College of Science and Health Theses and Dissertations

Date of Award

Spring 6-14-2019

Degree Type

Thesis

Degree Name

Master of Science (MS)

First Advisor

Jesus Pando, PhD

Second Advisor

Eric Landahl, PhD

Third Advisor

Gabriela Gonzalez Aviles, PhD

Abstract

This study looked to identify features related to thermal stability and function in the amino acid chains of short globular proteins from mesophile and thermophile species, within the constraint that the protein fold to perform a speci_c function. To do so 540 homologous pairs of proteins were studied. The amino acid chains were con-verted to hydrophobicity signals by assigning a hydropathy score to each residue in the polypeptide. The hydrophobicity signals were passed through a wavelet packet transform and the resulting spectra analyzed. Bootstrapping was used to gener-ate a control data set to determine if the true ordering of amino acids codes for a non-random uctuation in hydropathy along the length of the polypeptide. A method to relate the spectral characteristics to the function of a protein making use of gene ontologies was developed as a proof of concept. As a group, mesophile and thermophile proteins have very similar total power. However, on a protein-to-protein basis the thermophile contains a greater total power in 489 of the 540 pairs (90.56%). The hydrophobicity scale used in this study is strongly correlated with Gibbs free energy. The total power of a protein is also strongly correlated to the Gibbs free energy, so that the thermophile protein contains a greater free energy than its corresponding mesophile partner. It has been noted in the experimental literature that thermophile proteins are stabilized by increasing their Gibbs free en-ergy. The statistical measures skew and kurtosis were adapted so that a spectrum of skew and kurtosis values were generated for each protein. These values indicate that the uctuation in hydropathy is non random and position dependent. Thermophile proteins have larger power at frequency bands 21 through 31 (average intervals of 100 to 77 amino acids), and 44 to 56 (on average 46 to 19 amino acids), which may contribute to their having greater total power in 90.56% of the pairs. Increases to the uctuation in hydropathy within certain lengths throughout the total amino acid chain of a protein may be a means of raising the temperature at which a protein denatures.

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