery, badminton, and tennis

Projects: Interplay of N-linked glycosylation and disulfides on protein refoldability

N-linked glycosylation is a post-translational modification that attaches an oligosaccharide to an asparagine in a protein. Secretory proteins always get N-linked glycosylated in endoplasmic reticulum (ER) where disulfide formation is allowed due to its oxidative environment. As both of these modifications exclusively happen in ER, we seek to study their intertwined effects on protein energy landscape with a variety of biophysical and biochemical techniques.

Yuqi Tang (Chem-3)

Education: B.S. Chemistry, Beijing Normal University, 2020; M.S Chemistry, Pennsylvania State University, 2021

Interests: Netflix, hiking, grocery shopping

Projects: Exploring the structural biology of proteins inside glycolytic bodies using crosslinking mass spectrometry

I am interested in applying XL-MS to study how glycolytic bodies form and the hidden mechanism of metabolic flux alteration under hypoxia.

Josh Beale (CMDB-2)

Education: B.S. Molecular, Cellular and Developmental Biology, Yale, 2023

Interests: TTRPGs, Coffee, and Reading

Projects: Studying the structural changes of the blood plasma proteome across age and disease states.

Caden (Chem-2)

Education: Chemistry with Pharmacology, University of Birmingham, 2020; MRes Drug Discovery and Development, Imperial College London, 2023

Interests: Story-writing, tennis, watching anime

Projects: The refoldability of the E. coli proteome using AAA-ATPase: My research focuses on utilizing physiologically relevant biological machinery as an alternative to traditional chemical denaturants in refoldability experiments. I’m curious about how chaperone systems in E. coli help refold misfolded or aggregated proteins, keeping the proteome in check.

Yixuan huang (CMDB-2)

Education: B.S. Biology, Shanghai Tech University, China

Interests: Video games, dogs

Projects: One of my projects is mainly about developing a new tool to study RNA-Protein interactions in biocondensates. I am also working on stable misfolded proteins in E.coli.

Ruby Ho (cbi-1)

Education: B.S. Chemical Biology, UC Berkeley, USA

Interests: Cooking, swimming, reading

Projects: Assessing the adaptability of protein refoldability in Vibrio natriegen via laboratory evolution

James Wu (chem-1)

Education: B.S. Biochemistry, University of Toronto, Canada

Interests: Painting, music, cooking, traveling

Projects: Assessing the adaptability of protein refoldability in Vibrio natriegen via laboratory evolution

Lina Blanco-Rodriguez (cmdb-1)

Education: B.S, Industrial Microbiology, University of Puerto Rico at Mayaguez

Interests: Exploring the city, food, history books

Projects: Exploring protein refoldability upon desiccation by LiP-MS in Deinococcus radiodurans.

Daniel Hortis (CHEMBE-1)

Education: B.S.E., Bioengineering, 2025

Interests: Boating, Biking, Swimming, Basketball

Projects: My research focuses on the ambiguous relationship between a conformational state of a protein and its ubiquitination status. I am developing a systematic approach to structurally characterize distinct ubiquitinated protein populations with the aim of clarifying whether structural changes precede ubiquitination or the tag itself stabilizes a non-native conformation.

Edward xu (ChemBe-1)

Education: B.S. Material and Nanoscience, University of Waterloo; B.S. Nanomaterial and Science, Beijing Jiaotong University

Interests: Basketball, Video games

Projects: Using structural proteomics to explore how ubiquitin remodels the shapes and structures of proteins

Undergraduate Students

Eli Lesher

Interests: Running, gardening, and hiking

Projects: Interplay of N-linked glycosylation and disulfides on protein refoldability.

Noelle Tornquist

Interests: Dance, skiing, and reading

Projects: My project aims to study the age- and cognition-dependent structural changes of CaMKII, including refoldability and mixed-assembly complexes.