Ravi Heugle

September 2013
A Crystallographic and Geometric Approach For The Computational Prediction of Conformational Epitopes
Committee Members: Advisor: Sandor Vajda, BME; Srikanth Gopalan, MSE/ME; Dimitri Kozakov, BME

Abstract: The conformational, antibody, or B-cell epitope(CE) is a spatially grouped cluster of residues belonging to an antigen to which an antibody or B cell binds. Accurate and reliable predictions of CEs are necessary for rational vaccine design and immunodiagnostics.

In this work, a new computational approach, named Crystal Contact Epitope Prediction Algorithm (CCEP), for predicting CEs is provided . The premise for CCEP is twofold: firstly that proteins establish specific crystal contacts to optimize the enthalpic contribution during crystallization and in doing so mark those residues with high binding affinity, and secondly that geometrically protrusive residues are more exposed and are therefore highly visible targets for antibody binding.

In turn we use a two-step approach to predict and rank residue clusters that might constitute a CE. The first step uses crystallographic information to find an antigen’s crystal contacts before calculating the buried surface area, energy of interaction, and number of participating residues for each crystal contact. The second step uses the computational package ElliPro to measure the protrusion index of an antigen’s residues which are summed to find the total protrusion index of each crystal contact. Thereafter, the crystal contacts are ranked based on a combined measure of their energy, size, average buried surface area, and average protrusion index, where the averaged values are calculated based on the number of residues involved in the contact. The residues native to the highest ranked contact are predicted to most likely belong to the conformational epitope. A second extended approach is also presented, for which a local search around each crystal contact is performed for residues to include in the predicted epitope provided they have protrusion indices and buried surface areas that exceed the average protrusion index and average buried surface area of the crystal contact respectively.