One of the goals of Dr. Cheung’s research is to discover interesting macromolecular dynamics under cell-like conditions by applying molecular simulation methods. The cellular milieu is a crowded, concentrated environment that impacts the behavior of macromolecules. It can affect the rate of protein folding, protein association, and the overall conformational changes that cannot be probed in dilute solutions. Her research uses a combined approach of coarse-grained molecular simulation, all-atomistic molecular simulation, and bioinformatic data mining to investigate the structural behavior and statistical properties of large biomolecules in the cellular milieu.
Dr. Cheung developed a state-of-the-art multiscale molecular simulation approach that integrates varying grains of models and uses high performance computing to facilitate detailed examination of macromolecular dynamics across multiple orders of magnitude in both space and time. She is particularly interested in the statistical properties and electronic structure of soft materials in a nanosized tight space or at the interfaces of liquid and solid phases to address behavior under harsh conditions wherein bulk analysis does not apply. Characterization of these structural conformations and self-assembled behavior at a nanoscale level is important to the nanotechnology and petroleum science industries.
Figure 1. The F0 portion of the ATP Synthase complex was placed in a POPE bilayer membrane and solvated. This image illustrates the inside of the mitochondrial matrix. The protein is barely visible (purple) buried in the hydrophobic chains of the lipids and covered by several angstroms of water molecules. The hydrophobicity of the membrane has prevented laboratory observation and has therefore been studied with molecular modelings
Figure 2. As the rotary c-subunit passes the stationary a-subunit in the f0 portion of the ATP Synthase motor, certain amino acid residues engage with each other at this interface. In this image, some residues of interest are highlighted in pink and limve. This image also gives a glimpse in to the crowded conditions of the cell, which is why this project has been difficult to study in labs and must be studied with molecular dynamics.