Date of Award
Master of Science
Biochemistry, Biophysics and Molecular Biology
Bioinformatics and Computational Biology
Robert L. Jernigan
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.
Chakraborty, Debkanta, "Immunoglobulin motions and antigen binding effects examined by elastic network models" (2012). Graduate Theses and Dissertations. 12923.