Impact of Geometrical Constraint and Interfacial Interactions on Hydrated Proteins under Confinement

Yang Zhang, University of Illinois at Urbana-Champaign

Usage Details

Proteins in vivo commonly perform biological functions in confined spaces. On the one hand, the confinement interface imposes geometrical constraint on the conformation space of proteins; on the other hand, it may also interact with protein via, e.g. hydrophobic and hydrophilic interactions. Understanding the interaction between proteins and confinement not only helps elucidate the behaviors of proteins in confined spaces but is also imperative to the development of a plethora of confinement-based biotechnologies. Thus, in this project, we propose to study the overall effects of confinement that differ in hydrophobicity and interfacial interactions on the behaviors of proteins. Replica exchange molecular dynamics (REMD) simulation will be used to obtain the long-timescale equilibrium properties of protein under confinement. Due to the highly demanding computational sources, especially the intensive parallelization by the REMD simulations, a petascale supercomputer such as Blue Waters is imperative for conducting this project.