Structural Chemistry

, Volume 24, Issue 4, pp 1145–1151 | Cite as

A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

  • Cristina Trujillo
  • Goar Sánchez-Sanz
  • Ibon Alkorta
  • José Elguero
Original Research

Abstract

Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4–5 kJ mol−1.

Keywords

Cyclol Green fluorescent protein GFP DFT calculations Solvent effects Water molecules 

References

  1. 1.
  2. 2.
    Shimomura O (2009) Angew Chem Int Ed 48:5590–5602CrossRefGoogle Scholar
  3. 3.
    Chalfie M (2009) Angew Chem Int Ed 48:5603–5611CrossRefGoogle Scholar
  4. 4.
    Tsien T (2009) Angew Chem Int Ed 48:5612–5626CrossRefGoogle Scholar
  5. 5.
    Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D (1994) Science 263:802–805CrossRefGoogle Scholar
  6. 6.
    Tsien R (1998) Annu Rev Biochem 67:509–544CrossRefGoogle Scholar
  7. 7.
    Reid BG, Flynn GC (1997) Biochemistry 36:6786–6791CrossRefGoogle Scholar
  8. 8.
    Heim R, Prasher DC, Tsien RY (1994) Proc Natl Acad Sci USA 91:12501–12504CrossRefGoogle Scholar
  9. 9.
    Nishiuchi Y, Inui T, Nishio H, Bódi J, Kimura T, Tsuji FI, Sakakibara S (1998) Proc Natl Acad Sci USA 95:13549–13554CrossRefGoogle Scholar
  10. 10.
    Cubitt AB, Heim R, Adams SR, Boyd AE, Gross LA, Tsien RY (1995) Trends Biochem Sci 20:448–455CrossRefGoogle Scholar
  11. 11.
    Zimmer M (2002) Chem Rev 102:759–781CrossRefGoogle Scholar
  12. 12.
    Mizuno H, Mal TK, Tong KI, Ando R, Furuta T, Ikura M, Miyawaki A (2003) Mol Cell 12:1051–1058CrossRefGoogle Scholar
  13. 13.
    Wood TI, Barondeau DP, Hitomi C, Kassmann CJ, Tainer JA, Getzoff ED (2005) Biochemistry 44:16211–16220CrossRefGoogle Scholar
  14. 14.
    Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED (2006) J Am Chem Soc 128:4685–4693CrossRefGoogle Scholar
  15. 15.
    Pakhomov AA, Martynov VI (2008) Chem Biol 15:755–764CrossRefGoogle Scholar
  16. 16.
    Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED (2003) Proc Natl Acad Sci USA 100:12111–12116CrossRefGoogle Scholar
  17. 17.
    Sniegowski JA, Lappe JW, Patel HN, Huffman HA, Wachter RM (2005) J Biol Chem 280:26248–26255CrossRefGoogle Scholar
  18. 18.
    Li B, Shahid R, Peshkepija P, Zimmer M (2012) Chem Phys 392:143–148CrossRefGoogle Scholar
  19. 19.
    Ma Y, Sun Q, Zhang H, Peng L, Yu JG, Smith SC (2010) J Phys Chem B 114:9698–9705CrossRefGoogle Scholar
  20. 20.
    Ma Y, Sun Q, Li Z, Yu JG, Smith SC (2012) J Phys Chem B 116:1426–1436CrossRefGoogle Scholar
  21. 21.
    Alkorta I, Sánchez-Sanz G, Trujillo C, Azofra LM, Elguero J (2012) Struct Chem 23:873–877CrossRefGoogle Scholar
  22. 22.
    Lucente G, Pinnen, F, Zanotti G, Fedeli W, Mazza F (1980) J Chem Soc Perkin Trans 1 1499–1560Google Scholar
  23. 23.
    Pinnen F, Zanotti G, Lucente G (1982) J Chem Soc Perkin Trans 1 6:1311–1316CrossRefGoogle Scholar
  24. 24.
    Calcagni A, Lucente G, Luisi G, Pinnen F, Rossi D, Gavuzzo E (1997) J Chem Soc Perkin Trans 1 15:2223–2229CrossRefGoogle Scholar
  25. 25.
    Helms V, Winstead C, Langhoff PW (2000) J Mol Struct 506:179–189CrossRefGoogle Scholar
  26. 26.
    He X, Bell AF, Tonge PJ (2002) Org Lett 4:1523–1526CrossRefGoogle Scholar
  27. 27.
    Wang S, Smith SC (2006) J Phys Chem B 110:5084–5093CrossRefGoogle Scholar
  28. 28.
    Filippi C, Zaccheddu M, Buda F (2009) J Chem Theory Comput 5:2074–2087CrossRefGoogle Scholar
  29. 29.
    Kang J, Zhao G, Xu J, Yang W (2010) Chem Commun 46:2868–2870CrossRefGoogle Scholar
  30. 30.
    Baldridge A, Solntsev KM, Song C, Tanioka T, Kowalik J, Hardcastle K, Tolbert LM (2010) Chem Commun 46:5686–5688CrossRefGoogle Scholar
  31. 31.
    Polyakov IV, Grigorenko BL, Epifanovsky E, Krylov AI, Nemukhin AV (2010) J Chem Theory Comput 6:2377–2387CrossRefGoogle Scholar
  32. 32.
    Wang D, Merz T, van Gunsteren WF (2010) Phys Chem Chem Phys 12:11051–11061CrossRefGoogle Scholar
  33. 33.
    Li Y, Shi L, Qin LX, Qu LL, Jing C, Lan M, James TD, Long YT (2011) Chem Commun 47:4361–4363CrossRefGoogle Scholar
  34. 34.
    Forbes MW, Nagy AM, Jockusch RA (2011) Int J Mass Spectrom 308:155–166CrossRefGoogle Scholar
  35. 35.
    Solntsev KM, Ghosh D, Amador A, Josowicz M, Krylov AI (2011) J Phys Chem Lett 2:2593–2597CrossRefGoogle Scholar
  36. 36.
    Rafiq S, Rajbongshi BK, Nair NN, Sen P, Ramanathan G (2011) J Phys Chem A 115:13733–13742CrossRefGoogle Scholar
  37. 37.
    Bravaya KB, Grigorenko BL, Nemukhin AV, Krylov AI (2012) Acc Chem Res 45:265–275CrossRefGoogle Scholar
  38. 38.
    Zhang H, Sun Q, Li Z, Nanbu S, Smith SS (2012) Comput Theor Chem 990:185–193CrossRefGoogle Scholar
  39. 39.
    Wall MA, Socolich M, Ranganathan R (2000) Nat Struct Biol 7:1133–1138CrossRefGoogle Scholar
  40. 40.
    Yoo HY, Boatz JA, Helms V, McCammon JA, Langhoff PW (2001) J Phys Chem B 105:2850–2857CrossRefGoogle Scholar
  41. 41.
    Gepshtein R, Huppert D, Agmon N (2006) J Phys Chem B 110:4434–4442CrossRefGoogle Scholar
  42. 42.
    Chen KY, Cheng YM, Lai CH, Hsu CC, Ho ML, Lee GH, Chou PT (2007) J Am Chem Soc 129:4534–4535CrossRefGoogle Scholar
  43. 43.
    Hsieh CC, Chou PT, Shih CW, Chuang WT, Chung MW, Lee J, Joo T (2011) J Am Chem Soc 133:2932–2943CrossRefGoogle Scholar
  44. 44.
    Tolbert LM, Baldridge A, Kowalik J, Solntsev KM (2011) Acc Chem Res 45:171–181CrossRefGoogle Scholar
  45. 45.
    Paige JS, Wu KY, Jaffrey SR (2011) Science 333:642–646CrossRefGoogle Scholar
  46. 46.
    Filippi C, Buda F, Guidoni L, Sinicropi A (2012) J Chem Theory Comput 8:112–114CrossRefGoogle Scholar
  47. 47.
    Steindal AH, Olsen JMH, Ruud K, Frediani L, Kongsted J (2012) Phys Chem Chem Phys 14:5440–5451CrossRefGoogle Scholar
  48. 48.
    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 Jr. JA, 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., WallingfordGoogle Scholar
  49. 49.
    Becke AD (1988) Phys Rev A 38:3098–3100CrossRefGoogle Scholar
  50. 50.
    Becke AD (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  51. 51.
    Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789CrossRefGoogle Scholar
  52. 52.
    Hariharan PA, Pople JA (1973) Theor Chim Acta 28:213–222CrossRefGoogle Scholar
  53. 53.
    McIver JW, Komornicki AK (1972) J Am Chem Soc 94:2625–2633CrossRefGoogle Scholar
  54. 54.
    Alkorta I, Popelier PLA (2011) Carbohydr Res 346:2933–2939CrossRefGoogle Scholar
  55. 55.
    Azofra LM, Alkorta I, Elguero J, Toro-Labbé A (2012) J Phys Chem A 116:8250–8259CrossRefGoogle Scholar
  56. 56.
    Contreras-Torres FF, Basiuk VA (2006) J Phys Chem A 110:7431–7440CrossRefGoogle Scholar
  57. 57.
    Elguero J, Marzin C, Katritzky AR, Linda P (1976) The tautomerism of heterocycles. Academic Press, New York, p 371Google Scholar
  58. 58.
    Minkin VI, Garnovskii AD, Elguero J, Katritzky AR, Denisko OV (2000) The tautomerism of heterocycles: five-membered rings with two or more heteroatoms. Adv Heterocycl Chem 76:157–323CrossRefGoogle Scholar
  59. 59.
    Bethencourt L, Vivas D, Núñez O (2010) J Phys Org Chem 23:931–937CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Cristina Trujillo
    • 1
    • 2
  • Goar Sánchez-Sanz
    • 1
  • Ibon Alkorta
    • 1
  • José Elguero
    • 1
  1. 1.Instituto de Química Médica (C.S.I.C.)MadridSpain
  2. 2.Departamento de Ciencia e Ingeniería de Materiales e Ingeniería QuímicaUniversidad Carlos IIILeganés, MadridSpain

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