Date of Award
5-12-2024
Degree Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Biomedical and Chemical Engineering
Advisor(s)
Shikha Nangia
Subject Categories
Chemical Engineering | Engineering
Abstract
Molecular dynamics (MD) simulations serve as crucial tools for unraveling the underlying physical principles governing the structure and functionality of biological macromolecules. Experimental techniques provide valuable results, but sometimes it is quite difficult to explain phenomena at atomic and molecular levels. MD simulations investigate physical motion of atoms and molecules over microsecond time scale and compute the equilibrium properties. In this work, I investigated the hydropathy of proteins, lipid-modified proteins, and self-defensive biomaterials with atomistic MD simulations and coarse-grained (CG) MD simulations. The method, Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) scale, is developed to characterize and quantify hydropathies of residues in a protein. It shows that the hydropathy of a residue in a protein is influenced by the number of its topological neighbors and the chemical identities of neighbors, which is important to understand protein surface and protein-protein interaction. Lipid-modified elastin-like polypeptides (ELPs) can integrate the functional capabilities into precisely engineered nano-biomaterials. Studying their thermoresponsive character enable the rational design of the biomaterials and therapeutics. Self-defensive antimicrobial surfaces are of interest because they can inhibit bacterial colonization while minimizing unnecessary antimicrobial release in the absence of a bacterial challenge. This work shows that the complexation between antibiotics and bacterial membrane is stronger than that between antibiotics and microgels. So, antibiotics get released from microgels to kill bacteria when bacteria make a contact, which proved experimental findings. Therefore, computational modeling and simulations provide valuable theoretical guidance for biomaterial design.
Access
Open Access
Recommended Citation
Ji, Jingjing, "Investigation of Hydropathy of Proteins, Lipid-modified Proteins, and Self-defensive Biomaterials" (2024). Dissertations - ALL. 1955.
https://surface.syr.edu/etd/1955
