Degree Type

Thesis

Date of Award

2012

Degree Name

Master of Science

Department

Biochemistry, Biophysics and Molecular Biology

Major

Bioinformatics and Computational Biology

First Advisor

Robert L. Jernigan

Abstract

Immunoglobulin motions are evaluated using Normal Mode Analysis with Elastic Network Models. By employing this approach, we learn about the important motions of the protein, for the domain motions and other internal motions, and see strong evidence of the dominance of the low frequency normal modes. We particularly investigate the CDR motions. The CDR loops tend to move with their attached domains. By finding internal distance changes, we determine which parts of the structure undergo more rigid body like motions and which parts encounter larger internal distance changes. It turns out that Fab undergoes a large extent of changes in its internal distances and the Fc part moves more rigidly. We also investigate the effects of sugar and antigen binding on the IgG structures. The antigen binding effect is highly significant in the CDR regions, since antigen binding seems to enhance the motions in this region, while the sugar effects are more localized to the Fc region. By performing Principal Component Analysis on the numerous available Fab structures, we gather information about motions apparent in this ensemble of conformations, the correspondence of Principal Components to the Normal Modes of the Elastic Network Models, the residue fluctuations in the first few Principal Components and other important information about Immunoglobulin Dynamics.

DOI

https://doi.org/10.31274/etd-180810-2846

Copyright Owner

Debkanta Chakraborty

Language

en

File Format

application/pdf

File Size

91 pages

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