Computational Modelling Group

Membrane-Protein Interactions: The Outer Membrane of Gram-Negative Bacteria

10th June 2013
Research Team
Pin-Chia Hsu
Syma Khalid

Outer membrane protein, OmpF embedded in DMPC membrane

Understanding the interaction between membrane protein and biological membrane and predicting its interaction sites is one of the most important and key challenge research article in the modern structural biology. There is about 20-30% of membrane protein in genome and around 50% of membrane proteins were estimated and predicted as the future drug target. Furthermore, membrane proteins have both biological and biomedical importance, which involves multiple physiological functions in membrane, such as ion/small molecule transportation, energy transduction, cellular signalling and etc. Moreover, lipid-protein interactions are important in stabilizing its structure and in the native environment, and it helps the membrane proteins assembly.

Molecular dynamic simulation method provides a means of complement available structural, dynamic, thermodynamic information for protein embedded in a physiological, realistic, and modeled membrane environment. Using high performance computer, Iridis4, with it’s great facilities, will shorten the simulation time and could lead to study the variety of outer membrane proteins that share the similar structures and provide the better comparison results.


Life sciences simulation: Biomolecular simulations, Systems biology

Simulation software: Gromacs

Visualisation and data handling software: VMD, Xmgrace

Software Engineering Tools: Emacs

Programming languages and libraries: Fortran

Computational platforms: Iridis, Mac OS X