Simulation studies of the glycosylation code
Open Access
- Author:
- Ellis, Christopher Ross
- Graduate Program:
- Chemistry
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- June 04, 2014
- Committee Members:
- William George Noid, Dissertation Advisor/Co-Advisor
William George Noid, Committee Chair/Co-Chair
James Bernhard Anderson, Committee Member
Scott A Showalter, Committee Member
Coray M Colina, Special Member - Keywords:
- glycosylation
toluene
ubiquitin - Abstract:
- This thesis reports computational studies that investigate the impact of protein- carbohydrate and protein-protein interactions upon protein structure and folding. The core of this thesis, which is found in Chapters 2 and 3, examines the biophysical consequences of glycosylation. In Chapter 2, replica-exchange molecular dynamics (REMD) simulations investigate the underlying mechanism for an experimentally observed conformational switch that is induced by the glycosylation of a short peptide. In order to distinguish between the effects of specific and nonspecific interactions with the carbohydrate, these simulations considered model peptides that were N-linked to a disaccharide and also to a steric crowder of the same shape. The simulations suggest that nonspecific steric crowding by the N-linked disaccharide did not significantly alter the peptide free energy surface. However, the combination of steric crowding with specific interactions, e.g. hydrogen bonding and aromatic-glycan stacking, dramatically impacts the peptide ensemble and stabilizes the conformational switch. Motivated by these results, Chapter 3 investigates sequence specific effects of N-linked glycosylation by performing a series of REMD simulations for peptides that correspond to point mutations from the sequence considered in Chapter 2. The simulations suggest that sequences with glycine adjacent to the glycosylation site readily form compact beta-turns upon glycosylation, while sequences with alanine in this location appear to be much less influenced by the glycan. Somewhat surprisingly, the simulations suggest that aromatic-glycan interactions are less significant for this conformational switch. In order to corroborate the REMD simulations, we also performed bioinformatic analysis of a dataset of glycoprotein structures. This analysis indicated that the simulations of short glycopeptides are quite predictive of the conformations adopted by glycosylated sequences in the context of full length glycoproteins. Chapters 4 and 5 address considerably different systems. Chapter 4 investigates the molecular interactions governing ubiquitin-ubiquilin binding via structure alignment and a series of conventional MD simulations. These simulations demonstrate that subtle differences between the hydrophobic binding pockets of ubiquitin and the ubiquitin- like domain dramatically alter their conformational ensemble and also their binding