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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
B. Alberts, A. Jonhson, J. Lewis, M. Raff, K. Roberts, P. Walter, Molecular Biology of the Cell (Garland Science, Taylor and Francis, 2002)
D. Koshland, Proc. Natl. Acad. Sci. U.S.A. 44, 98 (1958)
H. Berman et al., Nucleic Acid Res. 28, 235 (2000) http://www.rcsb.org/pdb/home
H. Berman, K. Henrick, H. Nakamura, Nature Struct. Biol. 10, 980 (2003) http://www.wwpdb.org
J.N. Israelachvili, Intermolecular and Surface Forces (Elsevier, 1992)
D. Leckband, J. Israelachvili, Q. Rev. Biophys. 34, 105 (2001)
M.K. Gilson, H.X. Zhou, Annu. Rev. Biophys. Biomol. Struct. 36, 21 (2007)
A. Kosmrlj, A.K. Jha, E.S. Huseby, M. Kardar, A.K. Chakraborty, Proc. Natl. Acad. Sci. U.S.A. 105, 16671 (2008)
M. Lewis, C. R. Biologie 328, 521 (2005)
R.J. Hawkins, T.C.B. McLeish, Phys. Rev. Lett. 93, 098104 (2004)
H. Behringer, A. Degenhard, F. Schmid, Phys. Rev. Lett. 97, 128101 (2006)
H. Behringer, A. Degenhard, F. Schmid, Phys. Rev. E 76, 031914 (2007)
H. Behringer, F. Schmid, Phys. Rev. E 78, 031903 (2008)
M.K. Gilson, J.A. Given, B.L. Bush, J. McCammon, Biophys. J. 72, 1047 (1997)
M. Mihailescu, M.K. Gilson, Biophys. J. 87, 23 (2004)
J. Janin, Proteins: Struct. Funct. Genet. 25, 438 (1996)
S. Edwards, P. Anderson, J. Phys. F: Metal Phys. 5, 965 (1975)
M. Mézard, G. Parisi, M. Virasoro, Spin Glass Theory and Beyond., Vol. 9 (World Scientific, 1987)
R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis (Cambridge University Press, 1998)
J.M. Lehn, Supramolecular Chemistry: Concepts and Perspectives (Wiley-VCH, 1995)
H. Leff, A.F. Rex (Editors), Maxwell’s Demon 2: Entropy, Classical and Quantum Information, Computing (Institute of Physics Publishing, 2003)
G.A. Jones, M.J. Jones, Information and Coding Theory, Springer Undergraduate Mathematics Series (Springer, 2000)
T. Bogner, A. Degenhard, F. Schmid, Phys. Rev. Lett. 93, 268108 (2004)
S. Sacquin-Mora, E. Laforet, R. Lavery, Proteins: Struct. Funct. Bioinform. 67, 350 (2007)
N. Sourlas, Nature 339, 693 (1989)
N. Sourlas, Physica A 302, 14 (2001)
H. Nishimori, Statistical Physics of Spin Glasses and Information Processing. An Introduction, International Series of Monographs in Physics 111 (Clarendon Press Oxford, 2001)
R. Monasson, Phys. Rev. Lett. 75, 2847 (1995)
M. Blatt, S. Wiseman, E. Domany, Phys. Rev. Lett. 76, 3251 (1996)
S. Wiseman, M. Blatt, E. Domany, Phys. Rev. E 57, 3767 (1998)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Thalmann, F. A schematic model for molecular affinity and binding with Ising variables. Eur. Phys. J. E 31, 441–454 (2010). https://doi.org/10.1140/epje/i2010-10600-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1140/epje/i2010-10600-9