Computational study of biological systems at multi-scale: protein structure, function, assemblies, networks, and cells

Jie Liang

Department of Bioengineering, the University of Illinois at Chicago

11am Friday, Feburary 3rd, 2012

International Center (CIP-115)

Although the genetic blueprint of many species are known, understanding how living organisms work require a multi-scale approach combining studies of individual gene/protein, interactions of multiple proteins, molecular network, and cellular/tissue pattern formation. At the molecular level, we discuss how new insights into protein functions can be gained by computation of signatures of enzyme binding pockets, and its implication for large scale comparative modeling of binding surfaces. We also describe a new framework for stuyding stability and assembly of beta barrel membrane proteins, including prediction of oligomerization state, protein-protein interaction interface, relative melting temperature, as well as general stabilization strategy that is applicable for design of stable nanopores on membrane. At the network level, we describe how to account for the full stochasticity of rare and small copy number events important for cell fate by characterizing the full state space and by solving the chemical master equation accurately without Gillespie simulation or Fokker-Planck/Langevin approximation. We show
how to relate the computed landscape probability to phenomenological characterization of networks such as bi-stability, and the robustness of wild type versus mutant lambda phages. At the cellular level, we describe a geometric model and an algorithm for simulating dynamic pattern formation of cell populations from single or multiple locations where cells can grow, divide, differentiate, die, with changes in mechanical or environment properties. We believe this multi-scale approach will be useful for future engineering of biological systems. (Please visit http://www.uic.edu/~jliang for further information).

Bio: Jie Liang is a professor in the Department of Bioengineering at the University of Illinois at Chicago. He joined UIC in 1999 as an assistant professor, and was promoted to associated professor in 2003, and to full professor in 2007. He was a visiting professor at the Systems Biomedicine Institute at Shanghai Jiaotong University in 2006. He received his B.S. degree from Fudan University in 1986, MCS and Ph.D. in Biophysics from the University of Illinois at Urbana-Champaign in 1994. He was an NSF CISE postdoctoral research associate (1994-1996) at the Beckman Institute and National Center for Supercomputing and its Applications (NCSA) in Urbana. He spent eight months as a visiting fellow at the NSF Institute of Mathematics and Applications at Minneapolis. From 1997 to 1999, he was an Investigator at SmithKline Beecham Pharmaceuticals in Philadelphia. He was a recipient of the NSF CAREER award in 2003. He was elected as an AIMBE fellow in 2007. He is currently a University Scholar at the University of Illinois at Chicago.

Dr. Liang's research interests include systems biology, computational bioengineering, bioinformatics, and computational biophysics, especially the areas of structural bioinformatics, computational proteomics, molecular networks, and cellular pattern formation. Current projects in his lab include stochastic network of biomolecules, gene circuits, protein function prediction, evolution assessment, membrane protein/nanodevice assembly, protein folding and design, and stochasticity in molecular networks. His recent work can be accessed at (http://www.uic.edu/~jliang).

Host: Dr. Yanni Sun