Julia Sweeney

Date of Award

2022

Document Type

Thesis

Degree Name

Bachelors

Department

Natural Sciences

First Advisor

Walstrom, Katherine

Area of Concentration

Chemistry

Abstract

A novel species of halophilic bacteria from a Florida marine environment (Zooshikella MI-3) was identified, its genome sequenced, and a likely Glucose-6-Phosphate Dehydrogenase (G6PD) identified by sequence similarity. In this thesis project, a three dimensional structure was proposed for this G6PD enzyme using sequence homology in SWISS-MODEL. The structure was refined and verified for accuracy using the YASARA, ProtParam, MolProbity, SAVES Verify3D and ProSA web servers. A biological assembly was created via structural homology using the dimer G6PD of L. mesenteroides. Surface interactions between protein chains were quantified in Chimera and ChimeraX and compared to those from known crystal structures of G6PD. The limitations of generating a correct biological assembly via template based homology were explored. Structural features of this protein were compared to known characteristics of halophilic proteins to gain insight as to what types of adaptations this species employs to survive in a high salt environment. The presence of the ectoine biosynthesis gene and the lack of acidic proteome signatures provided evidence that this halophile employs ectoine as a compatible solute instead of importing potassium and chloride ions. The structural model showed the active site residues in very similar locations as G6PDs from crystal structures. This model predicts fewer ionic interactions between subunits compared to other G6PD structures.

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