Multiscale Simulation for Biomolecular Engineering: Protein Allostery and Cellulose Deconstruction
Multiscale modeling and simulation are becoming indispensible tools for bimolecular engineering. I will present two examples of applying computational methods to develop mechanistic understanding that is difficult to acquire otherwise. The first is the phenomena of protein allostery, the coupling between different motifs that enables proteins to function as molecular machines. The intra-protein communication in a serine protease subtilisin is employed as an example to illustrate how Ca2+ binding affects the structures and flexibility of other regions. We also establish a tight connection between physics-based and informatics-based representation of inter-residue coupling. Application of this framework to resolve the mechanism of enzyme acting on the interfaces of biomaterials will also be addressed. The second example is to elucidate why certain ionic liquids have high potency is dissolving crystalline cellulose but water does not. First, we compute the free-energy profiles of peeling off a glucose chain in water and in an ionic liquid. The potentials of mean forces between the moieties of solvent and cellulose are then computed to dissect the interaction forces that led to the different behaviors. We show that both the cations and anions of ionic liquid play essential roles in dissolving cellulose, in contrast to the dominant emphasis of anions in the literature.
Jhih-Wei Chu is Assistant Professor of Chemical and Biomolecular Engineering at the University of California, Berkeley. For more information, please visit: http://www.cchem.berkeley.edu/chugrp/Group_Members/Entries/2009/9/1_Jhih-Wei_Chu_-_assistant_professor_of_chemical_engineering.html.