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

Large-scale First-Principles molecular dynamics simulations with electrostatic embedding: application to acetylcholinesterase catalysis
Jean-Luc Fattebert, Edmond Y Lau, Brian J. Bennion, Patrick Huang, and Felice C Lightstone
J. Chem. Theory Comput. (2015) 11, In press.

Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography
Geoffrey K. Feld, Michael Heymann, W. Henry Benner, Tommaso Pardini, Ching-Ju Tsai, Sébastien Boutet, Matthew A. Coleman, Mark S. Hunter, Xiaodan Li, Marc Messerschmidt, Achini Opathalage, Bill Pedrini, Garth J. Williams, Bryan A. Krantz, Seth Fraden, Stefan Hau-Riege, James E. Evans, Brent W. Segelke, and Matthias Frank
J. Appl. Cryst. (2015) 48, 1072-1079.

Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance
Mimi C. Yung, Dan M. Park, K. Wesley Overton, Matthew J. Blow, Cindi A. Hoover, John Smit, Sean R. Murray, Dante P. Ricci, Beat Christen, Grant R. Bowman, Yongqin Jiao
J. Bacteriol. (2015) 197, 3160-72.

A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
Brian J. Bennion, Sebnem G. Essiz, Edmond Y. Lau, Jean-Luc Fattebert, Aiyana Emigh, Felice C. Lightstone
PLoS ONE (2015) 10(4): e0121092.

Molecular Dynamics Simulations of Ligand Recognition Upon Binding Antithrombin: A MM/GBSA Approach
Xiaohua Zhang, Horacio Péréz-Sánchez, and Felice C. Lightstone
Bioinformatics and Biomedical Engineering (2015) 9044, 584-593.

Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses
Stefan P. Hau-Riege and Brian J. Bennion
Phys Rev E (2015) 91(2).

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 (2015) 31(12), 3563–3568.

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw 
Christopher W. Simmons, Amitha P. Reddy, Patrik D’haeseleer, Jane Khudyakov, Konstantinos Billis, Amrita Pati, Blake A, Simmons, Michael P. Thelen and Jean S. VanderGheynst
Biotechnology for Biofuels (2014) 7, 495.

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) 289, 30668.

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, 4953.

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.