Date of Award

8-2010

Document Type

Thesis

Degree Name

Master of Science (MS)

Legacy Department

Bioengineering

Advisor

Latour, Robert A

Committee Member

Vertegel , Alexey

Committee Member

Dean , Delphine

Abstract

In any molecular simulation of protein-surface interaction, the selection of the initial orientation with which the protein would interact with the surface must be first made and is found to be critical in the determination of the bioactive state of the adsorbed protein. While various molecular simulation methods have been developed to identify the preferred orientation, these methods are generally computationally expensive and time consuming, especially for large molecules thereby motivating the current study.
The computational implementation for identifying a preferred orientation was done in MATLAB¨ and directly addresses the current research problem by assuming the protein to be rigid and mapping the number of solvent accessible residues that would interact with the surface as a function of orientation, thereby yielding a topography map that would reveal the potential minimum energy orientations for a given protein-interface interaction system. The protein orientation prediction has been performed for a wide range of proteins (11kDa-300kDa) and surfaces (hydrophobic, hydrophilic, charged, biological-membranes) with the total runtime involved usually averaging in minutes. These results were also found to be in good agreement with the experimental and simulation results reported in the literature for biological and man-made materials.
Besides the intended application for the support to molecular simulations, this method also has the general application of surface design to control the bioactive state of adsorbed proteins and to selectively target and immobilize protein in a controlled orientation.

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