Date of Award
2024
Document Type
Thesis
Degree Name
MS in Chemistry
Department
Chemistry
First Advisor
Francisco Vazquez
Second Advisor
Erica Jacobs
Third Advisor
Joseph M Serafin
Abstract
The study aimed to utilize molecular dynamics (MD) simulation to investigate intrinsically disordered protein (IDP) molecules and regions, focusing on IDPs such as alpha-synuclein and the SAR-CoV-2 nucleocapsid linker segment and their variants. Methodologically, the research employed MD simulation with implicit solvent methods, GaMD enhanced sampling, Python-based analysis, and VMD visualization. The study's significance lies in revealing structural dynamics insights of IDP regions. Key findings include the average structures of target sequences from k-means clustering analysis. The impact of mutations in alpha-synuclein KTKEGV repeat mutations is also revealed. Mutations introducing hydrophobic residues, like KGV and KLK, increased surface hydrophobicity, with KGV over-stabilized due to added positive charges. The research also explored the rigidity fluctuations of SAR-CoV-2 linker segments, comparing those from the Wuhan strain to those with r203k/g204r mutation and various phosphorylation levels.
Recommended Citation
Yeung, Coby, "MOLECULAR DYNAMICS STUDY OF ALPHA-SYNUCLEIN REPEAT MUTATIONS AND SARS-COV-2 NUCLEOCAPSID LINKER PHOSPHORYLATION" (2024). Theses and Dissertations. 755.
https://scholar.stjohns.edu/theses_dissertations/755