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Influence of model resolution on geometric simulations of antibody aggregation

Published online by Cambridge University Press:  13 May 2016

Kasra Manavi ,
Bruna Jacobson ,
Brittany Hoard  and
Lydia Tapia
Kasra Manavi
Affiliation:
Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails: kazaz@cs.unm.edu, bjacobson@cs.unm.edu, bhoard@cs.unm.edu
Bruna Jacobson
Affiliation:
Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails: kazaz@cs.unm.edu, bjacobson@cs.unm.edu, bhoard@cs.unm.edu
Brittany Hoard
Affiliation:
Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails: kazaz@cs.unm.edu, bjacobson@cs.unm.edu, bhoard@cs.unm.edu
Lydia Tapia*
Affiliation:
Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails: kazaz@cs.unm.edu, bjacobson@cs.unm.edu, bhoard@cs.unm.edu
*
*Corresponding author. E-mail: tapia@cs.unm.edu
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Summary

It is estimated that allergies afflict up to 40% of the world's population. A primary mediator for allergies is the aggregation of antigens and IgE antibodies bound to cell-surface receptors, FcεRI. Antibody/antigen aggregate formation causes stimulation of mast cells and basophils, initiating cellular degranulation and releasing immune mediators which produce an allergic or anaphylactic response. Understanding the shape and structure of these aggregates can provide critical insights into the allergic response. We have previously developed methods to geometrically model, simulate and analyze antibody aggregation inspired by rigid body robotic motion simulations. Our technique handles the large size and number of molecules involved in aggregation, providing an advantage over traditional simulations such as molecular dynamics (MD) and coarse-grained energetic models. In this paper, we study the impact of model resolution on simulations of geometric structures using both our previously developed Monte Carlo simulation and a novel application of rule-based modeling. These methods complement each other, the former providing explicit geometric detail and the latter providing a generic representation where multiple resolutions can be captured. Our exploration is focused on two antigens, a man-made antigen with three binding sites, DF3, and a common shrimp allergen (antigen), Pen a 1. We find that impact of resolution is minimal for DF3, a small globular antigen, but has a larger impact on Pen a 1, a rod-shaped molecule. The volume reduction caused by the loss in resolution allows more binding site accessibility, which can be quantified using a rule-based model with implicit geometric input. Clustering analysis of our simulation shows good correlation when compared with available experimental results. Moreover, collisions in all-atom reconstructions are negligible, at around 0.2% at 90% reduction.

Keywords

Antibody AggregationResolution StudyRule-Based Modeling
Type
Articles
Information
Robotica , Volume 34 , Issue 8 , August 2016 , pp. 1754 - 1776
Copyright
Copyright © Cambridge University Press 2016 

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