Abstract
Jianzhong Wu: „Random Thoughts: Hydrophobicity, Protein Folding and Genome Packaging”
Department of Chemical and Environmental Engineering, University of California, USA
A deductive model for biological systems typically starts with semi-empirical descriptions of molecules based on classical mechanics. Despite immense success over the last three decades, the atomistic methods often fall short of a faithful representation of the molecular behavior and intermolecular interactions on the microscopic scales and yet are limited by the computational capacity to describe biological events at the meso/macroscopic scales that are of interest for practical applications. Nevertheless, molecular modeling of biological systems can be fruitful by a synergistic combination of theory, coarse-grained modeling, and experiments.
In this presentation, I will discuss three examples from an engineering perspective on how experiment and molecular modeling can mutually benefit from each other toward understanding hydrophobicity, dynamically-stimulated protein folding, and electrostatic regulation of genome packaging. The first example illustrates that the hydrophobic effect is primarily a local phenomenon and that the hydrophobic interaction can be simply represented by a pairwise additive potential. The second example shows results from molecular simulations for the effects of confinement and dynamic control on the kinetic pathways of protein folding and how the modeling effort leads to the design of a novel experimental procedure for effective protein recovery from inclusion bodies. The third example demonstrates the power of a new molecular theory and coarse-grained models in making near quantitative predictions of electrostatic regulation of genome packaging in bacterial and human viruses.