Date of Award
Doctor of Philosophy (PhD)
Donald T. Haynie
Polypeptides constitute half of the dry mass of the cell, they form the bulk of the extracellular matrix (ECM), and they are a common element of extra- and intracellular signaling pathways. There is increasing interest in the development of computational methods in polypeptide and protein engineering on all length scales. This research concerns the development of computational methods for study of polypeptide interactions related to cell attachment in vivo and in vitro.
Polypeptides are inherently biocompatible, and an astronomical range of unique sequences can be designed and realized in massive quantities by modern methods of synthesis and purification. These macromolecules therefore constitute an intriguing class of polyelectrolyte for biomedically-oriented multilayer film engineering (Haynie et al., 2005), Applications of such films include artificial cells, drug delivery systems, and implant device coatings, cell/tissue scaffolds (ECM mimics). The plasma membrane-associated cytoplasmic protein tensin is involved in cell attachment, cell migration, embryogenesis, and wound healing. The tensin polypeptide comprises several modular domains implicated in signal transduction. It has been shown that the N-terminal region of tensin is a close homolog of a tumor suppressor that is highly mutated in glioblastomas, breast cancer, and other cancers.
There are two related areas of development in this work: Polypeptide multilayer films, a type of ECM mimics, and the molecular physiology of tensin. Two studies have been carried out on polypeptide multilayer films: aggregates of the model polypeptides poly(L-lysine) (PLL) and poly(L-glutamic acid) (PLGA), and interpolyelectrolytes complexes (IPECs) of designed peptides. Molecular models of all known domain of tensin have been developed by homology modeling. The binding properties of the two domain of tensin have been studied.
Molecular dynamics (MD) simulations of PLL/PLGA aggregates suggest that both hydrophobic interactions and electrostatics interactions play a significant role in stabilizing polypeptide multilayer structures. The approach provides a general means to determine how non-covalent interactions contribute to the structure and stability of polypeptide multilayer films. MD simulations of designed polypeptide complexes have been carried out in vacuum and in implicit solvent. The simulation results correlate with experimental data on the same peptides. Energy minimization and MD study of tensin domain-peptide complexes has provided insight on biofunctionality of the tensin molecule and thereby its role in cell adhesion. Such knowledge will be important for determining the molecular basis of cell adhesion in health and disease and engineering treatments of abnormalities involving cell attachment.
Zhao, Wanhua, "" (2006). Dissertation. 540.