Dry and wet interfaces: Influence of solvent particles on molecular recognition

Taktikos J, Behringer H (2009)
PHYSICAL REVIEW E 79(4).

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We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our basic model showing that the selectivity of the recognition process can be enhanced by considering the explicit influence of single solvent particles. When the number of cavities at the interface of a protein-protein complex is fixed as an intrinsic geometric constraint, there typically exists a characteristic fraction that should be filled with water molecules such that the selectivity exhibits a maximum. In addition, the optimum fraction depends on the hydrophobicity of the interface so that one has to distinguish between dry and wet interfaces.
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Taktikos J, Behringer H. Dry and wet interfaces: Influence of solvent particles on molecular recognition. PHYSICAL REVIEW E. 2009;79(4).
Taktikos, J., & Behringer, H. (2009). Dry and wet interfaces: Influence of solvent particles on molecular recognition. PHYSICAL REVIEW E, 79(4).
Taktikos, J., and Behringer, H. (2009). Dry and wet interfaces: Influence of solvent particles on molecular recognition. PHYSICAL REVIEW E 79.
Taktikos, J., & Behringer, H., 2009. Dry and wet interfaces: Influence of solvent particles on molecular recognition. PHYSICAL REVIEW E, 79(4).
J. Taktikos and H. Behringer, “Dry and wet interfaces: Influence of solvent particles on molecular recognition”, PHYSICAL REVIEW E, vol. 79, 2009.
Taktikos, J., Behringer, H.: Dry and wet interfaces: Influence of solvent particles on molecular recognition. PHYSICAL REVIEW E. 79, (2009).
Taktikos, Johannes, and Behringer, Hans. “Dry and wet interfaces: Influence of solvent particles on molecular recognition”. PHYSICAL REVIEW E 79.4 (2009).
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44 References

Data provided by Europe PubMed Central.

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
Miyazawa, Macromolecules 18(3), 1985
A lattice statistical mechanics model of the conformational and sequence spaces of proteins
Lau, Macromolecules 22(10), 1989
Hydration of protein-protein interfaces.
Rodier F, Bahadur RP, Chakrabarti P, Janin J., Proteins 60(1), 2005
PMID: 15856483
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
Water mediation in protein folding and molecular recognition.
Levy Y, Onuchic JN., Annu Rev Biophys Biomol Struct 35(), 2006
PMID: 16689642
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
Water at biomolecular binding interfaces.
Li Z, Lazaridis T., Phys Chem Chem Phys 9(5), 2007
PMID: 17242738
Macromolecular recognition in the Protein Data Bank.
Janin J, Rodier F, Chakrabarti P, Bahadur RP., Acta Crystallogr. D Biol. Crystallogr. 63(Pt 1), 2007
PMID: 17164520
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
Einfluss der Configuration auf die Wirkung der Enzyme
Fischer, Berichte der deutschen chemischen Gesellschaft 27(3), 1894
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
Influence of correlations on molecular recognition.
Behringer H, Schmid F., Phys Rev E Stat Nonlin Soft Matter Phys 78(3 Pt 1), 2008
PMID: 18851061
Cavities and atomic packing in protein structures and interfaces.
Sonavane S, Chakrabarti P., PLoS Comput. Biol. 4(9), 2008
PMID: 19005575
Cavities and packing at protein interfaces.
Hubbard SJ, Argos P., Protein Sci. 3(12), 1994
PMID: 7756979

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