Influence of correlations on molecular recognition

Behringer H, Schmid F (2008)
Physical Review E 78(3): 031903.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
;
Abstract
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealized coarse-grained lattice models. A general two-stage approach is utilized where an ensemble of probe molecules is designed first and the recognition ability of the probe ensemble is related to the free energy of association with both the target molecule and a different rival molecule in a second step. The influence of correlation effects are investigated using numerical Monte Carlo techniques and mean field methods. Correlations lead to different optimum characteristic lengths of the hydrophobic and polar patches for the mutual design of the two biomolecules on the one hand and their recognition ability in the presence of other molecules on the other hand.
Publishing Year
ISSN
PUB-ID

Cite this

Behringer H, Schmid F. Influence of correlations on molecular recognition. Physical Review E. 2008;78(3):031903.
Behringer, H., & Schmid, F. (2008). Influence of correlations on molecular recognition. Physical Review E, 78(3), 031903. doi:10.1103/PhysRevE.78.031903
Behringer, H., and Schmid, F. (2008). Influence of correlations on molecular recognition. Physical Review E 78, 031903.
Behringer, H., & Schmid, F., 2008. Influence of correlations on molecular recognition. Physical Review E, 78(3), p 031903.
H. Behringer and F. Schmid, “Influence of correlations on molecular recognition”, Physical Review E, vol. 78, 2008, pp. 031903.
Behringer, H., Schmid, F.: Influence of correlations on molecular recognition. Physical Review E. 78, 031903 (2008).
Behringer, Hans, and Schmid, Friederike. “Influence of correlations on molecular recognition”. Physical Review E 78.3 (2008): 031903.
This data publication is cited in the following publications:
This publication cites the following data publications:

2 Citations in Europe PMC

Data provided by Europe PubMed Central.

A schematic model for molecular affinity and binding with Ising variables.
Thalmann F., Eur Phys J E Soft Matter 31(4), 2010
PMID: 20480964
Dry and wet interfaces: influence of solvent particles on molecular recognition.
Taktikos J, Behringer H., Phys Rev E Stat Nonlin Soft Matter Phys 79(4 Pt 1), 2009
PMID: 19518257

42 References

Data provided by Europe PubMed Central.

Polymer adsorption onto random planar surfaces: interplay of polymer and surface correlations.
Polotsky A, Schmid F, Degenhard A., J Chem Phys 121(10), 2004
PMID: 15332921
A new approach to Monte Carlo simulations in statistical physics: Wang-Landau sampling
Landau, American Journal of Physics 72(10), 2004
Quantifying biological specificity: The statistical mechanics of molecular recognition
Janin, Proteins Structure Function and Genetics 25(4), 1996
Molecular recognition in a lattice model: an enumeration study.
Bogner T, Degenhard A, Schmid F., Phys. Rev. Lett. 93(26 Pt 1), 2004
PMID: 15698030
A docking analysis of the statistical physics of protein-protein recognition.
Bernauer J, Poupon A, Aze J, Janin J., Phys Biol 2(2), 2005
PMID: 16204845
Substrate specificity of peptide adsorption: a model study.
Bachmann M, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 73(2 Pt 1), 2006
PMID: 16605320
Application of a Theory of Enzyme Specificity to Protein Synthesis.
Koshland DE., Proc. Natl. Acad. Sci. U.S.A. 44(2), 1958
PMID: 16590179
Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system.
Lancet D, Sadovsky E, Seidemann E., Proc. Natl. Acad. Sci. U.S.A. 90(8), 1993
PMID: 8475121
Coarse-grained lattice model for molecular recognition.
Behringer H, Degenhard A, Schmid F., Phys. Rev. Lett. 97(12), 2006
PMID: 17026000
THE NATURE OF THE INTERMOLECULAR FORCES OPERATIVE IN BIOLOGICAL PROCESSES.
Pauling L, Delbruck M., Science 92(2378), 1940
PMID: 17733330
Statistically enhanced self-attraction of random patterns.
Lukatsky DB, Zeldovich KB, Shakhnovich EI., Phys. Rev. Lett. 97(17), 2006
PMID: 17155509
Developing and analyzing idealized models for molecular recognition.
Behringer H, Bogner T, Polotsky A, Degenhard A, Schmid F., J. Biotechnol. 129(2), 2007
PMID: 17368607
Coarse-grained lattice model for investigating the role of cooperativity in molecular recognition.
Behringer H, Degenhard A, Schmid F., Phys Rev E Stat Nonlin Soft Matter Phys 76(3 Pt 1), 2007
PMID: 17930278
Statistically enhanced promiscuity of structurally correlated patterns.
Lukatsky DB, Shakhnovich EI., Phys Rev E Stat Nonlin Soft Matter Phys 77(2 Pt 1), 2008
PMID: 18351980
Selective Adsorption of Heteropolymer onto Heterogeneous Surfaces: Interplay between Sequences and Surface Patterns
Ziebarth, Macromolecules 41(13), 2008
The statistical-thermodynamic basis for computation of binding affinities: a critical review.
Gilson MK, Given JA, Bush BL, McCammon JA., Biophys. J. 72(3), 1997
PMID: 9138555

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 18851061
PubMed | Europe PMC

Search this title in

Google Scholar