Proteins perform an incredible array of functions facilitated by a diverse
set of biochemical properties. Changing these properties is an essential molecular
mechanism of evolutionary change, with major questions in protein evolution
surrounding this topic. How do new functional biochemical features evolve? How
do proteins change following gene duplication events? I used the S100 protein
family as a model to probe these aspects of protein evolution. The S100s are
signaling proteins that play a diverse range of biological roles binding Calcium
ions, transition metal ions, and other proteins. Calcium drives a conformational
change allowing S100s to bind to diverse peptide regions of target proteins. I used
a phylogenetic approach to understand the evolution of these diverse biochemical
features. Chapter I comprises an introduction to the disseration. Chapter II is
a co-authored literature review assessing available evidence for global trends in
protein evolution. Chapter III describes mapping of transition metal binding
onto a maximum likelihood S100 phylogeny. Transition metal binding sites and
metal-driven structural changes are a conserved, ancestral features of the S100s.
However, they are highly labile at the amino acid level. Chapter IV further characterizes the biophysics of metal binding in the S100A5 lineage, revealing
that the oft–cited Ca2+/Cu2+ antagonism of S100A5 is likely due to an experimental
artifact of previous studies. Chapter V uses the S100 family to investigate the
evolution of binding specificity. Binding specificity for a small set of peptides
in the duplicate S100A5 and S100A6 clades. Ancestral sequence reconstruction
reveals a pattern of clade-level conservation and apparent subfunctionalization
along both lineages. In chapter VI, peptide phage display, deep-sequencing, and
machine-learning are combined to quantitatively reconstruct the evolution of
specificity in S100A5 and S100A6. S100A5 has subfunctionalized from the ancestor,
while S100A6 specificity has shifted. The importance of unbiased approaches to
measure specificity are discussed. This work highlights the lability of conserved
functions at the biochemical level, and measures changes in specificity following
gene duplication. Chapter VII summarizes the results of the dissertation, considers
the implications of these results, and discusses limitations and future directions.
This dissertation includes both previously published/unpublished and co-
authored material.
| Identifer | oai:union.ndltd.org:uoregon.edu/oai:scholarsbank.uoregon.edu:1794/23178 |
| Date | 10 April 2018 |
| Creators | Wheeler, Lucas |
| Contributors | Harms, Michael |
| Publisher | University of Oregon |
| Source Sets | University of Oregon |
| Language | en_US |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Rights | All Rights Reserved. |
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