1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
f
Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
Rent:
Rent this article for
Access full text Article
/content/aip/journal/jcp/137/14/10.1063/1.4757021
1.
1. A. R. Portis and M. A. J. Parry, Photosynth. Res. 94(1), 121143 (2007).
http://dx.doi.org/10.1007/s11120-007-9225-6
2.
2. W. W. Cleland, T. J. Andrews, S. Gutteridge, F. C. Hartman, and G. H. Lorimer, Chem. Rev. 98(2), 549 (1998).
http://dx.doi.org/10.1021/cr970010r
3.
3. M. A. J. Parry, P. J. Andralojc, R. A. C. Mitchell, P. J. Madgwick, and A. J. Keys, J. Exp. Bot. 54(386), 13211333 (2003).
http://dx.doi.org/10.1093/jxb/erg141
4.
4. R. J. Spreitzer and M. E. Salvucci, Annu. Rev. Plant Biol. 53, 449475 (2002).
http://dx.doi.org/10.1146/annurev.arplant.53.100301.135233
5.
5. R. F. Sage, D. A. Way, and D. S. Kubien, J. Exp. Bot. 59(7), 15811595 (2008).
http://dx.doi.org/10.1093/jxb/ern053
6.
6. J. R. Evans, R. Kaldenhoff, B. Genty, and I. Terashima, J. Exp. Bot. 60(8), 22352248 (2009).
http://dx.doi.org/10.1093/jxb/erp117
7.
7. K. A. Mott and I. E. Woodrow, J. Exp. Bot. 51, 399406 (2000).
http://dx.doi.org/10.1093/jexbot/51.suppl_1.399
8.
8. L. Xu, X. Liu, W. Zhao, and X. Wang, J. Phys. Chem. B 113(41), 1359613603 (2009).
http://dx.doi.org/10.1021/jp902597t
9.
9. F. Leroux, S. Dementin, B. Burlat, L. Cournac, A. Volbeda, S. Champ, L. Martin, B. Guigliarelli, P. Bertrand, and J. Fontecilla-Camps, Proc. Natl. Acad. Sci. U.S.A. 105(32), 11188 (2008).
http://dx.doi.org/10.1073/pnas.0803689105
10.
10. D. Calhoun, J. Vanderkooi, G. Woodrow III, and S. Englander, Biochemistry 22(7), 15261532 (1983).
http://dx.doi.org/10.1021/bi00276a002
11.
11. R. Baron, C. Riley, P. Chenprakhon, K. Thotsaporn, R. T. Winter, A. Alfieri, F. Forneris, W. J. H. Van Berkel, P. Chaiyen, and M. W. Fraaije, Proc. Natl. Acad. Sci. U.S.A. 106(26), 1060310608 (2009).
http://dx.doi.org/10.1073/pnas.0903809106
12.
12. J. Z. Ruscio, D. Kumar, M. Shukla, M. G. Prisant, T. Murali, and A. V. Onufriev, Proc. Natl. Acad. Sci. U.S.A. 105(27), 9204 (2008).
http://dx.doi.org/10.1073/pnas.0710825105
13.
13. J. Cohen, A. Arkhipov, R. Braun, and K. Schulten, Biophys. J. 91(5), 18441857 (2006).
http://dx.doi.org/10.1529/biophysj.106.085746
14.
14. R. Elber and M. Karplus, J. Am. Chem. Soc. 112(25), 91619175 (1990).
http://dx.doi.org/10.1021/ja00181a020
15.
15. A. A. Gusev, S. Arizzi, U. W. Suter, and D. J. Moll, J. Chem. Phys. 99, 2221 (1993).
http://dx.doi.org/10.1063/1.465283
16.
16. J. Cohen and K. Schulten, Biophys. J. 93(10), 35913600 (2007).
http://dx.doi.org/10.1529/biophysj.107.108712
17.
17. M. A. Scorciapino, A. Robertazzi, M. Casu, P. Ruggerone, and M. Ceccarelli, J. Am. Chem. Soc. 131(33), 1182511832 (2009).
http://dx.doi.org/10.1021/ja9028473
18.
18. D. A. Mooney and J. M. D. MacElroy, J. Chem. Phys. 110(22), 1108711093 (1999).
http://dx.doi.org/10.1063/1.479044
19.
19. J. Saam, I. Ivanov, M. Walther, H. G. Holzhütter, and H. Kuhn, Proc. Natl. Acad. Sci. U.S.A. 104(33), 13319 (2007).
http://dx.doi.org/10.1073/pnas.0702401104
20.
20. S. Orlowski and W. Nowak, J. Mol. Model. 13(6), 715723 (2007).
http://dx.doi.org/10.1007/s00894-007-0203-x
21.
21. X. G. Zhu, A. Portis Jr., and S. Long, Plant, Cell Environ. 27(2), 155165 (2004).
http://dx.doi.org/10.1046/j.1365-3040.2004.01142.x
22.
22. R. J. Ellis, Nature (London) 463(7278), 164165 (2010).
http://dx.doi.org/10.1038/463164a
23.
23. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, Eur. J. Biochem. 80(2), 319324 (1977).
http://dx.doi.org/10.1111/j.1432-1033.1977.tb11885.x
24.
24. I. Andersson, J. Mol. Biol. 259(1), 160174 (1996).
http://dx.doi.org/10.1006/jmbi.1996.0310
25.
25. M. A. Marti-Renom, A. C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali, Annu. Rev. Biophys. Biomol. Struct. 29, 291325 (2000).
http://dx.doi.org/10.1146/annurev.biophys.29.1.291
26.
26. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117(19), 51795197 (1995).
http://dx.doi.org/10.1021/ja00124a002
27.
27. J. Gumbart, L. G. Trabuco, E. Schreiner, E. Villa, and K. Schulten, Structure 17, 14531464 (2009).
http://dx.doi.org/10.1016/j.str.2009.09.010
28.
28. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14(1), 3338 (1996).
http://dx.doi.org/10.1016/0263-7855(96)00018-5
29.
29. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, J. Comput. Chem. 26(16), 17811802 (2005).
http://dx.doi.org/10.1002/jcc.20289
30.
30. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79(2), 926 (1983).
http://dx.doi.org/10.1063/1.445869
31.
31. Y. P. Pang, Proteins 45(3), 183189 (2001).
http://dx.doi.org/10.1002/prot.1138
32.
32. J. G. Harris and K. H. Yung, J. Phys. Chem. 99(31), 1202112024 (1995).
http://dx.doi.org/10.1021/j100031a034
33.
33. K. E. Anderson, S. L. Mielke, J. I. Siepmann, and D. G. Truhlar, J. Phys. Chem. A 113(10), 20532059 (2009).
http://dx.doi.org/10.1021/jp808711y
34.
34. C. Nieto-Draghi, T. de Bruin, J. Pérez-Pellitero, J. B. Avalos, and A. D. Mackie, J. Chem. Phys. 126, 064509 (2007).
http://dx.doi.org/10.1063/1.2434960
35.
35. N. Foloppe and A. D. MacKerell Jr., J. Comput. Chem. 21(2), 86104 (2000).
http://dx.doi.org/10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
36.
36. A. D. MacKerell Jr. and N. K. Banavali, J. Comput. Chem. 21(2), 105120 (2000).
http://dx.doi.org/10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
37.
37. O. Allnér, L. Nilsson, and A. Villa, J. Chem. Theory Comput. 8(4), 14931502 (2012).
http://dx.doi.org/10.1021/ct3000734
38.
38. Y. Lu, Y. Mei, J. Z. H. Zhang, and D. Zhang, J. Chem. Phys. 132, 131101 (2010).
http://dx.doi.org/10.1063/1.3360769
39.
39. P. Oelschlaeger, M. Klahn, W. A. Beard, S. H. Wilson, and A. Warshel, J. Mol. Biol. 366(2), 687701 (2007).
http://dx.doi.org/10.1016/j.jmb.2006.10.095
40.
40. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98(12), 1008910092 (1993).
http://dx.doi.org/10.1063/1.464397
41.
41. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
42.
42. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23(3), 327341 (1977).
http://dx.doi.org/10.1016/0021-9991(77)90098-5
43.
43. G. J. Martyna, D. J. Tobias, and M. L. Klein, J. Chem. Phys. 101, 4177 (1994).
http://dx.doi.org/10.1063/1.467468
44.
44. G. S. Grest and K. Kremer, Phys. Rev. A 33(5), 3628 (1986).
http://dx.doi.org/10.1103/PhysRevA.33.3628
45.
45. S. E. Feller, Y. Zhang, R. W. Pastor, and B. R. Brooks, J. Chem. Phys. 103, 4613 (1995).
http://dx.doi.org/10.1063/1.470648
46.
46. X. Zhang and T. C. Bruice, Biochemistry 46(51), 1483814844 (2007).
http://dx.doi.org/10.1021/bi7014579
47.
47. W. A. King, J. E. Gready, and T. J. Andrews, Biochemistry 37(44), 1541415422 (1998).
http://dx.doi.org/10.1021/bi981598e
48.
48. O. Tapia, J. Andres, and V. S. Safont, J. Mol. Struct.: THEOCHEM. 342, 131140 (1995).
http://dx.doi.org/10.1016/0166-1280(95)90101-9
49.
49. M. Oliva, V. S. Safont, J. Andres, and O. Tapia, Chem. Phys. Lett. 340(5–6), 391399 (2001).
http://dx.doi.org/10.1016/S0009-2614(01)00242-1
50.
50. M. Oliva, V. S. Safont, J. Andres, and O. Tapia, J. Phys. Chem. A 103(30), 60096016 (1999).
http://dx.doi.org/10.1021/jp9907342
51.
51. M. Oliva, V. S. Safont, J. Andres, and O. Tapia, J. Phys. Chem. A 103(43), 87258732 (1999).
http://dx.doi.org/10.1021/jp992052k
52.
52. B. Kannappan and J. E. Gready, J. Am. Chem. Soc. 130(45), 1506315080 (2008).
http://dx.doi.org/10.1021/ja803464a
53.
53. A. D. Becke, J. Chem. Phys. 98(7), 56485652 (1993).
http://dx.doi.org/10.1063/1.464913
54.
54. C. T. Lee, W. T. Yang, and R. G. Parr, J. Mol. Struct.: THEOCHEM 40, 305313 (1988).
http://dx.doi.org/10.1016/0166-1280(88)80397-X
55.
55. C. T. Lee, W. T. Yang, and R. G. Parr, Phys. Rev. B 37(2), 785789 (1988).
http://dx.doi.org/10.1103/PhysRevB.37.785
56.
56. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 09, Revision A.1, Gaussian Inc., Wallingford, CT, 2009.
57.
57.NBO Version 3.1, E. D. Glendening, A. E. Reed, J. E. Carpenter, and F. Weinhold.
58.
58. S. Dapprich and G. Frenking, J. Phys. Chem. 99(23), 93529362 (1995).
http://dx.doi.org/10.1021/j100023a009
59.
59. G. Frenking and N. Frohlich, Chem. Rev. 100(2), 717774 (2000).
http://dx.doi.org/10.1021/cr980401l
60.
60. K. Kitaura and K. Morokuma, Int. J. Quantum Chem. 10(2), 325340 (1976).
http://dx.doi.org/10.1002/qua.560100211
61.
61. T. Ziegler and A. Rauk, Theor. Chim. Acta 46(1), 110 (1977).
http://dx.doi.org/10.1007/BF02401406
62.
62. S. I. Gorelsky, AOMix, version 6.5, program for molecular orbital analysis, University of Ottawa, 2011, see http://www.sg-chem.net/.
63.
63. S. Gorelsky, J. Organomet. Chem. 635, 187196 (2001).
http://dx.doi.org/10.1016/S0022-328X(01)01079-8
64.
64. P. L. Cummins and J. E. Gready, J. Comput. Chem. 19(8), 977988 (1998).
http://dx.doi.org/10.1002/(SICI)1096-987X(199806)19:8<977::AID-JCC15>3.0.CO;2-4
65.
65. S. B. Ku and G. E. Edwards, Plant Physiol. 59(5), 986 (1977).
http://dx.doi.org/10.1104/pp.59.5.986
66.
66. R. K. Monson, M. A. Stidham, G. J. Williams III, G. E. Edwards, and E. G. Uribe, Plant Physiol. 69(4), 921 (1982).
http://dx.doi.org/10.1104/pp.69.4.921
67.
67. M. W. Denny, Air and Water: The Biology and Physics of Life's Media (Princeton University Press, 1993).
68.
68. O. Tapia, M. Oliva, V. S. Safont, and J. Andrés, Chem. Phys. Lett. 323(1), 2934 (2000).
http://dx.doi.org/10.1016/S0009-2614(00)00500-5
69.
69. O. Tapia, H. Fidder, V. S. Safont, M. Oliva, and J. Andrés, Int. J. Quantum Chem. 88(1), 154166 (2002).
http://dx.doi.org/10.1002/qua.10116
70.
journal-id:
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/14/10.1063/1.4757021
Loading
/content/aip/journal/jcp/137/14/10.1063/1.4757021
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/jcp/137/14/10.1063/1.4757021
2012-10-09
2014-07-13

Abstract

Molecular dynamics (MD) at the molecular mechanical level and geometry optimisation at the quantum mechanical level have been performed to investigate the transport and fixation of oxygen and carbon dioxide in the cavity of ribulose-1,5-bisphosphate carboxylase/oxygenase, or Rubisco. Multiple MD simulations have been carried out to study the diffusive behaviour of O and CO molecules from the Mg 2+ cation in Rubisco at 298 K and 1 bar, being one step in the overall process of carboxylation/oxygenation in Rubisco. In addition to this work, in order to gain additional perspective on the role of chemical reaction rates and thermodynamics, oxygen, and carbon dioxide uptake mechanisms have also been investigated by the aid of quantum chemical calculations. The results indicate that the activation barrier for carboxylation is slightly lower than that of oxygenation. This agrees qualitatively with experimental findings, and rationalises the observed competition between both catalytic processes in nature. Finally, the longer-lived persistence of CO in the vicinity of the active centre (i.e., slower self-diffusion) may serve to explain, in part, why carboxylation is the more kinetically favoured on an overall basis compared to oxygenation.

Loading

Full text loading...

/deliver/fulltext/aip/journal/jcp/137/14/1.4757021.html;jsessionid=1sk3vksqyx9s9.x-aip-live-03?itemId=/content/aip/journal/jcp/137/14/10.1063/1.4757021&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/jcp
true
true
This is a required field
Please enter a valid email address
This feature is disabled while Scitation upgrades its access control system.
This feature is disabled while Scitation upgrades its access control system.
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/14/10.1063/1.4757021
10.1063/1.4757021
SEARCH_EXPAND_ITEM