Eur. Phys. J. E (2010) 31: 441-454
https://doi.org/10.1140/epje/i2010-10600-9

Regular Article

A schematic model for molecular affinity and binding with Ising variables

Institut Charles Sadron, Université de Strasbourg, 23 rue du Loess, F-67034, Strasbourg Cedex, France

^* e-mail: thalmann@ics.u-strasbg.fr

Received: 10 June 2009
Revised: 7 February 2010
Accepted: 24 March 2010
Published online: 27 April 2010

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 or softening. The affinity of a ligand for its receptor is shown to depend on the details of its 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 out. Connection with other spin models, in particular spin glasses is mentioned in the conclusion.