Date of Graduation

5-2025

Document Type

Thesis

Degree Name

Bachelor of Science in Chemistry

Degree Level

Undergraduate

Department

Chemistry & Biochemistry

Advisor/Mentor

Moradi, Mahmoud

Committee Member

Hershberger, Margaret

Second Committee Member

Chen, Jiahui

Third Committee Member

Mantero, Paolo

Abstract

The envelope glycoprotein (Env), present on the viral surface of human immunodeficiency virus type 1 (HIV-1) facilitates host cell infection, making it a critical target for immune responses and vaccine development. Env is able to transition through three prevalent prefusion conformational states, state-1 (pre-triggered), state-2 (closed), and state-3 (open). By transitioning through these conformation states, Env can successfully evade immune responses and initiate viral entry into the host cell. This study uses molecular dynamics (MD) simulations to analyze the conformational dynamics of the mature, cleaved Env glycoprotein in the state-2 conformation (PDB ID: 4ZMJ). Simulations were conducted with five replicates, each simulation running for 500 nanoseconds. Structural stability and flexibility were assessed through root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and salt bridge analyses. Results indicate that the variable loop regions, particularly V2 in gp120, contribute significantly to Env flexibility, while gp41 remains rigid. Strong hydrogen bonds and salt bridges were identified. These findings enhance the understanding of Env conformational dynamics and highlight critical structural elements that could contribute to laying a foundation for a functional HIV-1 vaccine.

Keywords

Molecular Dynamics; Protein; Human Immunodeficiency Virus

Download

Included in

Chemistry Commons

Share

COinS