Journal of Chemical Biology

, Volume 4, Issue 4, pp 167–184 | Cite as

Effect of computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii

  • Emanuel Peter
  • Bernhard Dick
  • Stephan A. Baeurle
Original Article

Abstract

LOV domains are the light-sensitive protein domains of plant phototropins and bacteria. They photochemically form a covalent bond between a flavin mononucleotide (FMN) chromophore and a cysteine, attached to the apo-protein, upon irradiation with blue light, which triggers a signal in the adjacent kinase. Although their signaling state has been well characterized through experimental means, their signal transduction pathway as well as dark-state activity are generally only poorly understood. Here we show results from molecular dynamics simulations where we investigated the effect of thermostating and long-range electrostatics on the solution structure and dynamical behavior of the wild-type LOV1 domain from the green algae Chlamydomonas reinhardtii in the dark. We demonstrate that these computational issues can dramatically affect the conformational fluctuations of such protein domains by suppressing configurations far from equilibrium or destabilizing local configurations, leading to artificial changes of the protein secondary structure as well as the H-bond network formed by the amino acids and the FMN. By comparing our calculation results with recent experimental data, we show that the non-invasive thermostating strategy, where the protein solute is only indirectly coupled to the thermostat via the solvent, in conjunction with the particle-mesh Ewald technique, provides dark-state conformers, which are in consistency with experimental observations. Moreover, our calculations indicate that the LOV1 domains can alter the intersystem crossing rate and rate of adduct formation by adjusting the population distribution of these dark-state conformers. This might permit them to function as a modulator of the signal intensity under low light conditions.

Keywords

Protein photosensor Phototropin Plant Bacteria LOV 

Supplementary material

12154_2011_60_MOESM1_ESM.pdf (1 mb)
ESM 1(PDF 1056 kb)

References

  1. 1.
    Hegemann P (2008) Algal sensory photoreceptors. Annu Rev Plant Biol 59:167–189CrossRefGoogle Scholar
  2. 2.
    Christie JM (2007) Phototropin blue-light receptors. Annu Rev Plant Biol 58:21–45CrossRefGoogle Scholar
  3. 3.
    Briggs WR (2007) The LOV domain: a chromophore module servicing multiple photoreceptors. J Biomed Sci 14:499–504CrossRefGoogle Scholar
  4. 4.
    Kottke T, Hegemann P, Dick B, Heberle J (2006) The photochemistry of the light-, oxygen-, and voltage-sensitive domains in the algal blue light receptor phot. Biopolymers 82:373–378CrossRefGoogle Scholar
  5. 5.
    Jones MA, Feeney KA, Kelly SM, Christie JM (2007) Mutational analysis of phototropin1 provides insights into the mechanism underlying LOV2 signal transmission. J Biol Chem 282:6405–6414CrossRefGoogle Scholar
  6. 6.
    Salomon M, Lempert U, Rüdiger W (2004) Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain. FEBS Lett 572:8–10CrossRefGoogle Scholar
  7. 7.
    Kutta RJ, Hofinger ESA, Preuss H, Bernhardt G, Dick B (2008) Blue-light induced interaction of LOV domains from Chlamydomonas reinhardtii. ChemBioChem 9:1931–1938CrossRefGoogle Scholar
  8. 8.
    Christie JM, Swartz TE, Bogomolni RA, Briggs WR (2002) Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. Plant J 32:205–219CrossRefGoogle Scholar
  9. 9.
    Kagawa T, Kasahara M, Abe T, Yoshida S, Wada M (2004) Function analysis of phototropin2 using fern mutants deficient in blue light-induced chloroplast avoidance movement. Plant Cell Physiol 45:416–426CrossRefGoogle Scholar
  10. 10.
    Sullivan S, Thomson CE, Lamont DJ, Jones MA, Christie JM (2008) In vivo phosphorylation site mapping and functional characterization of Arabidopsis phototropin1. Mol Plant 1:178–194CrossRefGoogle Scholar
  11. 11.
    Kottke T, Heberle J, Hehn D, Dick B, Hegemann P (2003) Phot-LOV1: photocycle of a blue-light receptor domain from the green alga Chlamydomonas reinhardtii. Biophys J 84:1192–1201CrossRefGoogle Scholar
  12. 12.
    Fedorov R, Schlichting I, Hartmann E, Domratcheva T, Fuhrmann M, Hegemann P (2003) Crystal structures and molecular mechanism of a light-induced signaling switch: the phot-LOV1 domain from Chlamydomonas reinhardtii. Biophys J 84:2474–2482CrossRefGoogle Scholar
  13. 13.
    Bednarz T, Losi A, Gärtner W, Hegemann P, Heberle J (2004) Functional variations among LOV domains as revealed by FT-IR difference spectroscopy. Photochem Photobiol Sci 3:575–579CrossRefGoogle Scholar
  14. 14.
    Schleicher E, Kowalczyk RM, Kay CWM, Hegemann P, Bacher A, Fischer M, Bittl R, Richter G, Weber S (2004) On the reaction mechanism of adduct formation in LOV domains of the plant blue-light receptor phototropin. J Am Chem Soc 126:11067–11076CrossRefGoogle Scholar
  15. 15.
    Sato Y, Nabeno M, Iwata T, Tokutomi S, Sakurai M, Kandori H (2007) Heterogeneous environment of the SH group of Cys966 near the flavin chromophore in the LOV2 domain of Adiantum neochrome1. Biochemistry 46:10258–10265CrossRefGoogle Scholar
  16. 16.
    Iwata T, Nozaki D, Tokutomi S, Kandori H (2005) Comparative investigation of the LOV1 and LOV2 domains in Adiantum phytochrome3. Biochemistry 44:7427–7434CrossRefGoogle Scholar
  17. 17.
    Iwata T, Nozaki D, Tokutomi S, Kagawa T, Wada M, Kandori H (2003) Light-induced structural changes in the LOV2 domain of Adiantum phytochrome3 studied by low temperature FTIR and UV–visible spectroscopy. Biochemistry 42:8183–8191CrossRefGoogle Scholar
  18. 18.
    Alexandre MTA, van Grondelle R, Hellingwerf KJ, Kennis JTM (2009) Conformational heterogeneity and propagation of structural changes in the LOV2/Jα domain from Avena sativa phototropin1 as recorded by temperature-dependent FTIR spectroscopy. Biophys J 97:238–247CrossRefGoogle Scholar
  19. 19.
    Neiss C, Saalfrank P (2003) Ab initio quantum chemical investigation of the first steps of the photocycle of phototropin: a model study. Photochem Photobiol 77:101–109CrossRefGoogle Scholar
  20. 20.
    Dittrich M, Freddolino PL, Schulten K (2005) When light falls in LOV: a quantum mechanical/molecular mechanical study of photoexcitation in phot-LOV1 of Chlamydomonas reinhardtii. J Phys Chem B 109:13006–13013CrossRefGoogle Scholar
  21. 21.
    Freddolino PL, Dittrich M, Schulten K (2006) Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophys J 91:3630–3639CrossRefGoogle Scholar
  22. 22.
    Neiss C, Saalfrank P (2004) Molecular dynamics simulation of the LOV2 domain from Adiantum capillus-veneris. J Chem Inf Comput Sci 44:1788–1793Google Scholar
  23. 23.
    Arai S, Togashi M, Shiozawa M, Inoue Y, Sakurai M (2005) Molecular dynamics simulation of the M intermediate of photoactive yellow protein in the crystalline state. Chem Phys Lett 414:230–233CrossRefGoogle Scholar
  24. 24.
    Lins RD, Röthlisberger U (2006) Influence of long-range electrostatic treatments on the folding of the N-terminal H4 histone tail peptide. J Chem Theory Comput 2:246–250CrossRefGoogle Scholar
  25. 25.
    Weber W, Hünenberger PH, McCammon JA (2000) Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B 104:3668–3675CrossRefGoogle Scholar
  26. 26.
    Hünenberger PH, McCammon JA (1999) Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem 78:69–88CrossRefGoogle Scholar
  27. 27.
    Sagui C, Darden TA (1999) Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct 28:155–179CrossRefGoogle Scholar
  28. 28.
    Loncharich RJ, Brooks BR (1989) The effects of truncating long-range forces on protein dynamics. Proteins Struct Funct Genet 6:32–45CrossRefGoogle Scholar
  29. 29.
    Bergdorf M, Peter C, Hünenberger PH (2003) Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study. J Chem Phys 119:9129–9144, and references thereinCrossRefGoogle Scholar
  30. 30.
    Baeurle SA (2009) Multiscale modeling of polymer materials using field-theoretic methodologies: a survey about recent developments. J Math Chem 46:363–426CrossRefGoogle Scholar
  31. 31.
    Lingenheil M, Denschlag R, Reichold R, Tavan P (2008) The “hot-solvent/cold-solute” problem revisited. J Chem Theory Comput 4:1293–1306CrossRefGoogle Scholar
  32. 32.
    Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Oxford University Press, OxfordGoogle Scholar
  33. 33.
    Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217CrossRefGoogle Scholar
  34. 34.
    Brooks CL III, Pettitt BM, Karplus M (1985) Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J Chem Phys 83:5897–5908CrossRefGoogle Scholar
  35. 35.
    Kim KS (1989) On effective methods to treat solvent effects in macromolecular mechanics and simulations. Chem Phys Lett 156:261–268CrossRefGoogle Scholar
  36. 36.
    Steinbach PJ, Brooks BR (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem 15:667–683CrossRefGoogle Scholar
  37. 37.
    Norberg J, Nilsson L (2000) On the truncation of long-range electrostatic interactions in DNA. Biophys J 79:1537–1553CrossRefGoogle Scholar
  38. 38.
    Barker JA, Watts RO (1973) Monte Carlo studies of the dielectric properties of waterlike models. Mol Phys 26:789–792CrossRefGoogle Scholar
  39. 39.
    Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451–5459CrossRefGoogle Scholar
  40. 40.
    Hünenberger PH, van Gunsteren WF (1998) Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: influence on the simulated energetic, structural, and dielectric properties of liquid water. J Chem Phys 108:6117–6134CrossRefGoogle Scholar
  41. 41.
    Ewald PP (1921) Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann Phys (Leipzig) 64:253–287Google Scholar
  42. 42.
    Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  43. 43.
    Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593CrossRefGoogle Scholar
  44. 44.
    Hockney RW, Eastwood JW (1988) Computer simulation using particles. Inst of Physics, BristolCrossRefGoogle Scholar
  45. 45.
    van der Spoel D, van Maaren PJ (2006) The origin of layer structure artifacts in simulations of liquid water. J Chem Theory Comput 2:1–11CrossRefGoogle Scholar
  46. 46.
    Yonetani Y (2005) A severe artifact in simulation of liquid water using a long cut-off length: appearance of a strange layer structure. Chem Phys Lett 406:49–53CrossRefGoogle Scholar
  47. 47.
    van Gunsteren WF, Berendsen HJC (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew Chem Int Ed Engl 29:992–1023CrossRefGoogle Scholar
  48. 48.
    Hummer G, Pratt LR, Garcia AE (1996) Free energy of ionic hydration. J Phys Chem 100:1206–1215CrossRefGoogle Scholar
  49. 49.
    Hummer G, Pratt LR, Garcia AE (1998) Molecular theories and simulation of ions and polar molecules in water. J Phys Chem A 102:7885–7895CrossRefGoogle Scholar
  50. 50.
    Hünenberger PH, McCammon JA (1999) Ewald artifacts in computer simulations of ionic solvation and ion–ion interaction: a continuum electrostatics study. J Chem Phys 110:1856–1872CrossRefGoogle Scholar
  51. 51.
    Baker NA, Hünenberger PH, McCammon JA (1999) J Chem Phys 110:10679–10692CrossRefGoogle Scholar
  52. 52.
    Baker NA, Hünenberger PH, McCammon JA (2000) Erratum: “Polarization around an ion in a dielectric continuum with truncated electrostatic interactions” [J. Chem. Phys. 110, 10679 (1999)]. J Chem Phys 113:2510–2511CrossRefGoogle Scholar
  53. 53.
    Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  54. 54.
    Mor A, Ziv G, Levy Y (2008) Simulations of proteins with inhomogeneous degrees of freedom: the effect of thermostats. J Comput Chem 29:1992–1998CrossRefGoogle Scholar
  55. 55.
    Rosta E, Buchete N-V, Hummer G (2009) Thermostat artifacts in replica exchange molecular dynamics simulations. J Chem Theory Comput 5:1393–1399CrossRefGoogle Scholar
  56. 56.
    Nosé S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81:511–519CrossRefGoogle Scholar
  57. 57.
    Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697CrossRefGoogle Scholar
  58. 58.
    Frenkel D, Smit B (2003) Understanding molecular simulation: from algorithms to applications. Academic, San DiegoGoogle Scholar
  59. 59.
    Peter E, Dick B, Baeurle SA (2010) Mechanism of signal transduction of the LOV2-Jα-photosensor from Avena sativa. Nat Commun 1:122CrossRefGoogle Scholar
  60. 60.
    Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317Google Scholar
  61. 61.
    Soares T, Daura X, Oostenbrink C, Smith L, van Gunsteren WF (2004) Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme. J Biomol NMR 30:407–422CrossRefGoogle Scholar
  62. 62.
    Todorova N, Legge FS, Treutlein H, Yarovsky I (2008) Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin. J Phys Chem B 112:11137–11146CrossRefGoogle Scholar
  63. 63.
    Alexandre MTA, van Grondelle R, Hellingwerf KJ, Robert B, Kennis JTM (2008) Perturbation of the ground-state electronic structure of FMN by the conserved cysteine in phototropin LOV2 domains. Phys Chem Chem Phys 10:6693–6702CrossRefGoogle Scholar
  64. 64.
    Nishina Y, Kitagawa T, Shiga K, Horiike K, Matsumura Y, Watari H, Yamano T (1978) Resonance Raman spectra of riboflavin and its derivatives in the bound state with egg riboflavin binding proteins. J Biochem 84:925–932Google Scholar
  65. 65.
    Nishina Y, Shiga K, Horiike K, Tojo H, Kasai S, Yanase K, Matsui K, Watari H, Yamano T (1980) Vibrational modes of flavin bound to riboflavin binding protein from egg white: resonance Raman spectra of lumiflavin and 8-substituted riboflavin. J Biochem 88:403–409Google Scholar
  66. 66.
    Dutta PK, Spencer R, Walsh C, Spiro TG (1980) Resonance Raman and coherent anti-stokes Raman scattering spectra of flavin derivatives. Vibrational assignments and the zwitterionic structure of 8-methylamino-riboflavin. Biochim Biophys Acta 623:77–83Google Scholar
  67. 67.
    Schopfer LM, Morris MD (1980) Resonance Raman spectra of flavin derivatives containing chemical modifications in positions 7 and 8 of the isoalloxazine ring. Biochemistry 19:4932–4935CrossRefGoogle Scholar
  68. 68.
    Crosson S, Moffat K (2001) Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction. Proc Natl Acad Sci USA 98:2995–3000CrossRefGoogle Scholar
  69. 69.
    Halavaty AS, Moffat K (2007) N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin1 from Avena sativa. Biochemistry 46:14001–14009CrossRefGoogle Scholar
  70. 70.
    Kennis JTM, Crosson S, Gauden M, van Stokkum IHM, Moffat K, van Grondelle R (2003) Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor. Biochemistry 42:3385–3392CrossRefGoogle Scholar
  71. 71.
    Holzer W, Penzkofer A, Fuhrmann M, Hegemann P (2002) Absorption and emission spectroscopic characterisation of the LOV2-His domain of phot from Chlamydomonas reinhardtii. Photochem Photobiol 75:479–487CrossRefGoogle Scholar
  72. 72.
    Schüttrigkeit TA, Kompa CK, Salomon M, Rudiger W, Michel-Beyerle ME (2003) Primary photophysics of the FMN binding LOV2 domain of the plant blue light receptor phototropin of Avena sativa. Chem Phys 294:501–508CrossRefGoogle Scholar
  73. 73.
    Swartz TE, Corchnoy SB, Christie JM, Lewis JW, Szundi I, Briggs WR, Bogomolni RA (2001) The photocycle of a flavin-binding domain of the blue-light photoreceptor phototropin. J Biol Chem 276:36493–36500CrossRefGoogle Scholar
  74. 74.
    Losi A, Polverini E, Quest B, Gärtner W (2002) First evidence for phototropin-related blue-light receptors in prokaryotes. Biophys J 82:2627–2634CrossRefGoogle Scholar
  75. 75.
    Losi A, Kottke T, Hegemann P (2004) Recording of blue light-induced energy and volume changes within the wild-type and mutated phot-LOV1 domain from Chlamydomonas reinhardtii. Biophys J 86:1051–1060CrossRefGoogle Scholar
  76. 76.
    Salzmann S, Tatchen J, Marian CM (2008) The photophysics of flavins: what makes the difference between gas phase and aqueous solution? J Photochem Photobiol A 198:221–231CrossRefGoogle Scholar
  77. 77.
    Salzmann S, Martinez-Junza V, Zorn B, Braslavsky SE, Mansurova M, Marian CM, Gärtner W (2009) Photophysical properties of structurally and electronically modified flavin derivatives determined by spectroscopy and theoretical calculations. J Phys Chem A 113:9365–9375CrossRefGoogle Scholar
  78. 78.
    Salzmann S, Silva-Junior MR, Thiel W, Marian CM (2009) Influence of the LOV domain on low-lying excited states of flavin: a combined quantum-mechanics/molecular mechanics investigation. J Phys Chem B 113:15610–15618CrossRefGoogle Scholar
  79. 79.
    Nakasako M, Zikihara K, Matsuoka D, Katsura H, Tokutomi S (2008) Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2. J Mol Biol 381:718–733CrossRefGoogle Scholar
  80. 80.
    Baeurle SA, Kiselev MG, Makarova ES, Nogovitsin EA (2009) Effect of the counterion behavior on the frictional compressive properties of chondroitin sulfate solutions. Polymer 50:1805–1813CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Emanuel Peter
    • 1
  • Bernhard Dick
    • 1
  • Stephan A. Baeurle
    • 1
  1. 1.Department of Chemistry and Pharmacy, Institute of Physical and Theoretical ChemistryUniversity of RegensburgRegensburgGermany

Personalised recommendations