Date of Award

8-2016

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Legacy Department

Bioengineering

Committee Member

Dr. Robert A. Latour, Committee Chair

Committee Member

Dr. Steven J. Stuart

Committee Member

Dr. Delphine Dean

Committee Member

Dr. Alexey Vertegel

Abstract

Protein adsorption at material surfaces is a fundamental concept in many scientific applications ranging from the biocompatibility of implant materials in bioengineering to cleaning environmental material surfaces from toxic proteins in the area of biodefense. Understanding the molecular-level details of protein-surface interactions is crucial for controlling protein adsorption. While a range of experimental techniques has been developed to study protein adsorption, these techniques cannot produce the fundamental molecular-level information of protein adsorption. 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 acids 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 molecular system as protein adsorption. This study, thus, attempted to further advance protein-adsorption simulation methods using high-density polyethylene as a model materials surface.

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