Development and Evaluation of Protein Design Methods for Functional Targets

Citation

Vizcarra, Christina Luisa (2008) Development and Evaluation of Protein Design Methods for Functional Targets. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/G16E-JZ97. https://resolver.caltech.edu/CaltechETD:etd-05292008-140215

Abstract

Computational protein design seeks to identify amino acid sequences that will fold into a specified three-dimensional structure. Extending this technique from identification of sequences that retain a native structure to the design of sequences that will carry out a function has been a significant challenge. Modeling the energetics of catalysis and binding requires considerations that may not be necessary for the design of folded, stable proteins. I have investigated models for protein electrostatics with the goal of improving current methods for the design of functional molecules. The work in this thesis is focused on the Poisson-Boltzmann model, a dielectric continuum model that describes the effect of solvent polarization on the electrostatic potential in a protein. I found that this model is amenable to design calculations, as judged by its ability to be decomposed into terms that are used in sequence selection.

Aside from energy estimation, there are a number of assumptions that are made in protein design in order to make the problem computationally tractable. Because of these assumptions, and also because of incomplete models of protein function, it is expected that many proteins sequences will need to be experimentally characterized to find one that meets a difficult design goal. To this end, I examined methods for using computational tools to produce libraries of protein sequences. These studies showed that (1) structure-based, computational library design methods can be used to generate libraries with a high number of folded proteins and (2) computational design is a promising tool for generating highly mutated proteins with a diverse range of functions.

Thesis Files