Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

Journal of Biological Inorganic Chemistry

Volumn 21, Issue 3, 2016, Pages 383-394

  Dong, Geng ^a   Ryde, Ulf ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Big QM calculations; Protonation; QM MM; Reaction mechanism; NiFe hydrogenase

Indexed keywords

CARBON MONOXIDE; CYANIDE; CYSTEINE; IRON; NICKEL; NICKEL IRON HYDROGENASE; HYDROGENASE; NICKEL-IRON HYDROGENASE; PROTON;

ARTICLE; CHEMICAL REACTION KINETICS; CHEMICAL STRUCTURE; GEOMETRY; HYDROGEN BOND; MATHEMATICAL COMPUTING; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTON TRANSPORT; QUANTUM MECHANICS; SIMULATION; CHEMISTRY; DESULFOVIBRIO VULGARIS; ENZYMOLOGY; METABOLISM; QUANTUM THEORY;

CYSTEINE; DESULFOVIBRIO VULGARIS; HYDROGEN BONDING; HYDROGENASE; PROTONS; QUANTUM THEORY;

EID: 84960115057     PISSN: 09498257     EISSN: 14321327     Source Type: Journal    
DOI: 10.1007/s00775-016-1348-9     Document Type: Article

References (77)

1. Turner JA (1999) Science 285:687–689
2. Bockris JOM (2013) Int J Hydrogen Energy 38:2579–2588
3. Matsumoto T, Kim K, Nakai H, Hibino T, Ogo S (2013) Chem Cat Chem 5:1368–1373
4. Yang JY, Bullock M, DuBois MR, DuBois DL (2011) MRS Bull 36:39–47
5. Penner SS (2006) Energy 31:33–43
6. Cammack R, Frey M, Robson R (2001) Hydrogen as a fuel: learning from nature. Taylor Francis, Beijing
7. Lubitz W, Ogata H, Ruediger O, Reijerse E (2014) Chem Rev 114:4081–4148
8. Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y (2007) Chem Rev 107:4273–4303
9. Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T (1999) Structure 7:549–556
10. De Lacey AL, Fernandez VM, Rousset M, Cammack R (2007) Chem Rev 107:4304–4330
11. Lubitz W, Reijerse E, van Gastel M (2007) Chem Rev 107:4331–4365
12. Vincent KA, Parkin A, Armstrong FA (2007) Chem Rev 107:4366–4413
13. Tard C, Pickett CJ (2009) Chem Rev 109:2245–2274
14. Bakhmutov VI (2005) Eur J Inorg Chem 2005:245-255
15. Fan H-J, Hall MB (2001) J Biol Inorg Chem 6:467–473
16. Bruschi M, Zampella G, Fantucci P, De Gioia L (2005) Coord Chem Rev 249:1620–1640
17. Siegbahn PEM, Tye JW, Hall MB (2007) Chem Rev 107:4414–4435
18. Kampa M, Lubitz W, van Gastel M, Neese F (2012) J Biol Inorg Chem 17:1269–1281
19. Kraemer T, Kamp M, Lubitz W, van Gastel M, Neese F (2013) Chem Bio Chem 14:1898–1905
20. Bruschi M, Tiberti M, Guerra A, De Gioia L (2014) J Am Chem Soc 136:1803–1814
21. Pandelia M-E, Ogata H, Lubitz W (2010) Chem Phys Chem 11:1127–1140
22. Fichtner C, van Gastel M, Lubitz W (2003) Phys Chem Chem Phys 5:5507–5513
23. Medina M, Hatchikian EC, Cammack R (1996) Biochim Biophys Acta 1275:227–236
24. Whitehead JP, Gurbiel RJ, Bagyinka C, Hoffman BM, Maroney MJ (1993) J Am Chem Soc 115:5629–5635
25. van der Zwaan JW, Albracht SPJ, Fontijn RD, Slater EC (1985) FEBS Lett 179:271–277
26. Hidalgo R, Ash PA, Healy AJ, Vincent KA (2015) Angewandte Chemie Int Ed 54:7110–7113
27. Murphy BJ, Hidalgo R, Roessler MM, Evans RM, Ash PA, Myers WK, Vincent KA, Armstrong FA (2015) J Am Chem Soc 137:8484–8489
28. Pavlov M, Siegbahn PEM, Blomberg MRA, Crabtree RH (1998) J Am Chem Soc 120:548–555
29. Nilsson Lill SO, Siegbahn PEM (2009) Biochemistry 48:1056–1066
30. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC (1995) Nature 373:580–587
31. Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA (2001) J Biol Inorg Chem 6:63–81
32. Volbeda A, Fontecilla-Camps JC (2005) Coord Chem Rev 249:1609–1619
33. Galvan IF, Volbeda A, Fontecilla-Camps JC, Field MJ (2008) Proteins 73:95–203
34. Ogata H, Kramer T, Wang H, Schilter D, Pelmenschikov V, van Gastel M, Neese F, Rauchfuss TB, Gee LB, Scott AD, Yoda Y, Tanaka Y, Lubitz W, Cramer SP (2015) Nat Commun 6:7890
35. Pardo A, De Lacey AL, Fernandez VM, Fan HJ, Fan YB, Hall MB (2006) J Biol Inorg Chem 11:286–306
36. Wu H, Hall MB (2008) CR Chim 11:790–804
37. Amara P, Volbeda A, Fontecilla-Camps JC, Field MJ (1999) J Am Chem Soc 121:4468–4477
38. Stein M, Lubitz W (2004) J Inorg Biochem 98:862–877
39. Söderhjelm P, Ryde U (2006) J Mol Struc (Theochem) 770:199–219
40. Ryde U, Nilsson K (2003) J Mol Struc (Theochem) 632:259–275
41. Ryde U, Nilsson K (2003) J Am Chem Soc 125:14232–14233
42. Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539–1546
43. Rod TH, Ryde U (2005) J Chem Theory Comput 1:1240–1251
44. Rod TH, Ryde U (2005) Phys Rev Lett 94:138302
45. Hu L, Eliasson J, Heimdal J, Ryde U (2009) J Phys Chem A 113:11793–11800
46. Hu L, Söderhjelm P, Ryde U (2011) J Chem Theory Comput 7:761–777
47. Hu L, Söderhjelm P, Ryde U (2013) J Chem Theory Comput 9:640–649
48. Sumner S, Söderhjelm P, Ryde U (2013) J Chem Theory Comput 9:4205–4214
49. Kaukonen M, Söderhjelm P, Heimdal J, Ryde U (2008) J Phys Chem B 112:12537–12548
50. Kaukonen M, Söderhjelm P, Heimdal J, Ryde U (2008) J Chem Theory Comput 4:985–1001
51. Delcey MG, Pierloot K, Phung QM, Vancoillie S, Lindh R, Ryde U (2014) Phys Chem Chem Phys 16:7927–7938
52. Ogata H, Nishikawa K, Lubitz W (2015) Nature 520:571–574
53. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) J Chem Theory Comput 7:525–537
54. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) Nucl Acids Res 33:W368–W371
55. Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz KM, Monard G, Needham P, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Salomon-Ferrer R, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, York DM, Kollman PA (2014) AMBER 14. University of California, San Francisco
56. TURBOMOLE V65 2013, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007. Available from http://www.turbomole.com
57. Tao J, Perdew JP, Staroverov VN, Scuseria GE (2003) Phys Rev Lett 91:146401
58. Becke AD (1993) J Chem Phys 98:5648–5652
59. Becke AD (1988) Phys Rev A 38:3098–3100
60. Lee CT, Yang WT, Parr RG (1988) Phys Rev B 37:785–789
61. Schäfer A, Horn H, Ahlrichs R (1992) J Chem Phys 97:2571–2577
62. Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297–3305
63. Rappoport D, Furche F (2010) J Chem Phys 133:134105
64. Eichkorn K, Treutler O, Öhm H, Häser M, Ahlrichs R (1995) Chem Phys Lett 240:283–290
65. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119–124
66. Ryde U (1996) J Comput-Aided Mol Des 10:153–164
67. Ryde U, Olsson MHM (2001) Int J Quantum Chem 81:335–347
68. Reuter N, Dejaegere A, Maigret B, Karplus M (2000) J Phys Chem A 104:1720–1735
69. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K (1996) J Phys Chem 100:19357–19363
70. dftd3 software http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english
71. Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) J Chem Theory Comput 11:3696–3713
72. Grimme S, Ehrlich S, Goerigk L (2011) J Comput Chem 32:1456–1465
73. Luzhkov V, Warshel A (1992) J Comput Chem 13:199–213
74. Heimdal J, Kaukonen M, Srnec M, Rulisek L, Ryde U (2011) Chem Phys Chem 12:3337–3347
75. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935
76. Kampa M, Pandelia M-E, Lubitz W, van Gastel M, Neese F (2013) J Am Chem Soc 135:3915–3925
77. Jayapal P, Sundararajan M, Hillier IH, Burton NA (2008) Phys Chem Chem Phys 10:4249–4257