Honors Capstone Project
Date of Submission
Radhakrishna Sureshkumar, Dept. Chair & Professor
Shikha Nangia, Assistant Professor
Biomedical and Chemical Engineering
Engineering and Computer Science
Capstone Prize Winner
Won Capstone Funding
Sciences and Engineering
Chemical Engineering | Other Chemical Engineering
Bacterial biofilms are a major cause of persistent infections and diseases with known antibiotic and host immune defense resistances. The interaction of signaling factors, namely small cytokines, with the biofilm and host cell is considered vital to the survival of bacterial biofilms. In this study, molecular dynamics (MD) simulations are performed using coarse-grained biomolecular systems to provide significant insight into medical therapeutic advancements in treating persistent and chronic infections. Specifically, MD simulations of the interaction between signaling factors tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) with a model biofilm matrix with detailed description were performed. Additional simulations were used to study TNF-α interaction with dextran polymer chains of varying monomer length. In each study, resultant potential of mean force curves were analyzed to quantify the energy associated with translocation of the signaling factors through the extracellular polymeric substances, as well as to highlight the effect of chain degradation on this translocation process. In some instances, polymer intramatrix interactions were studied to better understand the translocation energy findings. The translocation of TNF-α across a lipid bilayer was also performed using MD simulation techniques, and the resultant potential of mean force curve highlights the energy barrier associated with this process. Qualitative and quantitative assessment of membrane damage was also performed.
DeSalvo, Stephen, "Probing Cell Membrane And Biofilm Extracellular Matrix Interactions With Tumor Necrosis Factor-Alpha and Interleukin-6 Through Molecular Dynamics Simulations Using A Detailed Chemical Description" (2014). Syracuse University Honors Program Capstone Projects. 761.
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