Year of Award
2025
Document Type
Thesis
Degree Type
Master of Science (MS)
Degree Name
Chemistry
Department or School/College
Department of Chemistry and Biochemistry
Committee Chair
Bruce E. Bowler
Commitee Members
Klara Briknarova, Kent Sugden, J. Stephen Lodmell, Travis Hughes
Subject Categories
Amino Acids, Peptides, and Proteins | Biological and Chemical Physics | Other Chemistry
Abstract
This study enhances protein stability prediction by refining EmCAST (Empirical C-Alpha Stability Tool), a computational tool used to identify stabilizing mutations in protein domains. We applied EmCAST to two model proteins: the α-helical ubiquitin-associated domain 2 (UBA(2)) and the α/β N-terminal domain of ribosomal protein L9 (NTL9). Protein stability is critical for proper function, and mutations can lead to misfolding and disease. To validate EmCAST’s predictions, guanidine hydrochloride-induced denaturation was monitored using circular dichroism (CD) spectroscopy for both wild-type and mutant variants. Results guided refinements to EmCAST’s algorithm, incorporating new experimental datasets to improve accuracy. Additionally, we examined the assumption that stabilizing mutations preserve global structure by attempting to crystallize wild-type UBA(2). This integrative approach bridges computational modeling and experimental validation, advancing the development of a strong framework for rational protein design and stability engineering.
Recommended Citation
Ghazi Esfahani, Bahar, "STRUCTURAL OPTIMIZATION AND STABILITY ENHANCEMENT OF UBA(2) AND NTL9 USING THE COMPUTATIONAL TOOL: EMCAST" (2025). Graduate Student Theses, Dissertations, & Professional Papers. 12478.
https://scholarworks.umt.edu/etd/12478
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Amino Acids, Peptides, and Proteins Commons, Biological and Chemical Physics Commons, Other Chemistry Commons
© Copyright 2025 Bahar Ghazi Esfahani