Journal of Molecular Modeling

, Volume 18, Issue 4, pp 1375–1388 | Cite as

Signals of LOV1: a computer simulation study on the wildtype LOV1-domain of Chlamydomonas reinhardtii and its mutants

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

Abstract

Phototropins are photoreceptors regulating the blue-light response in plants and bacteria. They consist of two LOV (light oxygen voltage sensitive) domains each containing a non-covalently bound flavin-mononucleotide (FMN) chromophore, which are connected to a serine/threonine-kinase. Upon illumination, the LOV-domains undergo conformational changes, triggering a signal cascade in the organism through kinase activation. Here, we present results from molecular dynamics simulations in which we investigate the signal transduction pathway of the wildtype LOV1-domain of Chlamydomonas reinhardtii and a methyl-mercaptan (MM) adduct of its Cys57Gly-mutant at the molecular level. In particular, we analyzed the effect of covalent-bond formation between the reactive cysteine Cys57 and the FMN-reaction center, as well as the subsequent charge redistribution, on the spatio-dynamical behavior of the LOV1-domain. We compare the calculation results with experimental data and demonstrate that these adduct state characteristics have an important influence on the response of this photosensor. The light-induced changes implicate primarily an alteration of the surface charge distribution through rearrangement of the highly flexible -, - and -helices including the Glu51-Lys91-salt bridge on the hydrophilic side of the protein domain and a β-sheet tightening process via coupling of the Aβ- and Bβ-strands. Our findings confirm the aptitude of the LOV1-domain to function as a dimerization partner, allowing the green alga to adapt its reproduction and growth speed to the environmental conditions.

Figure

This theoretical study elucidates the light-induced structural changes taking place in the LOV1-domain of Chlamydomonas reinhardtii after blue-light photoexcitation and confirms its aptitude to function as a dimerization partner

Keywords

LOV1-domain of Chlamydomonas reinhardtii Signal transduction mechanism Blue-light photoreceptor protein Phototropin Molecular dynamics simulation 

References

  1. 1.
    Scott JD, Pawson T (2009) Signaling through scaffold, anchoring, and adaptor proteins. Science 326:1220–1224CrossRefGoogle Scholar
  2. 2.
    Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM (2009) A genetically encoded photoactivable Rac controls the motility in living cells. Nature 461:104–108CrossRefGoogle Scholar
  3. 3.
    Kaganman I (2009) ’Blue’ lighting cell signaling research. Nat Methods 6:694–695CrossRefGoogle Scholar
  4. 4.
    Hegemann P (2008) Algal sensory photoreceptors. Annu Rev Plant Biol 59:167–189CrossRefGoogle Scholar
  5. 5.
    Christie JM (2007) Phototropin blue-light receptors. Annu Rev Plant Biol 58:21–45CrossRefGoogle Scholar
  6. 6.
    Briggs WR (2007) The LOV domain: a chromophore module servicing multiple pho-toreceptors. J Biomed Sci 14:499–504CrossRefGoogle Scholar
  7. 7.
    Kottke T, Hegemann P, Dick B, Heberle J (2006) The photochemistry of the LOV domains in the algal blue light receptor phot. Biopolymers 82:373–378CrossRefGoogle Scholar
  8. 8.
    Jones MA, Feeney KA, Kelly SM, Christie JM (2007) Mutational analysis of phototropin 1 provides insights into the mechanism underlying LOV2 signal transmission. J Biol Chem 282:6405–6414CrossRefGoogle Scholar
  9. 9.
    Harper SM, Neil LC, Gardner KH (2003) Structural basis of a phototropin light switch. Science 301:1541–1544CrossRefGoogle Scholar
  10. 10.
    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
  11. 11.
    Nakasako M, Iwata T, Matsuoka D, Tokutomi S (2004) Light-induced structural changes of LOV domain-containing polypeptides from Arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering. Biochemistry 43:14881–14890CrossRefGoogle Scholar
  12. 12.
    Briggs WR, Tseng T-S, Cho H-Y, Swartz TE, Sullivan S, Bogomolni RA, Kaiserli E, Christie JM (2007) Phototropins and their LOV domains: versatile plant blue-light receptors. J Integr Plant Biol 49:4–10CrossRefGoogle Scholar
  13. 13.
    Kutta RJ, Hofinger ESA, Preuss H, Bernhardt G, Dick B (2008) Blue-light induced in-teraction of LOV domains from Chlamydomonas reinhardtii. ChemBioChem 9:1931–1938CrossRefGoogle Scholar
  14. 14.
    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
  15. 15.
    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
  16. 16.
    Sullivan S, Thomson CE, Lamont DJ, Jones MA, Christie JM (2008) In vivo phosphorylation site mapping and functional characterization of Arabidopsis phototopin 1. Mol Plant 1:178–194CrossRefGoogle Scholar
  17. 17.
    Kaiserli E, Sullivan S, Jones MA, Feeney KA, Christie JM (2009) Domain swapping to assess the mechanistic basis of Arabidopsis phototropin 1 receptor kinase activation and endocytosis by blue light. Plant Cell 21:3226–3244CrossRefGoogle Scholar
  18. 18.
    Harper SM, Christie JM, Gardner KH (2004) Disruption of the LOV-Jα helix interaction activates phototropin kinase activity. Biochemistry 43:16184–16192CrossRefGoogle Scholar
  19. 19.
    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 46:14001–14009CrossRefGoogle Scholar
  20. 20.
    Nash AI, Ko W-H, Harper SM, Gardner KH (2008) A conserved glutamine plays a central role in LOV domain signal transmission and its duration. Biochemistry 47:13842–13849CrossRefGoogle Scholar
  21. 21.
    Peter E, Dick B, Baeurle SA (2010) Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa. Nat Commun 1:122CrossRefGoogle Scholar
  22. 22.
    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
  23. 23.
    Lanzl K, Nöll G, Dick B (2008) LOV1 protein from Chlamydomonas reinhardtii is a template for the photoadduct formation of FMN and methylmercaptan. ChemBioChem 9:861–864CrossRefGoogle Scholar
  24. 24.
    Lanzl K, von Sanden-Flohe M, Kutta R-J, Dick B (2010) Photoreaction of mutated LOV photoreceptor domains from Chlamydomonas reinhardtii with aliphatic mercap-tans: implications for the mechanism of wild type LOV. Phys Chem Chem Phys 12:6594–6604CrossRefGoogle Scholar
  25. 25.
    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
  26. 26.
    Ataka K, Hegemann P, Heberle J (2003) Vibrational spectroscopy of an algal phot-LOV1 domain probes the molecular changes associated with blue-light reception. Biophys J 84:466–474CrossRefGoogle Scholar
  27. 27.
    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
  28. 28.
    Guo H, Kottke T, Hegemann P, Dick B (2005) The phot LOV2 domain and its interaction with LOV1. Biophys J 89:402–412CrossRefGoogle Scholar
  29. 29.
    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
  30. 30.
    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
  31. 31.
    Freddolino PL, Dittrich M, Schulten K (2006) Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophys J 91:3630–3639CrossRefGoogle Scholar
  32. 32.
    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
  33. 33.
    Soares T, Daura X, Oostenbrink C, Smith L, Gunsteren W (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
  34. 34.
    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
  35. 35.
    Frenkel D, Smit B (2003) Understanding molecular simulation: from algorithms to applications. Academic, San DiegoGoogle Scholar
  36. 36.
    Peter E, Dick B, Baeurle SA (2011) Effect of the computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii. J Chem Biol. doi:10.1007/s12154-011-0060-z
  37. 37.
    Neiss C, Saalfrank P (2004) Molecular dynamics simulation of the LOV2 domain from Adiantum capillus-veneris. J Chem Inf Comput Sci 44:1788–1793CrossRefGoogle Scholar
  38. 38.
    Tatke SS, Loong CK, D’Souza N, Schoephoerster RT, Prabhakaran M (2008) Large scale motions in a biosensor protein glucose oxidase: a combined approach by QENS, normal mode analysis, and molecular dynamics studies. Biopolymers 89:582–594CrossRefGoogle Scholar
  39. 39.
    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
  40. 40.
    Crosson S, Rajagopal S, Moffat K (2003) The LOV domain family: photoresponsive signaling modules coupled to diverse output domains. Biochemistry 42:2–10CrossRefGoogle Scholar
  41. 41.
    Yao X, Rosen MK, Gardner KH (2008) Estimation of the available free energy in a LOV2-Jα photoswitch. Nat Chem Biol 4:491–497CrossRefGoogle Scholar
  42. 42.
    Vendruscolo M (2008) Protein dynamics under light control. Nat Chem Biol 4:449–450CrossRefGoogle Scholar
  43. 43.
    Matsuoka D, Tokutomi S (2005) Blue light-regulated molecular switch of Ser/Thr kinase in phototropin. Proc Natl Acad Sci USA 102:13337–13342CrossRefGoogle Scholar
  44. 44.
    Huang K, Beck CF (2003) Phototropin is the blue-light receptor that controls multiple steps in the sexual life cycle of the green alga Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 100:6269–6274CrossRefGoogle Scholar
  45. 45.
    Khrenova M, Domratcheva T, Grigorenko B, Nemukhin A (2011) Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1. J Mol Model 17:1579–1578. doi:10.1007/s00894-010-0842-1 Google Scholar
  46. 46.
    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
  47. 47.
    Cho H-Y, Tseng T-S, Kaiserli E, Sullivan S, Christie JM, Briggs WR (2007) Physiological roles of the light, oxygen, or voltage domains of phototropin 1 and phototropin 2 in Arabidopsis. Plant Physiol 143:517–529CrossRefGoogle Scholar
  48. 48.
    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 UVvisible spectroscopy. Biochemistry 42:8183–8191CrossRefGoogle Scholar
  49. 49.
    Möglich A, Ayers RA, Moffat K (2009) Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17:1282–1294CrossRefGoogle Scholar
  50. 50.
    Hahn K, Kuhlman B (2010) Hold me tightly LOV. Nat Methods 7:595–597CrossRefGoogle Scholar
  51. 51.
    Strickland D, Yao X, Gawlak G, Rosen MK, Gardner KH, Sosnick TR (2010) Rationally improving LOV domain-based photoswitches. Nat Methods 7:623–626CrossRefGoogle Scholar
  52. 52.
    Strickland D, Moffat K, Sosnick TR (2008) Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci USA 105:10709–10714CrossRefGoogle 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