The effect of MM polarization on the QM/MM transition state stabilization: Application to chorismate mutase

Molecular Physics

Volumn 106, Issue 12-13, 2008, Pages 1511-1515

  Illingworth, C J R ^a   Parkes, K E ^b   Snell, C R ^b   Marti, S ^c   Moliner, V ^c   Reynolds, C A ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

^b MEDIVIR AB   (Sweden)

^c UNIVERSITAT JAUME I   (Spain)

Author keywords

Chorismate mutase; Induced charge; Polarization; QM MM; Transition state stabilization

Indexed keywords

ENZYMES; FOOD ADDITIVES; MECHANISMS; MOLECULAR MECHANICS; POLARIZATION; RATE CONSTANTS; SPEED; STABILIZATION;

AQUEOUS REACTIONS; CHORISMATE; CHORISMATE MUTASE; CUT-OFF; ENERGY-BARRIER; EXPECTED VALUES; INDUCED CHARGE; INDUCED CHARGES; MOLECULAR LEVELS; QM/MM; RATE ENHANCEMENT; STABILIZATION ENERGIES; TRANSITION STATE STABILIZATION; TRANSITION STRUCTURE; UPPER-END;

METHOD OF MOMENTS;

EID: 52149095458     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268970802077850     Document Type: Article

References (35)

1. L. Pauling, Chem. Eng. News 24, 1375 (1946).
2. L. Gan, M.R. Seyedsayamdost, S. Shuto, et al., Biochemistry 42, 857 (2003).
3. M.J. Costanzo, S.C. Yabut, H.R. Almond Jr., et al., J. Med. Chem 46, 3865 (2003).
4. S.P. Dharmasena, D.S. Wimalasena, and K. Wimalasena, Biochemistry 41, 12414 (2002).
5. G.A. Kicska, P.C. Tyler, G.B. Evans, et al., J. Biol. Chem. 277, 3226 (2002).
6. I. Basu, G. Cordovano, I. Das, et al., J. Biol. Chem. 282, 21477 (2007).
7. R.E. Rigsby, C.L. Rife, K.L. Fillgrove, et al., Biochemistry 43, 13666 (2004).
8. C.J. Illingworth, S.R. Gooding, P.J. Winn, et al., J. Phys. Chem. A 110, 6487 (2006).
9. L. Pauling, Nature 161, 707 (1948).
10. S. Marti, J. Andres, V. Moliner, et al., J. Am. Chem. Soc. 123, 1709 (2001).
11. P.D. Lyne, A.J. Mulholland, and W.G. Richards, J. Amer. Chem. Soc. 117, 11345 (1995).
12. K.E. Ranaghan, L. Ridder, B. Szefczyk, et al., Mol. Phys. 101, 2695 (2003).
13. S. Hur and T.C. Bruice, Proc. Natl. Acad. Sci. USA 100, 12015 (2003).
14. S. Hur and T.C. Bruice, J. Am. Chem. Soc. 125, 10540 (2003).
15. S. Hur and T.C. Bruice, J. Am. Chem. Soc. 125, 5964 (2003).
16. F. Claeyssens, K.E. Ranaghan, F.R. Manby, et al., Chem. Commun. 5068 (2005).
17. K.E. Ranaghan, L. Ridder, B. Szefczyk, et al., Org. Biomol. Chem. 2, 968 (2004).
18. F. Claeyssens, J.N. Harvey, F.R. Manby, et al., Angew. Chem. Int. Edn. 45, 6856 (2006).
19. P. Kast, M. AsifUllah, and D. Hilvert, Tetrahedron Lett. 37, 2691 (1996).
20. M. Barbany, H. Gutierrez-de-Teran, F. Sanz, et al., Chembiochem. 4, 277 (2003).
21. S.R. Gooding, P.J. Winn, R.I. Maurer, et al., J. Comput. Chem. 21, 478 (2000).
22. P.J. Winn, G.G. Ferenczy, and C.A. Reynolds, J. Comput. Chem. 20, 704 (1999).
23. J.H. Wu, P.J. Winn, G.G. Ferenczy, et al., Int. J. Quant. Chem. 73, 229 (1999).
24. S. Marti, J. Andres, V. Moliner, et al., J. Phys. Chem. B 104, 11308 (2000).
25. Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, et al., J. Comput. Chem. 24, 1999 (2003).
26. M.J. Frisch, G.W. Trucks, H.B. Shlegel, et al., Gaussian 03, Revision C.02 (Gaussian, Wallingford CT, 2004).
27. A.D. Becke, J. Chem. Phys. 98, 5648 (1993).
28. W.J. Hehre, R. Ditchfield, and J.A. Pople, J. Chem. Phys. 56, 2257 (1972).
29. A.J. Stone, J. Chem. Theory Comput. 1, 1128 (2005).
30. G.G. Ferenczy, J. Comput. Chem. 12, 913 (1991).
31. G.G. Ferenczy, P.J. Winn, and C.A. Reynolds, J. Phys. Chem. A 101, 5446 (1997).
32. P.J. Winn, G.G. Ferenczy, and C.A. Reynolds, J. Phys. Chem. A 101, 5437 (1997).
33. A.J. Stone, A. Dullweber, O. Engkvist, et al., Orient: A Program for Studying Interactions Between Molecules, Version 4.5 (University of Cambridge, 2005). Enquiries to AJ Stone, ajs1@cam.ac.uk. 2006.
34. K.J. Miller and J.A. Savchik, J. Am. Chem. Soc. 101, 7206 (1979).
35. B. Szefczyk, F. Claeyssens, A.J. Mulholland, et al., Int. J. Quantum Chem. 107, 2274 (2007).