Immunoglobulin G: Solution Dynamics, Carbohydrate Structure, and Self-association From Atomistic and Coarse-grained Simulations

Open Access
Author:
Fortunato, Michael Edward
Graduate Program:
Materials Science and Engineering
Degree:
Master of Science
Document Type:
Master Thesis
Date of Defense:
October 29, 2014
Committee Members:
  • Coray M Colina, Thesis Advisor
  • Scott A Showalter, Thesis Advisor
  • Ralph H Colby, Thesis Advisor
Keywords:
  • IgG
  • protein
  • simulation
  • molecular
  • dynamics
  • carbohydrate
Abstract:
Immunoglobulin molecules are extremely effective at providing protection from foreign molecules or viruses; however, in certain cases the naturally occurring immune system cannot provide adequate protection. Monoclonal antibodies are designed to fill these gaps by engineering antigen binding regions capable of targeting and eliminating dangerous molecules. The monoclonal antibodies can function when isolated and able to travel through the blood stream. However, immunoglobulin efficiency decreases upon self-association for two reasons. First, the immune system may recognize the associated molecules and eliminate them depending on the size of the aggregates. Second, if the molecules associate in such a way that the antigen binding regions are no longer accessible they will be unable to function. This thesis discusses molecular simulation techniques that can be used to study the structural changes that occur due to intrinsic molecular flexibility in immunoglobulin molecules as well as the structure of small aggregates that form through self-association. One solvated immunoglobulin molecule was studied by explicitly representing every atom however coarse-graining techniques were required in order to study multiple molecules in the same system. The role of terminal galactose residues in the carbohydrate attached to the Fc domain in an atomisitc model of an antibody molecule was studied in this work. Carbohydrate mobility as well as the protein–carbohydrate hydrogen bonding interactions were compared between simulations with and without terminal galactose residues. It was shown that one of the two biantennary terminal galactose residues preferentially interacts with the protein when both were present; however, when both were removed the carbohydrate structure changed such that new protein–carbohydrate interactions formed. This change in solvent accessible protein surfaces will be an important area of study to both increase effector functions and decrease self-association involving the Fc domain. Understanding through which residues immunoglobulin molecules interact will lead to better designed monoclonal antibodies with increased aggregation resistance. To aid in this understanding, a previously developed residue level coarse-grained model was employed using the same model molecule from the previous atomistic studies. The residues most often involved in self-association of the antibody were individually mutated to alanine and the resulting association frequencies were compared to the “native” immunoglobulin results to determine the residues most important in self-association. Because of the asymmetry in the three-dimensional structure of the model immunoglobulin molecule used in this work, differences in aggregation behavior between two domains with identical amino acid sequence indicated that molecular structure can play a significant role in self-association. These simulation techniques were shown to be effective at studying molecular flexibility and protein–carbohydrate interactions with great chemical detail as well as the self-association with resolution at the residue level. The future combination of results from these types of studies will increase the understanding of the solution behavior of immunoglobulin molecules in order to develop more effective monoclonal antibodies.