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Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

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Abstract

The first biochemical and structural characterization of the full-length active photoreceptor BlrP1 from Klebsiella pneumoniae was recently reported by Barends et al. [Nature 459:1015–1018, (2009)]. The light-regulated catalytic function of its C-terminal c-di-guanosine monophosphate phosphodiesterase, the EAL (Glu-Ala-Leu) domain, is activated by the N-terminal sensor of blue light using the flavin adenine dinucleotide (BLUF) domain. We performed molecular dynamics simulations on the dimeric BlrP1 protein in order to examine the coupling regions that are presumably involved in transmitting light-induced structural changes which occur in the BLUF domain to the EAL domain. According to the results of simulations and an analysis of the hydrogen bonding between the respective polypeptide chains, the region containing the site on the α3α4 loop of BLUF is responsible for communication between the photosensing and catalytic domains in the dimeric BlrP1 protein.

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References

  1. Jenal U, Malone J (2006) Annu Rev Genet 40:385–407

    Article  CAS  Google Scholar 

  2. Tarutina M, Ryjenkov DA, Gomelsky M (2006) J Biol Chem 281:34751–34758

    Article  CAS  Google Scholar 

  3. Römling U, Amikam D (2006) Curr Opin Microbiol 9:218–228

    Article  Google Scholar 

  4. Cotter PA, Stibitz S (2007) Curr Opin Microbiol 10:17–23

    Article  CAS  Google Scholar 

  5. Römling U, Gomelsky M, Galperin MY (2007) Mol Microbiol 57:629–639

    Article  Google Scholar 

  6. Hisert KB, MacCoss M, Shiloh MU, Darwin KH, Singh S, Jones RA, Ehrt S, Zhang Z, Gaffney BL, Gandotra S, Holden DW, Murray D, Nathan C (2005) Mol Microbiol 56:1234–1245

    Article  CAS  Google Scholar 

  7. Hoffman LR, D'Argenio DA, MacCoss MJ, Zhang Z, Jones RA, Miller SI (2005) Nature 436:1171–1175

    Article  CAS  Google Scholar 

  8. Kulasakara H, Lee V, Brencic A, Liberati N, Urbach J, Miyata S, Lee DG, Neely AN, Hyodo M, Hayakawa Y, Ausubel FM, Lory S (2006) Proc Natl Acad Sci USA 103:2839–2844

    Article  Google Scholar 

  9. Schmidt AJ, Ryjenkov DA, Gomelsky M (2005) J Bacteriol 187:4774–4781

    Article  CAS  Google Scholar 

  10. Rao F, Yang Y, Qi Y, Liang Z-X (2008) J Bacteriol 190:3622–3631

    Article  CAS  Google Scholar 

  11. Barends TR, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I (2009) Nature 459:1015–1018

    Article  CAS  Google Scholar 

  12. Gomelsky M, Klug G (2002) Trends Biochem Sci 27:497–500

    Article  CAS  Google Scholar 

  13. Jung A, Domratcheva T, Tarutina M, Wu Q, Ko W-H, Shoeman RL, Gomelsky M, Gardner KH, Schlichting I (2005) Proc Natl Acad Sci USA 102:12350–12355

    Article  CAS  Google Scholar 

  14. Jung A, Reinstein J, Domratcheva T, Shoeman RL, Schlichting I (2006) J Mol Biol 362:717–732

    Article  CAS  Google Scholar 

  15. Anderson S, Dragnea V, Masuda S, Ybe J, Moffat K, Bauer C (2005) Biochemistry 44:7998–8005

    Article  CAS  Google Scholar 

  16. Kita A, Okajima K, Morimoto Y, Ikeuchi M, Miki K (2005) J Mol Biol 349:1–9

    Article  CAS  Google Scholar 

  17. Yuan H, Anderson S, Masuda S, Dragnea V, Moffat K, Bauer C (2006) Biochemistry 45:12687–12694

    Article  CAS  Google Scholar 

  18. Tyagi A, Penzkofer A, Griese J, Schlichting I, Kirienko NV, Gomelsky M (2008) Chem Phys 354:130–141

    Article  CAS  Google Scholar 

  19. Gomelsky M, Kaplan S (1998) J Biol Chem 273:35319–35325

    Article  CAS  Google Scholar 

  20. Domratcheva T, Grigorenko BL, Schlichting I, Nemukhin AV (2008) Biophys J 94:3872–3879

    Article  CAS  Google Scholar 

  21. Gauden M, van Stokkum IH, Key JM, Lührs DC, van Grondelle R, Hegemann P, Kennis JT (2006) Proc Natl Acad Sci USA 103:10895–10900

    Article  CAS  Google Scholar 

  22. Wu Q, Ko WH, Gardner KH (2008) Biochemistry 47:10271–10280

    Article  CAS  Google Scholar 

  23. Schroeder C, Werner K, Otten H, Krätzig S, Schwalbe H, Essen L-O (2008) ChemBioChem 9:2463–2473

    Article  CAS  Google Scholar 

  24. Wu Q, Gardner KH (2009) Biochemistry 48:2620–2629

    Article  CAS  Google Scholar 

  25. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) J Comput Chem 26:1781–1802

    Article  CAS  Google Scholar 

  26. Wang J, Wang W, Kollman PA, Case DA (2006) J Mol Graphics 25:247–260

    Article  Google Scholar 

  27. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25:1157–1174

    Article  CAS  Google Scholar 

  28. Humphrey W, Dalke A, Schulten K (1996) J Molec Graphics 14:33–38

    Article  CAS  Google Scholar 

  29. McDonald IK, Thornton JM (1994) J Mol Biol 238:777–793

    Article  CAS  Google Scholar 

  30. Torshin IY, Weber IT, Harrison RW (2002) Protein Eng 15:359–363

    Google Scholar 

  31. Fabiola F, Bertran R, Korostelev A, Chapman MS (2002) Protein Sci 11:1415–1423

    Article  CAS  Google Scholar 

  32. Aakeröy KB, Evans TA, Seddon KR, Pálinkó I (1999) New J Chem 23:145–152

    Google Scholar 

  33. Rao F, Qi Y, Chong HS, Kotaka M, Li B, Li J, Lescar J, Tang K, Liang Z-X (2009) J Bacteriol 191:4722–4731

    Article  CAS  Google Scholar 

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Acknowledgments

We are very grateful to Dr. Ilme Schlichting for helpful discussions. This work was supported in part by grants from the Deutsche Forschungsgemeinschaft FOR526 and from the Russian Foundation for Basic Research (project no. 10-03-00139). The Russian team is grateful for the use of the facilities of the supercomputing complex of the Research Computing Center of M.V. Lomonosov Moscow State University and the SKIF-GRID program for providing computational resources.

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Authors and Affiliations

  1. Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation

    Maria Khrenova, Bella Grigorenko & Alexander Nemukhin

  2. Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany

    Tatiana Domratcheva

  3. N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation

    Alexander Nemukhin

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  1. Maria Khrenova
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  2. Tatiana Domratcheva
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  3. Bella Grigorenko
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  4. Alexander Nemukhin
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Correspondence to Alexander Nemukhin.

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Khrenova, M., Domratcheva, T., Grigorenko, B. et al. Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1. J Mol Model 17, 1579–1586 (2011). https://doi.org/10.1007/s00894-010-0842-1

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  • DOI: https://doi.org/10.1007/s00894-010-0842-1

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