Date of Award
2024
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Biotechnology Science and Engineering
Committee Chair
Jerome Baudry
Committee Member
Joseph Ng
Committee Member
Luis Cruz-Vera
Committee Member
Ahmed Lawan
Committee Member
Daniel Adamek
Research Advisor
Jerome Baudry
Subject(s)
Inflammation, T cells--Receptors, Computational biology
Abstract
Computational tools are useful in the interpretation and analysis of experimental data. In the world of structural biophysics, computational tools go a bit further: they can simulate atomic motions and molecular interactions based on experimentally-determined biomolecule structures, therein describing natural phenomena, and inspiring the formulation of new hypotheses. In this work, computational structural biology tools are used to answer questions about molecules of inflammatory importance. Quantum chemistry computational tools are used to determine the electronic structure of sesamin, a component of many diets which may be a modulator of an enzyme involved in the metabolism of inflammation mediators. Virtual docking of small molecules is conducted on the SARS-CoV-2 polymerase to determine potential lead molecules’ interactions in the catalytic site. Select compounds are identified as promising inhibitors and are suggested for wet lab study in anti-viral assays. Finally, molecular modeling and dynamics simulations are performed on T cell receptors whose sequences are specific to individuals with PTSD. Structural differences in the receptors after long timescale dynamics simulations suggest a reason to investigate whether a functional discrepancy may exist as an immune marker of PTSD.
Recommended Citation
Jackson, Sara W., "The structural basis of inflammation : computational characterization of molecular mechanisms" (2024). Dissertations. 412.
https://louis.uah.edu/uah-dissertations/412