Degree Type

Thesis

Date of Award

2007

Degree Name

Master of Science

Department

Theses & dissertations (Interdisciplinary)

Major

Bioinformatics and Computational Biology

First Advisor

Xun Gu

Second Advisor

Karin Dorman

Abstract

In this study, I use animal G-protein alpha subunit family as an example to illustrate a comprehensive analytical pipeline for detecting different types of functional divergence of protein families, which is phylogeny-dependent, combined with ancestral sequence inference and available protein structure information. In particular, I focus on (i) Type-I functional divergence, or site-specific rate shift, as typically exemplified by amino acid residue highly conserved in a subset of homologous genes but highly variable in a different subset of homologous genes, and (ii) Type-II functional divergence, or the shift of cluster-specific amino acid property, as exemplified by a radical shift of amino acid property between duplicate genes, which is otherwise evolutionally conserved. We utilized the software DIVERGE2 to carry out these analyses. In the case of G-protein alpha subunit gene family, I have tested the significance of functional divergence between subfamily Gq and Gs, and predicted the candidate amino acid residues related to either Type-I or Type-II functional divergence. Then, the inferred ancestral sequences and current amino acid configuration of these candidate sites were combined with phylogenies to explore the trends of functional divergence. Finally, these predicted residues are mapped to the protein structures to test whether these residues may have structures or solvent accessibility preferences.

DOI

https://doi.org/10.31274/rtd-180813-16197

Publisher

Digital Repository @ Iowa State University, http://lib.dr.iastate.edu/

Copyright Owner

Ying Zheng

Language

en

Proquest ID

AAI1446062

OCLC Number

181086145

ISBN

9780549142270

File Format

application/pdf

File Size

37 pages

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