Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Computational and Systems Biology

Language

English (en)

Date of Award

Spring 4-8-2014

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

James J Havranek

Abstract

One of the key properties of proteins is that they exhibit remarkable affinities and specificities for small-molecule and peptide binding partners. To improve the success rate of rational, computational protein design and widen the scope of potential applications, it is useful to define generalized strategies and automated methodology to improve and/or alter the affinity and specificity of interactions. I have implemented several strategies for engineering protein-small molecule interactions including: improvement of substrate accessibility, stabilization of the bound state, truncation and surface engineering, and transplantation of residue level, native (or native-like) interactions. Each strategy was applied to one or more model protein, and the resulting changes in affinity, specificity, and activity were characterized experimentally. Finally, we designed a biomolecular tool-kit, consisting of 17 engineered proteins for amino acid side-chain recognition and a single enzyme to catalyze the Edman degradation. We profiled the affinity and specificity of each protein, and implemented a computational framework that demonstrates its utility for amino acid calling in a single molecule protein sequencing assay.

DOI

https://doi.org/10.7936/K7610X9N

Comments

This work is not available online per the author’s request. For access information, please contact digital@wumail.wustl.edu or visit http://digital.wustl.edu/publish/etd-search.html.

Permanent URL: http://dx.doi.org/10.7936/K7610X9N

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