A model study of sequential enzyme reactions and electrostatic channeling

Journal of Chemical Physics

Volumn 140, Issue 10, 2014, Pages

  Eun, Changsun ^a   Kekenes Huskey, Peter M ^b   Metzger, Vincent T ^a   McCammon, J Andrew ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; CATALYSIS; ELECTROSTATICS; REACTION KINETICS; SUBSTRATES;

BIOCHEMICAL NETWORK; DIRECTIONAL PROPERTIES; ELECTROSTATIC POTENTIALS; ENZYME-CATALYZED REACTIONS; INTERMEDIATE SUBSTRATES; LONG RANGE INTERACTIONS; PRODUCT GENERATION; SEQUENTIAL REACTION;

ENZYMES;

ENZYME;

CHEMICAL STRUCTURE; CHEMISTRY; KINETICS; STATIC ELECTRICITY;

ENZYMES; KINETICS; MODELS, MOLECULAR; STATIC ELECTRICITY;

EID: 84896342239     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4867286     Document Type: Article

References (36)

1. A. P. Somlyo and A. V. Somlyo, Nature 372, 231 (1994). 10.1038/372231a0
2. S. S. Shen-Orr, R. Milo, S. Mangan, and U. Alon, Nat. Gen. 31, 64 (2002). 10.1038/ng881
3. E. H. Davidson, J. P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.-H. Yuh, T. Minokawa, G. Amore, V. Hinman, and C. Arenas-Mena, Science 295, 1669 (2002). 10.1126/science.1069883
4. P. A. Srere, Annu. Rev. Biochem. 56, 89 (1987). 10.1146/annurev.bi.56. 070187.000513
5. A. Arkin and J. Ross, Biophys. J. 67, 560 (1994). 10.1016/S0006-3495(94) 80516-8
6. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási, Nature (London) 407, 651 (2000). 10.1038/35036627
7. J. A. Papin, J. L. Reed, and B. O. Palsson, Trends Biochem. Sci. 29, 641 (2004). 10.1016/j.tibs.2004.10.001
8. G. Shinar and M. Feinberg, Science 327, 1389 (2010). 10.1126/science. 1183372
9. W. W. Chen, M. Niepel, and P. K. Sorger, Genes Dev. 24, 1861 (2010). 10.1101/gad.1945410
10. J. J. Tyson and B. Novák, Annu. Rev. Phys. Chem. 61, 219 (2010). 10.1146/annurev.physchem.012809.103457
11. H.-X. Zhou, Q. Rev. Biophys. 43, 219 (2010). 10.1017/S0033583510000120
12. C. Eun, P. M. Kekenes-Huskey, and J. A. McCammon, J. Chem. Phys. 139, 044117 (2013). 10.1063/1.4816522
13. E. W. Miles, S. Rhee, and D. R. Davies, J. Biol. Chem. 274, 12193 (1999). 10.1074/jbc.274.18.12193
14. X. Huang, H. M. Holden, and F. M. Raushel, Annu. Rev. Biochem. 70, 149 (2001). 10.1146/annurev.biochem.70.1.149
15. Y.-H. P. Zhang, Biotechnol. Adv. 29, 715 (2011). 10.1016/j.biotechadv. 2011.05.020
16. D. R. Knighton, C.-C. Kan, E. Howland, C. A. Janson, Z. Hostomska, K. M. Welsh, and D. A. Matthews, Nat. Struct. Mol. Biol. 1, 186 (1994). 10.1038/nsb0394-186
17. R. M. Stroud, Nat. Struct. Biol. 1, 131 (1994). 10.1038/nsb0394-131
18. A. H. Elcock, M. J. Potter, D. A. Matthews, D. R. Knighton, and J. A. McCammon, J. Mol. Biol. 262, 370 (1996). 10.1006/jmbi.1996.0520
19. T. D. Meek, E. P. Garvey, and D. V. Santi, Biochemistry 24, 678 (1985). 10.1021/bi00324a021
20. P.-H. Liang and K. S. Anderson, Biochemistry 37, 12195 (1998). 10.1021/bi9803168
21. Y. Cheng, C.-E. A. Chang, Z. Yu, Y. Zhang, M. Sun, T. S. Leyh, M. J. Holst, and J. A. McCammon, Biophys. J. 95, 4659 (2008). 10.1529/biophysj.108. 140038
22. M. Trujillo, R. G. Donald, D. S. Roos, P. J. Greene, and D. V. Santi, Biochemistry 35, 6366 (1996). 10.1021/bi952923q
23. A. H. Elcock and J. A. McCammon, Biochemistry 35, 12652 (1996). 10.1021/bi9614747
24. S. A. Rice, Comprehensive Chemical Kinetics. Diffusion-Limited Reactions, Vol. 25 (Elsevier, Amsterdam, 1985).
25. K. M. Hong and J. Noolandi, J. Chem. Phys. 68, 5163 (1978). 10.1063/1.435636
26. K. M. Hong and J. Noolandi, J. Chem. Phys. 68, 5172 (1978). 10.1063/1.435581
27. S. A. Rice, P. R. Butler, M. J. Pilling, and J. K. Baird, J. Chem. Phys. 70, 4001 (1979). 10.1063/1.438020
28. H.-X. Zhou, Phys. Biol. 2, R1-R25 (2005). 10.1088/1478-3975/2/3/R01
29. S. C. Brenner and R. Scott, The Mathematical Theory of Finite Element Methods (Springer Verlag, New York, 2008).
30. J. Hake, A. G. Edwards, Z. Yu, P. M. Kekenes-Huskey, A. P. Michailova, J. A. McCammon, M. J. Holst, M. Hoshijima, and A. D. McCulloch, J. Physiol. 590, 4403 (2012). 10.1113/jphysiol.2012.227926
31. P. M. Kekenes-Huskey, A. Gillette, J. Hake, and J. A. McCammon, Comput. Sci. Discovery 5, 014015 (2012). 10.1088/1749-4699/5/1/014015
32. A. Logg, K.-A. Mardal, and G. Wells, Automated Solution of Differential Equations by the Finite Element Method (Springer, Heidelberg, 2012).
33. N. McDonald and W. Strieder, J. Chem. Phys. 118, 4598 (2003). 10.1063/1.1543937
34. P. Bauler, G. Huber, T. Leyh, and J. A. McCammon, J. Phys. Chem. Lett. 1, 1332 (2010). 10.1021/jz1002007
35. C. C. Hyde, S. A. Ahmed, E. A. Padlan, E. W. Miles, and D. R. Davies, J. Biol. Chem. 263, 17857 (1988).
36. J. B. Thoden, H. M. Holden, G. Wesenberg, F. M. Raushel, and I. Rayment, Biochemistry 36, 6305 (1997). 10.1021/bi970503q