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

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 Wong, Felice 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 Ng, Benjamin Stewart, Sergio Wong, Felice 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.

High Power Density Microbial Fuel Cell with Flexible 3D Graphene-Nickel Foam as Anode
Hanyu Wang, Gongming Wang, Yichuan Ling, Fang Qian, Yang Song, Xihong Lu, Shaowei Chen, Yexiang Tong, Yat Li
Nanoscale (2013) 5, 10283-10290.

Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses
Amitha Reddy, Christopher Simmons, Patrik D'haeseleer, Jane Khudyakov, Helcio Burd, Masood Hadi, Blake Simmons, Steven Singer, Michael Thelen, Jean VanderGheynst
PLoS ONE (2013) 8, e77985.

Self-biased Solar-Microbial Device for Sustainable Hydrogen Generation
Hanyu Wang, Fang Qian, Gongming Wang, Yongqin Jiao, Zen He and Yat Li
ACS Nano (2013) 7, 8728-8735.

Identification of a Possible Secondary Picrotoxin-Binding Site on the GABAA-Receptor
Tim Carpenter, Ed Lau, Felice Lightstone
Chemical Research in Toxicology (2013) 26, 1444-1454.

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Patrik D'haeseleer, John Gladden, Martin Allgaier, Patrik Chain, Susannah Tringe, Stephanie Malfatti, Joshua Aldrich, Carrie Nicora, Errol Robinson, Ljiljana Paša-Tolić, Philip Hugenholtz, Blake Simmons, Steven Singer
PLoS ONE (2013) 8(7), e68465.

Lignin depletion enhances the digestibility of cellulose in cultured xylem cells
Catherine Lacayo, Mona Hwang, Shi-You Ding, Michael Thelen
PLoS ONE (2013) 8(7), e68266.

Comparison and Analysis of Zinc and Cobalt-based Systems as Catalytic Entities for the Hydration of Carbon Dioxide
Ed Lau, Sergio Wong, Sarah Baker, Jane Bearinger, Lucas Koziol, Carlos Valdez, Joe Satcher, Roger Aines, Felice Lightstone
PLoS ONE (2013) 8(6): e66187.