Date of Award
12-2025
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Physics and Astronomy
Committee Chair/Advisor
Dr Hugo Sanabria Hernandez
Committee Member
Dr Emil Alexov
Committee Member
Dr Feng Ding
Committee Member
Dr Kasra Sardasthi
Abstract
Proteins, RNA, and DNA form the essential molecular machinery that drives the processes of life. The long-standing view that biological function arises solely from molecular structure has expanded with the understanding that biomolecules are dynamic entities whose motions are fundamental to regulation and activity. Structural flexibility, conformational transitions, and transient interactions together define how biological systems operate at the molecular scale. In this thesis, I present an integrated investigation of the relationship between structure, dynamics, and function in ARID1A, a chromatin remodeling protein frequently mutated in human cancers. ARID1A is a central component of the SWI/SNF complex, which modulates chromatin architecture and controls transcription of genes involved in cell-cycle regulation and DNA repair. Missense mutations within its DNA-binding ARID domain are recurrent in ovarian, endometrial, and gastric cancers, yet their molecular consequences remain largely unexplored. My research combines experimental fluorescence spectroscopy with computational modeling to examine how pathogenic substitutions alter ARID1A stability and DNA-binding behavior. Thermal and chemical denaturation experiments, supported by replica exchange discrete molecular dynamics (rexDMD) simulations, reveal that specific mutations destabilize the ARID helix bundle and modify folding energetics. Complementary single- and ensemble-fluorescence measurements, including proximity ratio assays and fluorescence anisotropy, show that these structural changes weaken DNA affinity and shift the binding mode from cooperative to noncooperative. Together, these results establish a molecular framework linking ARID1A stability to its regulatory function in chromatin remodeling. The findings demonstrate how subtle energetic perturbations introduced by missense mutations can propagate from atomic-level distortions to large-scale transcriptional dysregulation. Understanding these mechanisms provides new insight into the role of ARID1A in genome maintenance and suggests potential strategies for restoring its function in cancer.
Recommended Citation
Goutam, Rajen K., "Cancer-Associated Pathogenic Missense Mutations in the Arid Domain of arid1a Reveal Biophysical Insights Into Structural Destabilization and DNA Binding" (2025). All Dissertations. 4163.
https://open.clemson.edu/all_dissertations/4163
Author ORCID Identifier
https://orcid.org/0009-0006-4080-7193
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Pathogenic Microbiology Commons, Physics Commons