Optimal design of a molecular recognizer: Molecular recognition as a Bayesian signal detection problem

IEEE Journal on Selected Topics in Signal Processing

Volumn 2, Issue 3, 2008, Pages 390-399

  Savir, Yonatan ^a   Tlusty, Tsvi ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Bayesian detection; Conformational changes; Molecular recognition; Specificity

Indexed keywords

COMPETITION; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; MOLECULES; NUCLEIC ACIDS; OPTIMAL SYSTEMS; ORGANIC ACIDS; SIGNAL DETECTION; SIGNAL PROCESSING;

BAYESIAN; BIOLOGICAL FUNCTIONS; CONFORMATIONAL CHANGES; ENZYMATIC CATALYSIS; IMMUNE RESPONSES; INTERACTION ENERGIES; OPTIMAL DESIGNS; OPTIMAL PROPERTIES; OVERALL PERFORMANCE; RECOGNITION PROCESS; REGULATORY NETWORKS; SIGNAL DETECTION THEORY; SIGNAL PROCESSING DEVICES; TARGET MOLECULES; TRANSITION (JEL CLASSIFICATIONS:E52 ,E41 ,E31);

CONFORMATIONS;

EID: 47049095258     PISSN: 19324553     EISSN: None     Source Type: Journal    
DOI: 10.1109/JSTSP.2008.923859     Document Type: Article

References (26)

1. L. Pauling, Science, vol. 92, pp. 77-79, 1940.
2. W. Kauzmann, "Some factors in the interpretation of protein denaturation," Adv. Protein Chem., vol. 14, pp. 1-63, 1959.
3. C. Tanford, "Interfacial free energy and the hydrophobic effect," Proc. Nat. Acad. Sci. USA, vol. 76, pp. 4175-4176, 1979.
4. T. Tlusty, "A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost," Phys. Biol., vol. 5, p. 016001, 2008.
5. T. Tlusty, "Rate-distortion scenario for the emergence and evolution of noisy molecular codes," Phys. Rev. Lett., vol. 100, pp. 048101-048104, 2008.
6. G. G. Hammes, "Multiple conformational changes in enzyme catalysis," Biochemistry, vol. 41, pp. 8221-8228, 2002.
7. R. Jimenez, G. Salazar, K. K. Baldridge, and F. E. Romesberg, "Flexibility and molecular recognition in the immune system," Proc. Nat. Acad. USA, vol. 100, pp. 92-97, 2003.
8. L. C. James and D. S. Tawfik, "Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition," Proc. Nat. Acad. USA, vol. 102, pp. 12730-12735, 2005.
9. S. Jones and J. M. Thornton, "Principles of protein-protein interactions," Proc. Nat. Acad. USA, vol. 93, pp. 13-20, 1996.
10. C. S. Goh, D. Milburn, and M. Gerstein, "Conformational changes associated with protein-protein interactions," Curr. Opin. Struct. Biol., vol. 14, pp. 104-109, 2004.
11. C. O. Pabo and R. T. Sauer, "Protein-DNA recognition," Annu. Rev. Biochem., vol. 53, pp. 293-321, 1984.
12. K. A. Johnson, "Conformational coupling in DNA polymerase fidelity," Annu. Rev. Biochem., vol. 62, pp. 685-713, 1993, [15].
13. J. R. Williamson, "Induced fit in RNA-protein recognition," Nat. Struct. Biol., vol. 7, pp. 834-837, 2000.
14. A. R. Fersht, "Catalysis, binding and enzyme-substrate complementarity," Proc. Roy. Soc. Lond. B, Biol. Sci., vol. 187, pp. 397-407, 1974.
15. A. R. Fersht, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: Freeman, 1998.
16. C. B. Post and W. J. Ray, Jr., "Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions," Biochemistry, vol. 34, pp. 15881-15885, 1995.
17. Y. Savir and T. Tlusty, "Conformational proofreading: The impact of conformational changes on the specificity of molecular recognition," PLoS ONE, vol. 2, p. e468, 2007.
18. D. Herschlag, "The role of induced fit and conformational changes of enzymes in specificity and catalysis," Bioorg. Chem., vol. 16, pp. 62-96, 1988.
19. C. W. Helstrom, Elements of Signal Detection and Estimation. Englewood Cliffs, NJ: Prentice-Hall, 1995.
20. M. M. Tirion, "Large amplitude elastic motions in proteins from a single-parameter, atomic analysis," Phys. Rev. Lett., vol. 77, pp. 1905-1908, 1996.
21. I. Bahar, A. R. Atilgan, and B. Erman, "Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential," Fold Des., vol. 2, pp. 173-181, 1997.
22. F. Tama and Y. H. Sanejouand, "Conformational change of proteins arising from normal mode calculations," Protein Eng., vol. 14, pp. 1-6, 2001.
23. D. Tobi and I. Bahar, "Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state," Proc. Nat. Acad. USA, vol. 102, pp. 18908-18913, 2005.
24. C. Kleanthous, Protein-Protein Recognition. Oxford, U.K.: Oxford Univ. Press, 2000.
25. L. Stryer, Biochemistry, 3rd ed. New York: Freeman, 1988.
26. Y. Savir and T. Tlusty, "DNA extension induced by RecA during homologous recombination as a possible conformational proofreading mechanism," to be published.