Conformational analysis and molecular dynamics of mannosylated peptides
Date
1996
Authors
Joshi, Anurag
Major Professor
Advisor
Reilly, Peter J.
Committee Member
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Research Projects
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Abstract
The objective of this project was to provide an insight into the conformational behavior of glycosylated peptides. The peptides that have been studied were composed of serine and threonine residues, as they form the majority of the amino acids in the GA linker region.
The molecular dynamics (MD) study carried out on the serine tetramers and the threonine pentamers was of an exploratory nature. Our aim was to study and understand the behavior of mannosylated serine and threonine oligopeptides as they form the majority of the residues (28 out of 43) in the glycosylated linker of A. niger GA. These initial studies were needed to get an idea of the behavior of the mannosylated peptides in water, to get an idea of the relaxation time scales involved for the dihedral angles of interest and also to find out if the initial conformation had an effect on the final structure. We also wanted to study the effect of the presence of the mannosyl residues on the flexibility of the peptide backbone.
The constrained conformational mapping study for regular tetramers and dimers of serine and threonines was aimed at providing an understanding of the conformational space available for these structures. It also attempted to show the effect of increasing peptide length on the conformational space. Regular structures that were identified from this conformational mapping as having low energy were then subjected to MD. This was an attempt to obtain a more realistic picture of the structures in their natural environment and could form the basis for extending this work to the whole linker, using preferred dihedral values as starting points to conduct dynamics.