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

On-Demand and Location Selective Particle Assembly for Fabricating Structures of High Energy
Fang Qian, Mihail Bora, T. Yong-Jin Han, Andrew J. Pascall, Shirui Guo, Sonny S. Ly, Marcus A. Worsley, Joshua D. Kuntz, Tammy Y. Olson
Langmuir (2014) In press.

Structure and function of REP34 implicates carboxypeptidase activity in Francisella tularensis host-cell invasion
Geoffrey K. Feld, Sahar El-Etr, Michele H. Corzett, Mark S. Hunter, Kamila Belhocine, Denise M. Monack, Matthias Frank, Brent W. Segelke and Amy Rasley
Journal of Biological Chemistry (2014) In press.

A room temperature low-threshold ultraviolet plasmonic nanolaser
Qing Zhang, Guangyuan Li, Xinfeng Liu, Fang Qian, Yat Li, Tze Chien Sum, Charles M. Lieber & Qihua Xiong
Nature Communications (2014) 5, In press.

Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest
Dan M. Park and Yongqin Jiao
Applied and Environmental Microbiology (2014) 80(18), 5680-5688.

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.

Fixed-target protein serial microcrystallography with an x-ray free electron laser
Mark S. Hunter, Brent Segelke, Marc Messerschmidt, Garth J. Williams, Nadia A. Zatsepin, Anton Barty, W. Henry Benner, David B. Carlson, Matthew Coleman, Alexander Graf, Stefan P. Hau-Riege, Tommaso Pardini, M. Marvin Seibert, James Evans, Sébastien Boutet & Matthias Frank
Scientific Reports (2014) 4, 6026.

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.

Fluorescence Correlation Spectroscopy at micromolar Concentrations without optical nanoconfinement. 
Ted A. Laurence, Sonny Ly, Feliza Bourguet, Nicholas O. Fischer, Matthew A. Coleman
Journal of Physical Chemistry B (2014) 118, 9662-9667. 

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.

Nanoparticles and antigen delivery: Understanding the benefits and drawbacks of different delivery platforms.
Nicholas O. Fischer, Amy Rasley, Craig D. Blanchette
Nanomedicine (Lond) (2014) 9(4), 373-376.

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.

Enhancing the efficacy of innate immune agonists: Could nanolipoprotein particles hold the key?
Nicholas O. Fischer, Craig D. Blanchette, Amy Rasley
Nanomedicine (Lond) (2014) 9(3), 369-372.

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.

Light-Directed Electrophoretic Deposition: A New Additive Manufacturing Technique for Arbitrarily Patterned 3D Composites
Andrew J. Pascall, Fang Qian, Gongming Wang, Marcus A. Worsley, Yat Li, Joshua D. Kuntz
Advanced Materials (2014) 26(14), 2252-2256.

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.