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A computational study of the statistical mechanics of antibody-antigen conformations

Patricia Theodosopoulos·Ted Theodosopoulos
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Abstract

We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the identification of shape attractors in the configuration space for the joint antibody / antigen combining site sequence. We parameterize configuration space in terms of Ramachandran angles. The shape attractors allow us to construct a Markov chain whose steady state distribution gives rise to the desired attachment probability. As a result we are able to delineate the enthalpic, entropic and kinetic components of affinity and study their interactions.

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Patricia Theodosopoulos, Ted Theodosopoulos. 2004-06-04. A computational study of the statistical mechanics of antibody-antigen conformations. https://arxiv.org/abs/q-bio/0406012

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