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

Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines
Montiago X. LaBute, Xiaohua Zhang, Jason Lenderman, Brian J. Bennion, Sergio E. Wong, Felice C. Lightstone
PLoS ONE (2014) 9(9): e106298.

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) 107(3), 630-641.

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source
Bill Pedrini, Ching-Ju Tsai, Guido Capitani, Celestino Padeste, Mark S. Hunter, Nadia A. Zatsepin, Anton Barty, W. Henry Benner, Sébastien Boutet, Geoffrey K. Feld, Stefan P. Hau-Riege, Richard A. Kirian, Christopher Kupitz, Marc Messerschmitt, John I. Ogren, Tommaso Pardini, Brent Segelke, Garth J. Williams, John C. H. Spence, Rafael Abela, Matthew Coleman, James E. Evans, Gebhard F. X. Schertler, Matthias Frank, Xiao-Dan Li
Philos Trans R Soc Lond B Biol Sci. (2014) 369(1647): 20130500.

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) 80(16), 4795-4804.

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.

Evaluation of Nanolipoprotein Particles (NLPs) as an In Vivo Delivery Platform
Nicholas O. Fischer, Dina R. Weilhammer, Alexis. Dunkle, Cynthia Thomas, Mona Hwang, Michele Corzett, Cheri Lychak, Wasima Mayer, Salustra Urbin, Nichole Collette, Jiun Chiun Chang, Gabriela G. Loots, Amy Rasley, Craig D. Blanchette
PLoS ONE (2014) 9(3): e93342.

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) 13 1833-1847.

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.

Quantifying Interactions of a Membrane Protein Embedded in a Lipid Nanodisc using Fluorescence Correlation Spectroscopy
Sonny Ly, Feliza Bourguet, Nicholas O. Fischer, Edmond Y. Lau, Matthew A. Coleman, Ted A. Laurence
Biophys. J. (2014) 106(2), L05-L08.

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.