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Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

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Marco Antonio Chaer Nascimento

Part of the book series: Highlights in Theoretical Chemistry ((HITC,volume 4))

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Abstract

The ground and excited state properties of copper proteins are studied and analyzed using hybrid quantum mechanics/molecular mechanics technique. Wildtype plastocyanin, characterized by an intense blue color, and wild-type nitrosocyanin, a red protein, are considered. These proteins differ from some ligands of the copper containing chromophore; we also studied the effects of selective mutations of one of the active site residue in plastocyanin. It is shown that this mutation is able to strongly modify the UV/VIS spectrum continuously modifying the absorption spectrum of the protein that from blue becomes red. Electrostatic and polarization effects of the macromolecular environment on the chromophore are taken into account using original techniques. Principal transitions are analyzed by mean of natural transition orbitals.

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References

  1. Holm RH, Kennepohl P, Solomon EI (1996) Chem Rev 96:2239

    Article  CAS  Google Scholar 

  2. Solomon EI, Hadt RG (2011) Coord Chem Rev 255:774

    Article  CAS  Google Scholar 

  3. Solomon EI, Szilagyi RK, De Beer S, Basumallick G, Basumallick L (2004) Chem Rev 104:419

    Article  CAS  Google Scholar 

  4. Gross EL (1993) Photosynth Res 37:103

    Article  CAS  Google Scholar 

  5. Skyes AG (1991) Adv Inorg Chem 36:377

    Article  Google Scholar 

  6. Mohamed MS, Fattah SA, Mostafa HM (2010) Curr Res J Biolog Sci 2:396

    CAS  Google Scholar 

  7. Book LD, Arnett DC, Hu H, Scherer NF (1998) J Phys Chem A 102:4350

    Article  CAS  Google Scholar 

  8. Xue Y, Ökvist M, Hansson Ö, Young S (1998) Protein Sci 7:2099

    Google Scholar 

  9. Gewirth AA, Solomon EI (1998) J Am Chem Soc 110:3811

    Article  Google Scholar 

  10. Nersissian AM, Nalbandyan RM (1988) Biochim Biophys Acta 957:446

    Article  Google Scholar 

  11. Gray HB, Malström BG, Williams RJP (2000) J Biol Inorg Chem 5:551

    Google Scholar 

  12. Lockwood DM, Cheng Y-K, Rossky PJ (2001) Chem Phys Lett 345:159

    Article  CAS  Google Scholar 

  13. Clark KM, YU Y, Marshall NM, Sieracki NA, Nilges MJ, Blackburn NJ, van der Donk WA, Lu Y (2010) J Am Chem Soc 132:10093

    Google Scholar 

  14. Ghosh S, Xie X, Dey A, Sun Y, Scholes CP, Solomon EI (2009) Proc Nat Acad Sci USA 106:4969

    Article  CAS  Google Scholar 

  15. Ando K (2010) J Chem Phys 133:175101

    Article  Google Scholar 

  16. Corni S, De Rienzo F, Di Felice R, Molinari E (2005) Int J Quant Chem 102:328

    Article  CAS  Google Scholar 

  17. Ryde U, Olsson MHM, Pierloot K, Roos BO (1996) J Mol Biol 261:586

    Article  CAS  Google Scholar 

  18. Olsson MHM, Ryde U (1999) J Biol Inorg Chem 4:654

    Article  CAS  Google Scholar 

  19. Ryde U, Olsoon MHM (2001) Int J Quant Chem 81:335

    Article  CAS  Google Scholar 

  20. Ando K (2004) J Phys Chem B 108:3940

    Article  CAS  Google Scholar 

  21. Pierloot K, De Kerpel JOA, Ryde U, Olsson MHM, Roos BO (1998) J Am Chem Soc 120:13156

    Article  CAS  Google Scholar 

  22. Sinnecker S, Neese F (2006) J Comput Chem 27:1463

    Article  CAS  Google Scholar 

  23. Cascella M, Cuendet MA, Tavernelli I, Rohtlisberger U (2007) J Phys Chem B 111:10248

    Article  CAS  Google Scholar 

  24. Le Bard DN, Matyushov DV (2008) J Phys Chem B 112:5218

    Google Scholar 

  25. Ando K (2008) J Phys Chem B 112:250

    Article  CAS  Google Scholar 

  26. Monari A, Very T, Rivail J-L, Assfeld X (2011) Comp Theor Chem. doi:10.1016/j.comptc.2011.11.026

  27. Lieberman RL, Arciero D, Hooper AB, Rosenzweig AC (2001) Biochemistry 40:5674

    Article  CAS  Google Scholar 

  28. Arciero DM, Pierce BS, Hendrich MP, Hooper AB (2002) Biochemistry 41:1703

    Article  CAS  Google Scholar 

  29. Basumalick L, Sarangi R, De Beer Giorgi S, Elmore B, Hooper AB, Hedmann B, Hodgson KO, Solomon EI (2004) J Am Chem Soc 127:3531

    Google Scholar 

  30. Besley NA, Robinson D (2011) Farady Discuss148:55

    Google Scholar 

  31. Berry SM, Bladhoim EL, Mostad EJ, Schenewerk AR (2011) J Biol Inorg Chem 16:473

    Article  CAS  Google Scholar 

  32. Laurent AD, Assfeld X (2010) Interdiscip Sci Comput Life Sci 2:38

    Article  Google Scholar 

  33. Loos P-F, Dumont E, Laurent AD, Assfeld X (2009) Chem Phys Lett 475:120

    Article  CAS  Google Scholar 

  34. Jacquemin D, Perpète EA, Laurent AD, Assfeld X, Adamo C (2009) Phys Chem Chem Phys 11:1258

    Article  CAS  Google Scholar 

  35. Dumont E, Laurent AD, Loos P-F, Assfeld X (2009) J Chem Theory Comput 5:1700

    Article  CAS  Google Scholar 

  36. Ambrosek D, Loos P-F, Assfeld X, Daniel C (2010) J Inorg Biochem 104:893

    Article  CAS  Google Scholar 

  37. Rodriguez-Ropero F, Zanuy D, Assfeld X, Aleman C (2009) Biomacromolecules 10:2338

    Article  CAS  Google Scholar 

  38. Dreuw A, Head-Gordon M (2005) Chem Rev 105:4009

    Article  CAS  Google Scholar 

  39. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.1. Gaussian Inc., Wallingford, CT

    Google Scholar 

  40. Ferré N, Assfeld X, Rivail J-L (2002) J Comput Chem 23:610

    Article  Google Scholar 

  41. Assfeld X, Rivail J-L (1996) Chem Phys Lett 266:100

    Article  Google Scholar 

  42. Tinker code package: http://dasher.wustl.edu/tinker/

  43. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187

    Article  CAS  Google Scholar 

  44. Hay PJ, Wadt WR (1985) J Chem Phys 82:270

    Article  CAS  Google Scholar 

  45. Hay PJ, Wadt WR (1985) J Chem Phys 82:284

    Article  Google Scholar 

  46. Hay PJ, Wadt WR (1985) J Chem Phys 82:299

    Article  CAS  Google Scholar 

  47. Becke AD (1993) J Chem Phys 98:1372

    Article  CAS  Google Scholar 

  48. Lee C, Yang W, Parr RG (1993) Phys Rev B 37:785

    Article  Google Scholar 

  49. Runge E, Gross EKU (1984) Phys Rev Lett 52:997

    Article  CAS  Google Scholar 

  50. Ditchfield R, Hehre WJ, Pople JA (1971) J Chem Phys 54:724

    Article  CAS  Google Scholar 

  51. Hehre WJ, Ditchfield R, Pople JA (1972) J Chem Phys 56:2257

    Article  CAS  Google Scholar 

  52. Rassolov VA, Ratner MA, Pople JA, Redfern PC, Curtiss LA (2001) J Comp Chem 22:976

    Article  CAS  Google Scholar 

  53. Hansen E, Bak KL (1999) Enantiomer 4:455

    CAS  Google Scholar 

  54. Warnke I, Furche F, Wire Inter Rev. doi:10.1002/wcms.55

  55. Yanai T, Tew D, Handy N (2004) Chem Phys Lett 393:51

    Article  CAS  Google Scholar 

  56. Chai J-D, Head-Gordon M (2008) Phys Chem Chem Phys 10:6615

    Article  CAS  Google Scholar 

  57. Adamo C, Barone VJ (1999) Chem Phys 110(110):6158

    CAS  Google Scholar 

  58. Martin RL (2003) J Chem Phys 118:4775

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Equipe de Chimie et Biochime Théoriques, SRSMC-UMR 7565, Université de Lorraine-Nancy and CNRS, 70239, 54506, Nancy-Vandoeuvre, France

    Antonio Monari, Thibaut Very, Jean-Louis Rivail & Xavier Assfeld

Authors
  1. Antonio Monari
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  2. Thibaut Very
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  3. Jean-Louis Rivail
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  4. Xavier Assfeld
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Corresponding authors

Correspondence to Antonio Monari or Jean-Louis Rivail .

Editor information

Editors and Affiliations

  1. Departamento de Química Fundamental, Instituto de Química, University of São Paulo, São Paulo, Brazil

    Fernando R. Ornellas

  2. REQUIMTE, Depart. de Química e Bioquimic, University of Porto, Faculty of Science, Porto, Portugal

    Maria João Ramos

Additional information

Dedicated to Professor Marco Antonio Chaer Nascimento and published as part of the special collection of articles celebrating his 65th birthday.

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© 2014 Springer-Verlag Berlin Heidelberg

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Monari, A., Very, T., Rivail, JL., Assfeld, X. (2014). Effects of mutations on the absorption spectra of copper proteins: a QM/MM study. In: Ornellas, F., João Ramos, M. (eds) Marco Antonio Chaer Nascimento. Highlights in Theoretical Chemistry, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41163-2_5

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