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Computational Spectroscopy, Dynamics, and Photochemistry of Photosensory Flavoproteins

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Flavins and Flavoproteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1146))

Abstract

Extensive interest in photosensory proteins stimulated computational studies of flavins and flavoproteins in the past decade. This review is dedicated to the three central topics of these studies: calculations of flavin UV–visible and IR spectra, simulated dynamics of photoreceptor proteins, and flavin photochemistry. Accordingly, this chapter is divided into three parts; each part describes corresponding computational protocols, summarizes computational results, and discusses the emerging mechanistic picture.

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References

  1. Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864–B871

    Google Scholar 

  2. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133–A1138

    Google Scholar 

  3. Pople JA, Binkley JS, Seeger R (1976) Theoretical models incorporating electron correlation. Int J Quantum Chem 10:1–19

    CAS  Google Scholar 

  4. Christiansen O, Koch H, Jørgensen P (1995) The second-order approximate coupled cluster singles and doubles model CC2. Chem Phys Lett 243:409–418

    CAS  Google Scholar 

  5. Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52:997–1000

    CAS  Google Scholar 

  6. Foresman JB, Head-Gordon M, Pople JA, Frisch MJ (1992) Toward a systematic molecular orbital theory for excited states. J Phys Chem 96:135–149

    CAS  Google Scholar 

  7. Rhee YM, Head-Gordon M (2007) Scaled second-order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods. J Phys Chem A 111:5314–5326

    PubMed  CAS  Google Scholar 

  8. Khrenova MG, Nemukhin AV, Grigorenko BL, Krylov AI, Domratcheva TM (2010) Quantum chemistry calculations provide support to the mechanism of the light-induced structural changes in the flavin-binding photoreceptor proteins. J Chem Theory Comput 6:2293–2302

    CAS  Google Scholar 

  9. Grimme S, Waletzke M (1999) A combination of Kohn–Sham density functional theory and multi-reference configuration interaction methods. J Chem Phys 111:5645–5655

    CAS  Google Scholar 

  10. Neiss C, Saalfrank P (2003) Ab initio quantum chemical investigation of the first steps of the photocycle of phototropin: a model study. Photochem Photobiol 77:101–109

    PubMed  CAS  Google Scholar 

  11. Salzmann S, Marian CM (2008) Effects of protonation and deprotonation on the excitation energies of lumiflavin. Chem Phys Lett 463:400–404

    CAS  Google Scholar 

  12. Salzmann S, Marian CM (2009) The photophysics of alloxazine: a quantum chemical investigation in vacuum and solution. Photochem Photobiol Sci 8:1655–1666

    PubMed  CAS  Google Scholar 

  13. 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 113:9365–9375

    PubMed  CAS  Google Scholar 

  14. Salzmann S, Silva 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 113:15610–15618

    PubMed  CAS  Google Scholar 

  15. 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 198:221–231

    CAS  Google Scholar 

  16. Neiss C, Saalfrank P, Parac M, Grimme S (2003) Quantum chemical calculation of excited states of flavin-related molecules. J Phys Chem A 107:140–147

    CAS  Google Scholar 

  17. Nakatsuji H (1979) Cluster expansion of the wavefunction. Electron correlations in ground and excited states by SAC (symmetry-adapted-cluster) and SAC CI theories. Chem Phys Lett 67:329–333

    CAS  Google Scholar 

  18. Hasegawa J, Bureekaew S, Nakatsuji H (2007) SAC-CI theoretical study on the excited states of lumiflavin: structure, excitation spectrum, and solvation effect. J Photochem Photobiol A 189:205–210

    CAS  Google Scholar 

  19. Roos B (1972) A new method for large-scale Cl calculations. Chem Phys Lett 15:153–159

    Google Scholar 

  20. Roos BO, Andersson K, Fülscher MP et al (2007) Multiconfigurational perturbation theory: applications in electronic spectroscopy. In: Prigogine I, Rice SA (eds) Advances in chemical physics: new methods in computational quantum mechanics. Wiley, New York, pp 219–331

    Google Scholar 

  21. Granovsky AA (2011) Extended multi-configuration quasi-degenerate perturbation theory: the new approach to multi-state multi-reference perturbation theory. J Chem Phys 134, Art.-No. 214113

    Google Scholar 

  22. Angeli C, Cimiraglia R, Evangelisti S, Leininger T, Malrieu JP (2001) Introduction of n-electron valence states for multireference perturbation theory. J Chem Phys 114:10252–10264

    CAS  Google Scholar 

  23. Climent T, Gonzalez-Luque R, Merchan M, Serrano-Andres L (2006) Theoretical insight into the spectroscopy and photochemistry of isoalloxazine, the flavin core ring. J Phys Chem A 110:13584–13590

    PubMed  CAS  Google Scholar 

  24. Domratcheva T, Fedorov R, Schlichting I (2006) Analysis of the primary photocycle reactions occurring in the light, oxygen, and voltage blue-light receptor by multiconfigurational quantum-chemical methods. J Chem Theory Comput 2:1565–1574

    CAS  Google Scholar 

  25. Udvarhelyi A, Domratcheva T (2011) Photoreaction in BLUF receptors: proton-coupled electron transfer in the flavin-Gln-Tyr system. Photochem Photobiol 87:554–563

    PubMed  CAS  Google Scholar 

  26. Solov’yov IA, Domratcheva T, Shahi ARM, Schulten K (2012) Decrypting cryptochrome: revealing the molecular identity of the photoactivation reaction. J Am Chem Soc 134:18046–18052

    PubMed Central  PubMed  Google Scholar 

  27. Sadeghian K, Bocola M, Schütz M (2008) A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors. J Am Chem Soc 130:12501–12513

    PubMed  CAS  Google Scholar 

  28. Sadeghian K, Bocola M, Schütz M (2010) A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form. Phys Chem Chem Phys 12:8840–8846

    PubMed  CAS  Google Scholar 

  29. Sadeghian K, Schütz M (2007) On the photophysics of artificial blue-light photoreceptors: an ab initio study on a flavin-based dye dyad at the level of coupled-cluster response theory. J Am Chem Soc 129:4068–4074

    PubMed  CAS  Google Scholar 

  30. Taylor WJ (1954) Distribution of kinetic and potential energy in vibrating molecules. J Chem Phys 22:1780

    CAS  Google Scholar 

  31. Pulay P, Fogarasi G (1992) Geometry optimization in redundant internal coordinates. J Chem Phys 96:2856–2860

    CAS  Google Scholar 

  32. Wolf MMN, Schumann C, Gross R, Domratcheva T, Diller R (2008) Ultrafast infrared spectroscopy of riboflavin: dynamics, electronic structure, and vibrational mode analysis. J Phys Chem B 112:13424–13432

    PubMed  CAS  Google Scholar 

  33. Wolf MMN, Zimmermann H, Diller R, Domratcheva T (2011) Vibrational mode analysis of isotope-labeled electronically excited riboflavin. J Phys Chem B 115:7621–7628

    PubMed  CAS  Google Scholar 

  34. Klaumünzer B, Kröner D, Saalfrank P (2010) (TD-)DFT calculation of vibrational and vibronic spectra of riboflavin in solution. J Phys Chem B 114:10826–10834

    PubMed  Google Scholar 

  35. Alexandre MTA, Domratcheva T, Bonetti C, van Wilderen LJGW, van Grondell R, Groot ML, Hellingwerf KJ, Kennis JTM (2009) Primary reactions of the LOV2 domain of phototropin studied with ultrafast mid-infrared spectroscopy and quantum chemistry. Biophys J 97:227–237

    PubMed Central  PubMed  CAS  Google Scholar 

  36. Martin CB, Shi XF, Tsao ML, Karweik D, Brooke J, Hadad CM, Platz MS (2002) The photochemistry of riboflavin tetraacetate and nucleosides. A study using density functional theory, laser flash photolysis, fluorescence, UV-vis, and time resolved infrared spectroscopy. J Phys Chem B 106:10263–10271

    CAS  Google Scholar 

  37. Martin CB, Tsao ML, Hadad CM, Platz MS (2002) The reaction of triplet flavin with indole. A study of the cascade of reactive intermediates using density functional theory and time resolved infrared spectroscopy. J Am Chem Soc 124:7226–7234

    PubMed  CAS  Google Scholar 

  38. Rieff B, Bauer S, Mathias G, Tavan P (2011) IR spectra of flavins in solution: DFT/MM description of redox effects. J Phys Chem B 115:2117–2123

    PubMed  CAS  Google Scholar 

  39. Unno M, Sano R, Masuda S, Ono TA, Yamauchi S (2005) Light-induced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy. J Phys Chem B 109:12620–12626

    PubMed  CAS  Google Scholar 

  40. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3094

    PubMed  CAS  Google Scholar 

  41. Klamt A, Schüürmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2:799–805

    Google Scholar 

  42. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227–249

    PubMed  CAS  Google Scholar 

  43. Rieff B, Bauer S, Mathias G, Tavan P (2011) DFT/MM description of flavin IR spectra in BLUF domains. J Phys Chem B 115:11239–11253

    PubMed  CAS  Google Scholar 

  44. Rieff B, Mathias G, Bauer S, Tavan P (2011) Density functional theory combined with molecular mechanics: the infrared spectra of flavin in solution. Photochem Photobiol 87:511–523

    PubMed  CAS  Google Scholar 

  45. Sikorska E, Khmelinskii I, Komasa A, Koput J, Ferreira LFV, Herance JR, Bourdelande JL, Williams SL, Worrall DR, Insinska-Rak M, Sikorski M (2005) Spectroscopy and photophysics of flavin related compounds: riboflavin and iso-(6,7)-riboflavin. Chem Phys 314:239–247

    CAS  Google Scholar 

  46. Zenichowski K, Gothe M, Saalfrank P (2007) Exciting flavins: absorption spectra and spin-orbit coupling in light-oxygen-voltage (LOV) domains. J Photochem Photobiol A Chem 190:290–300

    CAS  Google Scholar 

  47. Haigney A, Lukacs A, Zhao RK, Stelling AL, Brust R, Kim RR, Kondo M, Clark I, Towrie M, Greetham GM, Illarionov B, Bacher A, Römisch-Margl W, Fischer M, Meech SR, Tonge PJ (2011) Ultrafast infrared spectroscopy of an isotope-labeled photoactivatable flavoprotein. Biochemistry 50:1321–1328

    PubMed  CAS  Google Scholar 

  48. Merz T, Sadeghian K, Schütz M (2011) Why BLUF photoreceptors with roseoflavin cofactors lose their biological functionality. Phys Chem Chem Phys 13:14775–14783

    PubMed  CAS  Google Scholar 

  49. Choe YK, Nagase S, Nishimoto K (2007) Theoretical study of the electronic spectra of oxidized and reduced states of lumiflavin and its derivative. J Comput Chem 28:727–739

    PubMed  CAS  Google Scholar 

  50. Ghisla S, Massey V, Lhoste JM, Mayhew SG (1974) Fluorescence and optical characteristics of reduced flavins and flavoproteins. Biochemistry 13:589–597

    PubMed  CAS  Google Scholar 

  51. Walsh JD, Miller AF (2003) Flavin reduction potential tuning by substitution and bending. J Mol Struct Theochem 623:185–195

    CAS  Google Scholar 

  52. Harbach PHP, Borowka J, Bohnwagner MV, Dreuw A (2010) DNA (6-4) photolesion repair occurs in the electronic ground state of the TT dinucleotide dimer radical anion. J Phys Chem Lett 1:2556–2560

    CAS  Google Scholar 

  53. Sadeghian K, Bocola M, Merz T, Schütz M (2010) Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase. J Am Chem Soc 132:16285–16295

    PubMed  CAS  Google Scholar 

  54. Freddolino PL, Dittrich M, Schulten K (2006) Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophys J 91:3630–3639

    PubMed Central  PubMed  CAS  Google Scholar 

  55. Neiss C, Saalfrank P (2004) Molecular dynamics simulation of the LOV2 domain from Adiantum capillus-veneris. J Chem Inf Comput Sci 44:1788–1793

    PubMed  CAS  Google Scholar 

  56. Masson F, Laino T, Rothlisberger U, Hutter J (2009) A QM/MM investigation of thymine dimer radical anion splitting catalyzed by DNA photolyase. ChemPhysChem 10:400–410

    PubMed  CAS  Google Scholar 

  57. Condic-Jurkic K, Smith AS, Zipse H, Smith DM (2012) The protonation states of the active-site histidines in (6-4) photolyase. J Chem Theory Comput 8:1078–1091

    CAS  Google Scholar 

  58. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38

    PubMed  CAS  Google Scholar 

  59. 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 84:2474–2482

    PubMed Central  PubMed  CAS  Google Scholar 

  60. 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 phototropin 1 from Avena sativa. Biochemistry 46:14001–14009

    PubMed  CAS  Google Scholar 

  61. Crosson S, Moffat K (2002) Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell 14:1067–1075

    PubMed Central  PubMed  CAS  Google Scholar 

  62. Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM, Dunlap JC, Crane BR (2007) Conformational switching in the fungal light sensor vivid. Science 316:1054–1057

    PubMed Central  PubMed  CAS  Google Scholar 

  63. Salomon M, Lempert U, Rüdiger W (2004) Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain. FEBS Lett 572:8–10

    PubMed  CAS  Google Scholar 

  64. Harper SM, Neil LC, Gardner KH (2003) Structural basis of a phototropin light switch. Science 301:1541–1544

    PubMed  CAS  Google Scholar 

  65. Peter E, Dick B, Baeurle SA (2010) Mechanism of signal transduction of the LOV2-Jalpha photosensor from Avena sativa. Nat Commun 1:122

    PubMed  Google Scholar 

  66. Peter E, Dick B, Baeurle SA (2011) Effect of computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii. J Chem Biol 4:167–184

    PubMed Central  PubMed  Google Scholar 

  67. Peter E, Dick B, Baeurle SA (2012) Illuminating the early signaling pathway of a fungal light-oxygen-voltage photoreceptor. Proteins 80:471–481

    CAS  Google Scholar 

  68. Peter E, Dick B, Baeurle SA (2012) Signals of LOV1: a computer simulation study on the wildtype LOV1-domain of Chlamydomonas reinhardtii and its mutants. J Mol Model 18:1375–1388

    PubMed  CAS  Google Scholar 

  69. Peter E, Dick B, Baeurle SA (2012) Signaling pathway of a photoactivable Rac1-GTPase in the early stages. Proteins 80:1350–1362

    PubMed  CAS  Google Scholar 

  70. Lingenheil M, Denschlag R, Reichold R, Tavan P (2008) The “hot-solvent/cold-solute” problem revisited. J Chem Theory Comput 4:1293–1306

    CAS  Google Scholar 

  71. Lanzl K, Noll G, Dick B (2008) LOV1 protein from Chlamydomonas reinhardtii is a template for the photoadduct formation of FMN and methylmercaptane. ChemBioChem 9:861–864

    PubMed  CAS  Google Scholar 

  72. Lanzl K, von Sanden-Flohe M, Kutta RJ, Dick B (2010) Photoreaction of mutated LOV photoreceptor domains from Chlamydomonas reinhardtii with aliphatic mercaptans: implications for the mechanism of wild type LOV. Phys Chem Chem Phys 12:6594–6604

    PubMed  CAS  Google Scholar 

  73. Song SH, Freddolino PL, Nash AI, Carroll EC, Schulten K, Gardner KH, Larsen DS (2011) Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site. Biochemistry 50:2411–2423

    PubMed Central  PubMed  CAS  Google Scholar 

  74. Jung A, Reinstein J, Domratcheva T, Schoeman RL, Schlichting I (2006) Crystal structures of the AppA BLUF domain photoreceptor provide insights into blue light-mediated signal transduction. J Mol Biol 362:717–732

    PubMed  CAS  Google Scholar 

  75. Anderson S, Dragnea V, Masuda S, Ybe J, Moffat K, Bauer C (2005) Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides. Biochemistry 44:7998–8005

    PubMed Central  PubMed  CAS  Google Scholar 

  76. Lukacs A, Haigney A, Brust R, Zhao RK, Stelling AL, Clark IP, Towrie M, Greetham DM, Meech SR, Tonge PJ (2011) Photoexcitation of the blue light using FAD photoreceptor AppA results in ultrafast changes to the protein matrix. J Am Chem Soc 133:16893–16900

    PubMed  CAS  Google Scholar 

  77. Unno M, Masuda S, Ono TA, Yamauchi S (2006) Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations. J Am Chem Soc 128:5638–5639

    PubMed  CAS  Google Scholar 

  78. Unno M, Kikuchi S, Masuda S (2010) Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance Raman spectroscopy. Biophys J 98:1949–1956

    PubMed Central  PubMed  CAS  Google Scholar 

  79. Domratcheva T, Grigorenko BL, Schlichting I, Nemukhin AV (2008) Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors. Biophys J 94:3872–3879

    PubMed Central  PubMed  CAS  Google Scholar 

  80. Götze J, Saalfrank P (2009) Serine in BLUF domains displays spectral importance in computational models. J Photochem Photobiol B 94:87–95

    PubMed  Google Scholar 

  81. Khrenova MG, Domratcheva T, Schlichting I, Grigorenko BL, Nemukhin AV (2011) Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor. Photochem Photobiol 87:564–573

    PubMed  CAS  Google Scholar 

  82. Meier K, Thiel W, van Gunsteren WF (2012) On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations. J Comput Chem 33:363–378

    PubMed  CAS  Google Scholar 

  83. Obanayama K, Kobayashi H, Fukushima K, Sakurai M (2008) Structures of the chromophore binding sites in BLUF domains as studied by molecular dynamics and quantum chemical calculations. Photochem Photobiol 84:1003–1010

    PubMed  CAS  Google Scholar 

  84. Khrenova MG, Nemukhin AV, Domratcheva T (2013) Photoinduced electron transfer facilitates tautomerization of the conserved signaling glutamine side chain in BLUF protein light sensors. J Phys Chem B 117:2369–2377

    PubMed  CAS  Google Scholar 

  85. Iwata T, Watanabe A, Iseki M, Watanabe M, Kandori H (2011) Strong donation of the hydrogen bond of tyrosine during photoactivation of the BLUF domain. J Phys Chem Lett 2:1015–1019

    CAS  Google Scholar 

  86. Udvarhelyi A, Domratcheva T (2013) Glutamine rotamers in BLUF photoreceptors: a mechanistic reappraisal. J Phys Chem B 117:2888–2897

    PubMed  CAS  Google Scholar 

  87. Grinstead JS, Hsu S-TD, Laan W, Bonvin AMJJ, Hellingwerf KJ, Boelens R, Kaptein R (2006) The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling. ChemBioChem 7:187–193

    PubMed  CAS  Google Scholar 

  88. Jung A, Domratcheva T, Tarutina M, Wu Q, Ko WH, Shoeman RL, Gomelsky M, Gardner KH, Schlichting I (2005) Structure of a bacterial BLUF photoreceptor: insights into blue light-mediated signal transduction. Proc Natl Acad Sci U S A 102:12350–12355

    PubMed Central  PubMed  CAS  Google Scholar 

  89. El-Sayed MA (1968) Triplet state. Its radiative and nonradiative properties. Acc Chem Res 1:8–16

    CAS  Google Scholar 

  90. 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 84:1192–1201

    PubMed Central  PubMed  CAS  Google Scholar 

  91. 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 42:3385–3392

    PubMed  CAS  Google Scholar 

  92. 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 276:36493–36500

    PubMed  CAS  Google Scholar 

  93. 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 109:13006–13013

    PubMed Central  PubMed  CAS  Google Scholar 

  94. Gauden M, van Stokkum IHM, Key JM, Lührs DC, van Grondelle R, Hegemann P, Kennis JTM (2006) Hydrogen-bond switching through a radical pair mechanism in a flavin-binding photoreceptor. Proc Natl Acad Sci U S A 103:10895–10900

    PubMed Central  PubMed  CAS  Google Scholar 

  95. Bonetti C, Mathes T, van Stokkum IHM, Mullen KM, Groot ML, van Grondelle R, Hegemann P, Kennis JTM (2008) Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy. Biophys J 95:4790–4802

    PubMed Central  PubMed  CAS  Google Scholar 

  96. Stelling AL, Ronayne KL, Nappa J, Tonge PJ, Meech SR (2007) Ultrafast structural dynamics in BLUF domains: transient infrared spectroscopy of AppA and its mutants. J Am Chem Soc 129:15556–15564

    PubMed  CAS  Google Scholar 

  97. Bonetti C, Stierl M, Mathes T, van Stokkum IHM, Mullen KM, Cohen-Stuart TA, van Grondelle R, Hegemann P, Kennis JTM (2009) The role of key amino acids in the photoactivation pathway of the Synechocystis Slr1694 BLUF domain. Biochemistry 48:11458–11469

    PubMed  CAS  Google Scholar 

  98. Dragnea V, Arunkumar AI, Yuan H, Giedroc DP, Bauer CE (2009) Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: addressing movement of tryptophan 104 in the signaling state. Biochemistry 48:9969–9979

    PubMed Central  PubMed  CAS  Google Scholar 

  99. Izmaylov AF, Tully JC, Frisch MJ (2009) Relativistic interactions in the radical pair model of magnetic field sense in CRY-1 protein of Arabidopsis thaliana. J Phys Chem A 113:12276–12284

    PubMed  CAS  Google Scholar 

  100. Domratcheva T (2011) Neutral histidine and photoinduced electron transfer in DNA photolyases. J Am Chem Soc 133:18172–18182

    PubMed  CAS  Google Scholar 

  101. Toh KC, van Stokkum IHM, Hendriks J, Alexandre MTA, Arenths JC, Perez MA, van Grondelle R, Hellingwerf KJ, Kennis JTM (2008) On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain. Biophys J 95:312–321

    PubMed Central  PubMed  CAS  Google Scholar 

  102. Mathes T, van Stokkum IHM, Stierl M, Kennis JTM (2012) Redox modulation of flavin and tyrosine determines photoinduced proton-coupled electron transfer and photoactivation of BLUF photoreceptors. J Biol Chem 287:31725–31738

    PubMed Central  PubMed  CAS  Google Scholar 

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Acknowledgments

We are very grateful to Prof. Ilme Schlichting (Max Planck Institute for Medical Research, Heidelberg, Germany) for long-term collaboration and support. We also acknowledge financial support from the MPI Minerva program (to T.D.), the Boehringer Ingelheim Fonds (to A.U.), and BIOMS-Heidelberg (to A.R.M.S.).

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Authors and Affiliations

  1. Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany

    Tatiana Domratcheva, Anikó Udvarhelyi & Abdul Rehaman Moughal Shahi

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  1. Tatiana Domratcheva
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  2. Anikó Udvarhelyi
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  3. Abdul Rehaman Moughal Shahi
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Correspondence to Tatiana Domratcheva .

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  1. Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany

    Stefan Weber

  2. Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany

    Erik Schleicher

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Domratcheva, T., Udvarhelyi, A., Shahi, A.R.M. (2014). Computational Spectroscopy, Dynamics, and Photochemistry of Photosensory Flavoproteins. In: Weber, S., Schleicher, E. (eds) Flavins and Flavoproteins. Methods in Molecular Biology, vol 1146. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0452-5_10

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  • DOI: https://doi.org/10.1007/978-1-4939-0452-5_10

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