Biological Research

Graduate students in the Division meld molecular and structural biology with physical, organic and analytical chemistry to understand the molecular basis of biological processes and human disease. Research in the Biological Division focuses on the structure, stability and function of proteins, membranes, DNA, RNA, macromolecular complexes and viruses, natural product biogenesis, synthetic biology, and genomics.

Students are a constant source of new hypotheses for mechanisms underlying cellular machines like the ribosome, spliceosome, and as well as protein and RNA folding. Students tackle these problems using biochemical methods, chemical biosensor technologies, protein and nucleic acid crystallography, in vitro and in vivo evolution, multi-dimensional NMR spectroscopy, surface chemistry, atomic-force microscopy, fluorescence spectroscopy, and high-resolution mass spectrometry.

Doctoral students in our Divsion leave the Department broadly trained for leadership roles in academia and industry.

Recent Research Results

Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP

Here, we present SHAPE-JuMP (selective 2′-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions.

SHAPE Directed Discovery of New Functions in Large RNAs

By applying comprehensive structure probing to diverse problems, we and others are showing that control of biological function mediated by RNA structure is ubiquitous across prokaryotic and eukaryotic organisms.

Physiologically relevant oxygen tensions differentially regulate hepatotoxic responses in HepG2 cells

This study evaluates the impact of physiologically relevant oxygen tensions on the response of HepG2 cells to known inducers and hepatotoxic drugs.

Representative Publications

Accounts of Chemical Research.
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SHAPE Directed Discovery of New Functions in Large RNAs Kevin M. Weeks Accounts of Chemical Research 2021 54 (10), 2502-2517 DOI: 10.1021/acs.accounts.1c00118

Toxicology in Vitro.
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Physiologically relevant oxygen tensions differentially regulate hepatotoxic responses in HepG2 cells Thomas J. DiProspero, Erin Dalrymple, Matthew R. Lockett, Toxicology in Vitro 2021 74, 0887-2333 DOI: 10.1016/j.tiv.2021.105156

ACS Applied Materials & Interfaces.
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Dye-Sensitized Nonstoichiometric Strontium Titanate Core–Shell Photocathodes for Photoelectrosynthesis Applications Caroline E. Reilly, Robert J. Dillon, Animesh Nayak, Shane Brogan, Taylor Moot, Matthew K. Brennaman, Rene Lopez, Thomas J. Meyer, and Leila Alibabaei ACS Applied Materials & Interfaces 2021 13 (13), 15261-15269 DOI: 10.1021/acsami.1c00933

Chemical Research in Toxicology.
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Toxicological Responses of α-Pinene-Derived Secondary Organic Aerosol and Its Molecular Tracers in Human Lung Cell Lines Faria Khan, Karina Kwapiszewska, Yue Zhang, Yuzhi Chen, Andrew T. Lambe, Agata Kołodziejczyk, Nasir Jalal, Krzysztof Rudzinski, Alicia Martínez-Romero, Rebecca C. Fry, Jason D. Surratt, and Rafal Szmigielski Chemical Research in Toxicology 2021 34 (3), 817-832 DOI: 10.1021/acs.chemrestox.0c00409

Current Opinion in Structural Biology.
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Protein-complex stability in cells and in vitro under crowded conditions Samantha S. Stadmiller and Gary J. Pielak Current Opinion in Structural Biology 2021 66, 183-192 DOI: 10.1016/j.sbi.2020.10.024

Proceedings of the National Academy of Sciences .
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The intracellular environment affects protein–protein interactions Shannon L. Speer, Wenwen Zheng, Xin Jiang, I-Te Chu, Alex J. Guseman, Maili Liu, Gary J. Pielak, Conggang Li Proceedings of the National Academy of Sciences Mar 2021, 118 (11) e2019918118 DOI: 10.1073/pnas.2019918118

ACS Chemical Biology.
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Pseudomonas Virulence Factor Pathway Synthesizes Autoinducers That Regulate the Secretome of a Pathogen Ashley M. Kretsch, Gina L. Morgan, Katie A. Acken, Sarah A. Barr, and Bo Li ACS Chemical Biology 2021 16 (3), 501-509 DOI: 10.1021/acschembio.0c00901

Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR.
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Crilly C, Brom J, Kowalewski M, Piszkiewicz S, Pielak, GJ. 2021. Dried protein structure revealed at the residue level by liquid-observed vapor exchange NMR Biochemistry 60, 152-159.

Journal of the American Chemical Society.
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Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA Jeffrey E. Ehrhardt and Kevin M. Weeks Journal of the American Chemical Society 2020 142 (44), 18735-18740 DOI: 10.1021/jacs.0c06221