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

  • Geng Dong
  • Ulf RydeEmail author
Original Paper


The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14–51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.


[NiFe] hydrogenase Protonation Reaction mechanism QM/MM Big-QM calculations 



This investigation has been supported by grants from the Swedish research council (project 2014-5540), the China Scholarship Council, and COST through Action CM1305 (ECOSTBio). The computations were performed on computer resources provided by the Swedish National Infrastructure for Computing (SNIC) at Lunarc at Lund University.

Supplementary material

775_2016_1348_MOESM1_ESM.pdf (118 kb)
Supplementary material 1 (PDF 117 kb)


  1. 1.
    Turner JA (1999) Science 285:687–689CrossRefPubMedGoogle Scholar
  2. 2.
    Bockris JOM (2013) Int J Hydrogen Energy 38:2579–2588CrossRefGoogle Scholar
  3. 3.
    Matsumoto T, Kim K, Nakai H, Hibino T, Ogo S (2013) Chem Cat Chem 5:1368–1373Google Scholar
  4. 4.
    Yang JY, Bullock M, DuBois MR, DuBois DL (2011) MRS Bull 36:39–47CrossRefGoogle Scholar
  5. 5.
    Penner SS (2006) Energy 31:33–43CrossRefGoogle Scholar
  6. 6.
    Cammack R, Frey M, Robson R (2001) Hydrogen as a fuel: learning from nature. Taylor Francis, BeijingCrossRefGoogle Scholar
  7. 7.
    Lubitz W, Ogata H, Ruediger O, Reijerse E (2014) Chem Rev 114:4081–4148CrossRefPubMedGoogle Scholar
  8. 8.
    Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y (2007) Chem Rev 107:4273–4303CrossRefPubMedGoogle Scholar
  9. 9.
    Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T (1999) Structure 7:549–556CrossRefPubMedGoogle Scholar
  10. 10.
    De Lacey AL, Fernandez VM, Rousset M, Cammack R (2007) Chem Rev 107:4304–4330CrossRefPubMedGoogle Scholar
  11. 11.
    Lubitz W, Reijerse E, van Gastel M (2007) Chem Rev 107:4331–4365CrossRefPubMedGoogle Scholar
  12. 12.
    Vincent KA, Parkin A, Armstrong FA (2007) Chem Rev 107:4366–4413CrossRefPubMedGoogle Scholar
  13. 13.
    Tard C, Pickett CJ (2009) Chem Rev 109:2245–2274CrossRefPubMedGoogle Scholar
  14. 14.
    Bakhmutov VI (2005) Eur J Inorg Chem 2005:245-255CrossRefGoogle Scholar
  15. 15.
    Fan H-J, Hall MB (2001) J Biol Inorg Chem 6:467–473CrossRefPubMedGoogle Scholar
  16. 16.
    Bruschi M, Zampella G, Fantucci P, De Gioia L (2005) Coord Chem Rev 249:1620–1640CrossRefGoogle Scholar
  17. 17.
    Siegbahn PEM, Tye JW, Hall MB (2007) Chem Rev 107:4414–4435CrossRefPubMedGoogle Scholar
  18. 18.
    Kampa M, Lubitz W, van Gastel M, Neese F (2012) J Biol Inorg Chem 17:1269–1281CrossRefPubMedGoogle Scholar
  19. 19.
    Kraemer T, Kamp M, Lubitz W, van Gastel M, Neese F (2013) Chem Bio Chem 14:1898–1905CrossRefGoogle Scholar
  20. 20.
    Bruschi M, Tiberti M, Guerra A, De Gioia L (2014) J Am Chem Soc 136:1803–1814CrossRefPubMedGoogle Scholar
  21. 21.
    Pandelia M-E, Ogata H, Lubitz W (2010) Chem Phys Chem 11:1127–1140PubMedGoogle Scholar
  22. 22.
    Fichtner C, van Gastel M, Lubitz W (2003) Phys Chem Chem Phys 5:5507–5513CrossRefGoogle Scholar
  23. 23.
    Medina M, Hatchikian EC, Cammack R (1996) Biochim Biophys Acta 1275:227–236CrossRefGoogle Scholar
  24. 24.
    Whitehead JP, Gurbiel RJ, Bagyinka C, Hoffman BM, Maroney MJ (1993) J Am Chem Soc 115:5629–5635CrossRefGoogle Scholar
  25. 25.
    van der Zwaan JW, Albracht SPJ, Fontijn RD, Slater EC (1985) FEBS Lett 179:271–277CrossRefPubMedGoogle Scholar
  26. 26.
    Hidalgo R, Ash PA, Healy AJ, Vincent KA (2015) Angewandte Chemie Int Ed 54:7110–7113CrossRefGoogle Scholar
  27. 27.
    Murphy BJ, Hidalgo R, Roessler MM, Evans RM, Ash PA, Myers WK, Vincent KA, Armstrong FA (2015) J Am Chem Soc 137:8484–8489CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Pavlov M, Siegbahn PEM, Blomberg MRA, Crabtree RH (1998) J Am Chem Soc 120:548–555CrossRefGoogle Scholar
  29. 29.
    Nilsson Lill SO, Siegbahn PEM (2009) Biochemistry 48:1056–1066CrossRefGoogle Scholar
  30. 30.
    Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC (1995) Nature 373:580–587CrossRefPubMedGoogle Scholar
  31. 31.
    Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA (2001) J Biol Inorg Chem 6:63–81CrossRefPubMedGoogle Scholar
  32. 32.
    Volbeda A, Fontecilla-Camps JC (2005) Coord Chem Rev 249:1609–1619CrossRefGoogle Scholar
  33. 33.
    Galvan IF, Volbeda A, Fontecilla-Camps JC, Field MJ (2008) Proteins 73:95–203Google Scholar
  34. 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 6:7890CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Pardo A, De Lacey AL, Fernandez VM, Fan HJ, Fan YB, Hall MB (2006) J Biol Inorg Chem 11:286–306CrossRefPubMedGoogle Scholar
  36. 36.
    Wu H, Hall MB (2008) CR Chim 11:790–804CrossRefGoogle Scholar
  37. 37.
    Amara P, Volbeda A, Fontecilla-Camps JC, Field MJ (1999) J Am Chem Soc 121:4468–4477CrossRefGoogle Scholar
  38. 38.
    Stein M, Lubitz W (2004) J Inorg Biochem 98:862–877CrossRefPubMedGoogle Scholar
  39. 39.
    Söderhjelm P, Ryde U (2006) J Mol Struc (Theochem) 770:199–219CrossRefGoogle Scholar
  40. 40.
    Ryde U, Nilsson K (2003) J Mol Struc (Theochem) 632:259–275CrossRefGoogle Scholar
  41. 41.
    Ryde U, Nilsson K (2003) J Am Chem Soc 125:14232–14233CrossRefPubMedGoogle Scholar
  42. 42.
    Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539–1546CrossRefPubMedGoogle Scholar
  43. 43.
    Rod TH, Ryde U (2005) J Chem Theory Comput 1:1240–1251CrossRefPubMedGoogle Scholar
  44. 44.
    Rod TH, Ryde U (2005) Phys Rev Lett 94:138302CrossRefPubMedGoogle Scholar
  45. 45.
    Hu L, Eliasson J, Heimdal J, Ryde U (2009) J Phys Chem A 113:11793–11800CrossRefPubMedGoogle Scholar
  46. 46.
    Hu L, Söderhjelm P, Ryde U (2011) J Chem Theory Comput 7:761–777CrossRefPubMedGoogle Scholar
  47. 47.
    Hu L, Söderhjelm P, Ryde U (2013) J Chem Theory Comput 9:640–649CrossRefPubMedGoogle Scholar
  48. 48.
    Sumner S, Söderhjelm P, Ryde U (2013) J Chem Theory Comput 9:4205–4214CrossRefPubMedGoogle Scholar
  49. 49.
    Kaukonen M, Söderhjelm P, Heimdal J, Ryde U (2008) J Phys Chem B 112:12537–12548CrossRefPubMedGoogle Scholar
  50. 50.
    Kaukonen M, Söderhjelm P, Heimdal J, Ryde U (2008) J Chem Theory Comput 4:985–1001CrossRefPubMedGoogle Scholar
  51. 51.
    Delcey MG, Pierloot K, Phung QM, Vancoillie S, Lindh R, Ryde U (2014) Phys Chem Chem Phys 16:7927–7938CrossRefPubMedGoogle Scholar
  52. 52.
    Ogata H, Nishikawa K, Lubitz W (2015) Nature 520:571–574CrossRefPubMedGoogle Scholar
  53. 53.
    Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) J Chem Theory Comput 7:525–537CrossRefPubMedGoogle Scholar
  54. 54.
    Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) Nucl Acids Res 33:W368–W371CrossRefPubMedPubMedCentralGoogle Scholar
  55. 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 FranciscoGoogle Scholar
  56. 56.
    TURBOMOLE V65 2013, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007. Available from
  57. 57.
    Tao J, Perdew JP, Staroverov VN, Scuseria GE (2003) Phys Rev Lett 91:146401CrossRefPubMedGoogle Scholar
  58. 58.
    Becke AD (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  59. 59.
    Becke AD (1988) Phys Rev A 38:3098–3100CrossRefGoogle Scholar
  60. 60.
    Lee CT, Yang WT, Parr RG (1988) Phys Rev B 37:785–789CrossRefGoogle Scholar
  61. 61.
    Schäfer A, Horn H, Ahlrichs R (1992) J Chem Phys 97:2571–2577CrossRefGoogle Scholar
  62. 62.
    Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297–3305CrossRefPubMedGoogle Scholar
  63. 63.
    Rappoport D, Furche F (2010) J Chem Phys 133:134105CrossRefPubMedGoogle Scholar
  64. 64.
    Eichkorn K, Treutler O, Öhm H, Häser M, Ahlrichs R (1995) Chem Phys Lett 240:283–290CrossRefGoogle Scholar
  65. 65.
    Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119–124CrossRefGoogle Scholar
  66. 66.
    Ryde U (1996) J Comput-Aided Mol Des 10:153–164CrossRefPubMedGoogle Scholar
  67. 67.
    Ryde U, Olsson MHM (2001) Int J Quantum Chem 81:335–347CrossRefGoogle Scholar
  68. 68.
    Reuter N, Dejaegere A, Maigret B, Karplus M (2000) J Phys Chem A 104:1720–1735CrossRefGoogle Scholar
  69. 69.
    Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K (1996) J Phys Chem 100:19357–19363CrossRefGoogle Scholar
  70. 70.
  71. 71.
    Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) J Chem Theory Comput 11:3696–3713CrossRefPubMedGoogle Scholar
  72. 72.
    Grimme S, Ehrlich S, Goerigk L (2011) J Comput Chem 32:1456–1465CrossRefPubMedGoogle Scholar
  73. 73.
    Luzhkov V, Warshel A (1992) J Comput Chem 13:199–213CrossRefGoogle Scholar
  74. 74.
    Heimdal J, Kaukonen M, Srnec M, Rulisek L, Ryde U (2011) Chem Phys Chem 12:3337–3347PubMedGoogle Scholar
  75. 75.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935CrossRefGoogle Scholar
  76. 76.
    Kampa M, Pandelia M-E, Lubitz W, van Gastel M, Neese F (2013) J Am Chem Soc 135:3915–3925CrossRefPubMedGoogle Scholar
  77. 77.
    Jayapal P, Sundararajan M, Hillier IH, Burton NA (2008) Phys Chem Chem Phys 10:4249–4257CrossRefPubMedGoogle Scholar

Copyright information

© SBIC 2016

Authors and Affiliations

  1. 1.Department of Theoretical ChemistryLund UniversityLundSweden

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