Abstract

The interaction of proteins with surfaces is a major problem involved in protein microarrays. Understanding protein/surface interactions is key to improving the performance of protein microarrays, but current understanding of the behavior of proteins on surfaces is lacking. Prevailing theories on the subject, which suggest that proteins should be stabilized when tethered to surfaces, do not explain the experimentally observed fact that proteins are often denatured on surfaces. In an attempt to develop some predictive capabilities with respect to protein/surface interactions, it was asked in previous works if the stabilization/destabilization of proteins on surfaces could be correlated to secondary structure and found that no link existed. However, further investigation has revealed that proteins with similar tertiary structure show predictable stabilization patterns. In this research, it is reported how five, alpha-helical, orthogonal-bundle proteins behave on the surface compared to the bulk. By measuring stabilization using melting temperatures and the Gibbs energies of folding, it is shown that the stability of proteins tethered to surfaces can be correlated to the shape of the loop region where the tether is placed and the free rotation ability of the part of proteins near surfaces. It is also shown that any destabilization that occurs because of the surface is an enthalpic effect and that surfaces always stabilize proteins entropically. Furthermore, the entropical stabilization effect comes from unfolded states of the tethered protein, while the enthalpical destabilization effect is from the folded states of protein. A further analysis of surface induced change of folding mechanism is also studied with a multi-state protein 7LZM in this research. The result showed that by tethering a protein on a surface, the melting temperature of part of the protein changed, which leads to a miss of state.

Degree

MS

College and Department

Ira A. Fulton College of Engineering and Technology; Chemical Engineering

Rights

http://lib.byu.edu/about/copyright/

Date Submitted

2010-06-29

Document Type

Thesis

Handle

http://hdl.lib.byu.edu/1877/etd3672

Keywords

simulation, thermodynamics, tertiary structure, interaction, protein microarray

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