Dartmouth Events

Protein adsorption to material surfaces is a fundamental concept in various scientific applications ranging from the biocompatibility of implant materials in bioengineering to cleaning the environmental material surfaces from toxic proteins in the area of biodefense. Understanding the basic molecular-level details of protein-surface interactions is, thus, crucial for controlling the protein adsorption. While a range of experimental techniques has been developed to study protein adsorption, these techniques alone are not capable of producing the dynamic molecular-level information of the protein adsorption process.

All-atom empirical force field molecular dynamics (MD) simulations hold great promise as a valuable tool for elucidating and predicting the mechanisms governing protein adsorption. However, current MD simulation methods have not been validated for this application. This research addresses three limitations of the standard MD when applied to the simulations of the protein-surface interactions: (1) representation of the force field parameters governing the interactions of protein amino-acid residues with the material surface; (2) cluster analysis of ensembles of adsorbed protein states obtained in protein-adsorption simulations, in which in addition to the conformation the orientation of the sampled states is also important; and (3) simulation time to ensure a significant level of conformational sampling to cover the entire rough energy landscape of such a large molecule system as protein adsorption. This study, thus, attempted to further advance protein-adsorption simulation methods using high-density polyethylene as a model materials surface.