Influence of correlations on molecular recognition

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

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
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Abstract / Bemerkung
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.
Erscheinungsjahr
Zeitschriftentitel
Physical Review E
Band
78
Ausgabe
3
Seite(n)
031903
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PUB-ID

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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.

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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

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 1994

AUTHOR UNKNOWN, 2000

AUTHOR UNKNOWN, 2005

AUTHOR UNKNOWN, 1991

AUTHOR UNKNOWN, ber dtsch chem ges b 27(), 1894

AUTHOR UNKNOWN, adv protein chem 61(), 2003

AUTHOR UNKNOWN, acta crystallogr sect d biol crystallogr 63(), 2007

AUTHOR UNKNOWN, 2006
The kinetics of protein-protein recognition.
Janin J., Proteins 28(2), 1997
PMID: 9188733
Disordered heteropolymers: models for biomimetic polymers and polymers with frustrating quenched disorder
Chakraborty, Physics Reports 342(1), 2001
Discussion
AUTHOR UNKNOWN, Chemical Physics Letters 280(1-2), 1997
Pattern recognition by polyelectrolytes
Muthukumar, The Journal of Chemical Physics 103(11), 1995
Principles of protein-protein interactions.
Jones S, Thornton JM., Proc. Natl. Acad. Sci. U.S.A. 93(1), 1996
PMID: 8552589
Simulation of biomimetic recognition between polymers and surfaces.
Golumbfskie AJ, Pande VS, Chakraborty AK., Proc. Natl. Acad. Sci. U.S.A. 96(21), 1999
PMID: 10518514
Nature of Driving Force for Protein Folding: A Result From Analyzing the Statistical Potential
Li, Physical Review Letters 79(4), 1997
Finite-size tests of hyperscaling.
Binder K, Nauenberg M, Privman V V, Young AP., Phys. Rev., B Condens. Matter 31(3), 1985
PMID: 9935926
Test of a statistical model for molecular recognition in biological repertoires.
Rosenwald S, Kafri R, Lancet D., J. Theor. Biol. 216(3), 2002
PMID: 12183121
Polymers and gels as molecular recognition agents.
Peppas NA, Huang Y., Pharm. Res. 19(5), 2002
PMID: 12069158

HULLER, International Journal of Modern Physics C 13(7), 2002
Statistical mechanics of finite three-dimensional Ising models
Binder, Physica 62(4), 1972
Calculation of free energy through successive umbrella sampling.
Virnau P, Muller M., J Chem Phys 120(23), 2004
PMID: 15268122
Morphology of protein-protein interfaces.
Larsen TA, Olson AJ, Goodsell DS., Structure 6(4), 1998
PMID: 9562553
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

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