Theoretical Chemistry Accounts

, 131:1286 | Cite as

Enzyme dynamics and catalysis in the mechanism of DNA polymerase

Regular Article

Abstract

This contribution contains the commentaries of the three authors about two papers in this issue of TCA that present alternative views of the role of conformational changes in the specificity of enzyme DNA polymerase β. Concepts such as dynamical effects, the induced fit model or the importance of sampling in modeling of enzymatic reactions are briefly revised within the context of the debate established in the two previous papers.

Keywords

Enzyme dynamics Enzymatic catalysis Dynamical effects DNA polymerase 

References

  1. 1.
    Nashine VC, Hammes-Schiffer S, Benkovic SJ (2010) Curr Op Chem Biol 14:644CrossRefGoogle Scholar
  2. 2.
    Pudney CR, Johannissen LO, Sutcliffe MJ, Hay S, Scrutton NS (2010) J Am Chem Soc 132:11329CrossRefGoogle Scholar
  3. 3.
    Pineda JRET, Antoniou D, Schwartz SD (2010) J Phys Chem B 114:15985CrossRefGoogle Scholar
  4. 4.
    Hay S, Scrutton NS (2012) Nat Chem 4:161CrossRefGoogle Scholar
  5. 5.
    Olsson MHM, Parson WW, Warshel A (2006) Chem Rev 106:1377CrossRefGoogle Scholar
  6. 6.
    Pisliakov AV, Cao J, Kamerlin SCL, Warshel A (2008) Proc Natl Acad Sci USA 106:17359CrossRefGoogle Scholar
  7. 7.
    DeCarlo L, Gowda ASP, Suo Z, Spratt TE (2008) Biochemistry 47:8157CrossRefGoogle Scholar
  8. 8.
    Guengerich FP (2006) Chem Rev 2006(106):420CrossRefGoogle Scholar
  9. 9.
    Mizrahi V, Henrie RN, Marlier JF, Johnson KA, Benkovic SJ (1985) Biochemistry 24:4010CrossRefGoogle Scholar
  10. 10.
    Greaves SJ, Wrede E, Goldberg NT, Zhang J, Miller DJ, Zare RN (2008) Nature 454:88CrossRefGoogle Scholar
  11. 11.
    Garcia-Viloca M, Truhlar DG, Gao J (2003) Biochemistry 42:13558CrossRefGoogle Scholar
  12. 12.
    Roca M, Moliner V, Tuñón I, Hynes JT (2006) J Am Chem Soc 128:6186CrossRefGoogle Scholar
  13. 13.
    Knapp MJ, Rickert K, Klinman JP (2002) J Am Chem Soc 124:3865CrossRefGoogle Scholar
  14. 14.
    Kanaan N, Ferrer S, Martí S, Garcia-Viloca M, Kohen A, Moliner V (2011) J Am Chem Soc 133:6692CrossRefGoogle Scholar
  15. 15.
    Glowacki DR, Harvey JN, Mulholland AJ (2012) Nat Chem 4:169CrossRefGoogle Scholar
  16. 16.
    Vilali J, Kern D (2010) Curr Opin Chem Biol 14:636CrossRefGoogle Scholar
  17. 17.
    Hammes GG, Benkovic SJ, Hammes-Schiffer S (2011) Biochemistry 50:10422CrossRefGoogle Scholar
  18. 18.
    Ruiz-Pernía JJ, Tuñón I, Moliner V, Hynes JT, Roca M (2008) J Am Chem Soc 130:7477CrossRefGoogle Scholar
  19. 19.
    Koshland DE Jr (1958) Proc Natl Acad Sci USA 44:98CrossRefGoogle Scholar
  20. 20.
    Ma BY, Nussinov R (2010) Cur Opin Chem Biol 14:652CrossRefGoogle Scholar
  21. 21.
    Zhou HX (2010) Biophys J 98:L15CrossRefGoogle Scholar
  22. 22.
    Vértessy BG, Orosz F (2011) BioEssays 33:30CrossRefGoogle Scholar
  23. 23.
    Schlick T, Arora K, Beard WA, Wilson SH (2012) Theor Chem Acc 131:1287Google Scholar
  24. 24.
    Prasad BR, Kamerlin SCL, Florian J, Warshel A (2012) Theor Chem Acc 131:1288Google Scholar
  25. 25.
    Wong I, Patel SS, Johnson KA (1991) Biochemistry 30:526CrossRefGoogle Scholar
  26. 26.
    Johnson KA (2008) J Biol Chem 283:26297CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Centre for Computational Chemistry, School of ChemistryUniversity of BristolBristolUK
  2. 2.Department of Chemistry and Quantum Theory ProjectUniversity of FloridaGainesvilleUSA
  3. 3.Departamento de Química FísicaUniversidad de ValenciaBurjasotSpain

Personalised recommendations