The structural basis of inflammation : computational characterization of molecular mechanisms

Author

Sara W. Jackson

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