Abstract
Quantum mechanical/molecular mechanical (QM/MM) theoretical calculations were performed for the pentacoordinate Mn(III) and water-bound resting states of the Mn-reconstituted mutant of cytochrome P450cam (Mn-P450cam) in order to obtain insights into their characters, especially, their spin state ordering. The QM/MM study was carried out by use of the B3LYP and BLYP density functional theory (DFT) methods coupled to the CHARMM force field. Although the relative energies of possible spin states for the Mn-P450cam species varied depending on the functional, this dependence was less significant compared with previous calculations on the corresponding intermediates of wild-type P450cam. The results suggested that both Mn-P450cam intermediates have quintet ground states. Additional time-dependent DFT (TDDFT) calculations were carried out for the quintet states of these species using the B3LYP and BP86 functionals with the electrostatic environmental effect included. The TDDFT results enabled us to assign the origins of the peaks observed in optical absorption spectra (Makris et al. in J. Inorg. Biochem. 100:507–518, 2006).
Similar content being viewed by others
References
Ortiz de Montellano PR (2005) Cytochrome P450: structure, mechanism, and biochemistry, 3rd edn. Kluwer Academic/Plenum Publishers, New York
Meunier B, de Visser SP, Shaik S (2004) Chem Rev 104:3947–3980
Shaik S, Kumar D, de Visser SP, Altun A, Thiel W (2005) Chem Rev 105:2279–2328
Groves GT (2006) J Inorg Biochem 100:434–447
Schlichting I, Berendzen J, Chu K, Stock AM, Maves SA, Benson DE, Sweet RM, Ringe D, Petsko GA, Sligar SG (2000) Science 287:1615–1622
Newcomb M, Toy PH (2000) Acc Chem Res 33:449–455
Makris TM, von Koenig K, Schlichting I, Sligar SG (2006) J Inorg Biochem 100:507–518
Gelb MH, Toscano WA Jr, Sligar SG (1982) Proc Natl Acad Sci USA 79:5578–5762
Jaguar 5.5 (2004) Schrödinger Inc., Portland
Becke AD (1992) J Chem Phys 96:2155–2160
Becke AD (1992) J Chem Phys 97:9173–9177
Becke AD (1993) J Chem Phys 98:5648–5652
Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789
Perdew JP (1986) Phys Rev B 33:8822–8824
Hay JP, Wadt WR (1985) J Chem Phys 82:299–310
Friesner RA, Murphy RB, Beachy MD, Ringnalda MN, Pollard WT, Dunietz BD, Cao Y (1999) J Phys Chem A 103:1913–1928
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586–3616
Altun A, Thiel W (2005) J Phys Chem B 109:1268–1280
Schöneboom JC, Thiel W (2004) J Phys Chem B 108:7468–7478
Schöneboom JC, Lin H, Reuter N, Thiel W, Cohen S, Ogliaro F, Shaik S (2002) J Am Chem Soc 124:8142–8151
Van Gunsteren WF, Berendsen HHC (1977) Mol Phys 34:1311
Ahlrichs R, Bar M, Häser M, Horn H, Kölmel C (1989) Chem Phys Lett 162:165–169
Ahlrichs R et al (2002) TURBOMOLE 55. University of Karlsruhe, Karlsruhe
Smith W, Forester TR (1996) J Mol Graph 14:136–141
Billeter SR, Turner AJ, Thiel W (2000) Phys Chem Chem Phys 2:2177–2186
Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow CRA, French SA, Sokol AA, Bromley ST, Thiel W, Turner AJ, Billeter S, Terstegen F, Thiel S, Kendrick J, Rogers SC, Casci J, Watson M, King F, Karlsen E, Sjøvoll M, Fahmi A, Schäfer A, Lennartz C (2003) J Mol Struct Theochem 632:1–28
Ghosh A (2006) J Biol Inorg Chem 11:711–724
Harvey JN (2006) Annu Rep Prog Chem C 102:203–226
Fouqueau A, Casida ME, Lawson Daku LM, Houser A, Neese F (2005) J Chem Phys 122:044110/1–044110/13
Debrunner PG (1989) In: Lever ABP, Gray HB (eds) Iron porphyrins part 3. Physical bioinorganic chemistry series, vol 4. VCH, New York
Davydov R, Makris TM, Kofman V, Werst DE, Sligar SG, Hoffman BM (2001) J Am Chem Soc 123:1403–1415
Lipscomb JD (1980) Biochemistry 19:3590–3599
Dawson JH, Sono M (1987) Chem Rev 87:1255–1276
Sharrock M, Debrunner PG, Schulz C, Liscomb JD, Marshall V, Gunsalus IC (1976) Biochim Biophys Acta 426:8
Tsai R, Ru CA, Gunsalus IC, Peisach J, Blumberg W, Orme-Johnson WH, Beinert H (1970) Proc Natl Acad Sci USA 66:1157–1163
Sligar SG (1976) Biochemistry 15:5399–5406
Sligar SG, Gunsalus IC (1979) Biochemistry 18:2290–2295
Horitani M, Yashiro H, Hagiwara M, Hori H (2007) J Inorg Biochem. doi:10.1016/j.jinorgbio.2007.11.015 (in press)
Nguyen KA, Pachter R (2001) J Chem Phys 114:10757–10767
Kozlowski PM, Kuta J, Ohta T, Kitagawa TJ (2006) Inorg Biochem 100:744–750
Gouterman M (1961) J Mol Spectrosc 16:138–163
Acknowledgments
The research of S.S. at the Hebrew University of Jerusalem is supported by an ISF grant. H.H. is a JSPS Postdoctoral Fellow for Research Abroad. Ilme Schlichting and Konstanze von König are acknowledged for early access to the PDB structures.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Hirao, H., Cho, KB. & Shaik, S. QM/MM theoretical study of the pentacoordinate Mn(III) and resting states of manganese-reconstituted cytochrome P450cam . J Biol Inorg Chem 13, 521–530 (2008). https://doi.org/10.1007/s00775-007-0340-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00775-007-0340-9