A schematic model for molecular affinity and binding with Ising variables

TL;DR

This paper introduces a schematic Ising chain model to study molecular affinity and binding, revealing how ligand and receptor rigidity profiles influence affinity and selectivity, with implications for information encoding.

Contribution

It presents a novel Ising chain model for ligand-receptor binding that explores the effects of rigidity and flexibility on affinity and selectivity.

Findings

Affinity depends on ligand and receptor rigidity profiles.

Bond hardening or softening can modulate affinity.

The model connects molecular recognition to spin systems like spin glasses.

Abstract

After discussing the relevance of statistical physics in molecular recognition processes, we present a schematic model for ligand-receptor association based on an Ising chain. We discuss the possible behaviors of the affinity when the stiffness of the ligand increases. We also consider the case of flexible receptors. A variety of interesting behaviors is obtained, including some affinity modulation upon bond hardening of softening. The affinity of a ligand for its receptor is shown to depend on the details of their rigidity profile, and we question the possibility of encoding information in the rigidities as well as in the shape. An exhaustive study of the selectivity of patterns with length $n<8$ is carried on. Connection with other spin models, in particular spin glasses is mentioned in conclusion.