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The properties of proteins with reduced sequence complexity--either in the form of primary structure symmetry or restricted amino acid alphabets--are controversial. Studies of protein biophysics and sequence analyses suggest that simplified proteins lack fundamental features of foldability and stability (generally considered to be prerequisites for functional protein structures). Conversely, models of protein emergence and evolution freely invoke simplified proteins and presume them to be stable, foldable, and structured. To resolve this apparent contradiction, two model proteins with key features of sequence simplification were developed and their folding properties analyzed. The first model protein is characterized by a symmetric sequence and is derived from the folding nucleus of a human protein, fibroblast growth factor-1. The second model protein, which also has a symmetric sequence, is greatly enriched for the amino acids that were present at the origin of life. Studies of the stability, folding, and structure of these model proteins suggest that (1) the folding nucleus is a key element of protein evolution and design, (2) symmetric sequences are compatible with protein folding, and can confer robustness to structural reengagements that facilitate protein structure evolution, and (3) the amino acid diversity present on the early earth was likely sufficient to encode complex protein architecture, especially within a halophile environment. In total, the data presented here support a crucial role for proteins with sequence symmetry or amino acid alphabet simplification in key biological processes.
Halophile, Origin of Life, Protein Design, Protein Evolution, Protein Folding, Proteogenesis
Date of Defense
November 4, 2014.
A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Includes bibliographical references.
Michael Blaber, Professor Directing Dissertation; Timothy Logan, Committee Member; Scott Stagg, Committee Member; Oliver Steinbock, Committee Member.
Florida State University
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