The Biochemical and Biophysical Systems Group

The Biochemical and Biophysical Systems Group is formed by experimental and computational biologists who use a wide range of expertise to approach cutting-edge problems in systems biology.  We use multidisciplinary approaches – ranging from molecular biology through proteomics to modeling – to investigate microbes and microbial communities as they respond to different perturbations, including those relevant to emerging issues in bioenergy, bioremediation, and pathogenesis.  In addition to developing computational tools to describe and predict biological systems, we are combining experimental efforts with modeling and simulation methods to design and develop safe and effective therapeutics.  Our principal unifying objective is to gain a predictive understanding of protein-mediated activities that are critical to cells and their interactions in living systems.

Recent Publications

A Method to Predict Blood-Brain Barrier Permeability of Drug-like Compounds Using Molecular Dynamics Simulations
Timothy S. Carpenter, Daniel A. Kirshner, Edmond Y. Lau, Sergio E. Wong, Jerome P. Nilmeier, and Felice C. Lightstone
Biophys. J., (2014) In press.

Development of a native Escherichia coli induction system for ionic liquid tolerance
Marijke Frederix, Kimmo Hütter, Jessica Leu, Tanveer S. Batth, William J. Turner, Thomas L. Rüegg, Harvey W. Blanch, Blake A. Simmons, Paul D. Adams, Jay D. Keasling, Michael P. Thelen, Mary J. Dunlop, Christopher J. Petzold, and Aindrila Mukhopadhyay
PLoS ONE, (2014) 9(7): e101115.

Photoenhanced Electrochemical Interaction between Shewanella and a Hematite Nanowire Photoanode
Fang Qian, Hanyu Wang, Yichuan Ling, Gongming Wang, Michael P. Thelen, and Yat Li
Nano Letters (2014) 14(6), 3688-3693.

Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus
Mimi Cho Yung and Yongqin Jiao
Appl. Environ. Microbiol. (2014) In press.

The GABAA Receptor Target of Tetramethylenedisulfotetramine
Chunqing Zhao, Sung Hee Hwang, Bruce A. Buchholz , Timothy S. Carpenter, Felice C. Lightstone, Jun Yang, Bruce D. Hammock, John E. Casida
Proc. Natl. Acad. Sci. USA (2014) 111(23), 8607-8612.

An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production
Thomas L. Ruegg, Eun-Mi Kim, Blake A. Simmons, Jay D. Keasling, Steven W. Singer, Taek Soon Lee, Michael P. Thelen
Nature Communications, (2014) 5, 3490.

Shotgun Proteomic Analysis Unveils Survival and Detoxification Strategies byCaulobacter crescentus during Exposure to Uranium, Chromium, and Cadmium
Mimi Cho Yung, Jincai Ma, Michelle Salemi, Brett S. Phinney, Grant R. Bowman, and Yongqin Jiao
J. Proteome Res. (2014) 131833-1847.

Understanding a Substrate’s Product Regioselectivity in a Family of Enzymes:  A Case Study of Acetaminophen Binding in Cytochrome P450s
Yue Yang, Sergio E. Wong and Felice C. Lightstone
PLoS ONE (2014) 9(2): e87058.

Developing an approach for first-principles catalyst design: application to carbon capture catalysis
Heather J. Kulik, Sergio E. Wong, Sarah E. Baker, Carlos A. Valdez, Joe H. Satcher, Roger D. Aines, and Felice C. Lightstone
Acta Crystallographica (2014) C70, 123-131.

Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment
Xiaohua Zhang, Sergio E. Wong, Felice C. Lightstone
J. Chem. Inf. Model. (2014), 54(1), 324-337.

Tricyclic GyrB/ParE (TriBE) Inhibitors: A New Class of Broad-Spectrum Dual-Targeting Antibacterial Agents
Leslie W. Tari, Xiaoming Li, Michael Trzoss, Daniel C. Bensen, Zhiyong Chen, Thanh Lam, Junhu Zhang, Suk Joong Lee, Grayson Hough, Doug Phillipson, Suzanne Akers-Rodriguez, Mark L. Cunningham, Bryan P. Kwan, Kirk J. Nelson, Amanda Castellano, Jeff B. Locke, Vickie Brown-Driver, Timothy M. Murphy, Voon S. Ong, Chris M. Pillar, Dean L. Shinabarger, Jay Nix, Felice C. Lightstone, Sergio E. Wong, Toan B. Nguyen, Karen J. Shaw, John Finn
PLoS ONE (2013) 8(12), e84409.

Molecular Recognition of Aromatic Rings by Flavin: Electrostatics and Dispersion Determine Ring Positioning Above Isoalloxazine
Lucas Koziol, Neeraj Kumar, Sergio E. Wong, Felice C. Lightstone
J. Phys. Chem. A (2013) 117, 12946-12952.

Quantitative in silico analysis of transient metabolism of acetaminophen and associated causes of hepatotoxicity in humans
Ali Navid, David M. Ng, Benjamin J. Stewart, Sergio E. Wong, Felice C. Lightstone
In Silico Pharmacology (2013) 1, 14.

The use of nanolipoprotein particles to enhance the immunostimulatory properties of innate immune agonists against lethal influenza challenge
Dina Weilhammer, Craig Blanchette, Nicholas Fischer, Shabnam Alam, Gabriela Loots, Michelle Corzett, Cynthia Thomas, Cheri Lychak, Alexis Dunkle, Joyce Ruitenberg, Smita Ghanekar, Andrea Sant, Amy Rasley
Biomaterials (2013) 34(38),10305-10318.