Theoretical prediction of the protein-protein interaction between Arabidopsis thaliana COP1 and UVR8

Theoretical Chemistry Accounts

Volumn 132, Issue 7, 2013, Pages 1-11

  Wu, Min ^a   Eriksson, Leif A ^a   Strid, Åke ^b  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b ÖREBRO UNIVERSITY   (Sweden)

Author keywords

Arabidopsis thaliana; COP1; Docking; Modeling; Mutation; Protein protein interaction; UVR8; WD40

Indexed keywords

EID: 84877088330     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-013-1371-7     Document Type: Article

References (45)

1. Hideg É, Jansen MAK, Strid Å.(2012)UV-Bexposure,ROSand stress: inseparable companions or loosely linked associates? Trends Plant Sci, in press. doi: 10.1021/ci300264u
2. Jansen MAK, Coffey AM, Prinsen E (2012) UV-B induced morphogenesis: four players or a quartet? Plant Signal Behav 7:1185-1187
3. Favory JJ, Stec A, Gruber H, Rizzini L, Oravecz A, Funk M, Albert A, Cloix C, Jenkins GI, Oakeley EJ et al (2009) Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J 28:591-601
4. Rizzini L, Favory JJ, Cloix C, Faggionato D, O'Hara A, Kaiserli E, Baumeister R, Schäfer E, Nagy F, Jenkins GI et al (2011) Perception of UV-B by the Arabidopsis UVR8 protein. Science 332:103-106
5. Brown BA, Cloix C, Jiang GH, Kaiserli E, Herzyk P, Kliebenstein DJ, Jenkins GI (2005) A UV-B-specific signaling compoent orchestrates plant UV protection. Proc Natl Acad Sci USA 102:18225-18230
6. Brown BA, Jenkins GI (2008) UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH. Plant Physiol 146:576-588
7. Kaiserli E, Jenkins GI (2007) UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus. Plant Cell 19:2662-2673
8. Jenkins GI (2009) Signal transduction in responses to UV-B radiation. Annu Rev Plant Biol 60:407-431
9. Wu M, Grahn E, Eriksson LA, Strid (2011) Computational Evidence for the role of Arabidopsis thaliana UVR8 as UV-B photoreceptor and identification of its chromophore amino acids. J Chem Inf Model 51:1287-1295
10. Christie JM, Arvai AS, Baxter KJ, Heilmann M, Pratt AJ, O'Hara A, Kelly SM, Hothorn M, Smith BO, Hitomi K et al (2012) Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335:1492-1496
11. Wu D, Hu Q, Yan Z, Chen W, Yan C, Huang X, Zhang J, Yang P, Deng H, Wang J et al (2012) Structural basis of ultraviolet-B perception by UVR8. Nature 484:214-419
12. Cloix C, Kaiserli E, Heilmann M, Baxter KJ, Brown BA, O'Hara A, Smith BO, Christie JM, Jenkins GI (2012) C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein. Proc Natl Acad Sci USA 109:16366-16370
13. Yi C, Deng XW (2005) COP1-from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol 15:618-625
14. Oravecz A, Baumann A, Máté Z, Brzezinska A, Molinier J, Oakeley EJ, Adám E, Schäfer E, Nagy F, Ulm R (2006) CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis. Plant Cell 18:1975-1990
15. Ang LH, Deng XW (1994) Regulatory hierarchy of photomorphogenic loci: allele-specific and light-dependent interaction between the HY5 and COP1 loci. Plant Cell 6:613-628
16. McNellis TW, von Arnim AG, Araki T, Komeda Y, Miséra S, Deng XW (1994) Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6:487-500
17. McNellis TW, von Arnim AG, Deng XW (1994) Overexpression of Arabidopsis COP1 results in partial suppression of lightmediated development: evidence for a light-inactivable repressor of photomorphogenesis. Plant Cell 6:1391-1400
18. Deng XW, Matsui M, Wei N, Wagner D, Chu AM, Feldmann KA, Quail PH (1992) COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G beta homologous domain. Cell 71:791-801
19. Laubinger S, Fittinghoff K, Hoecker U (2004) The SPA quartet: a family of WD-repeat proteins with a central role in suppression of photomorphogenesis in arabidopsis. Plant Cell 16:2293-2306
20. Holm M, Ma LG, Qu LJ, Deng XW (2002) Two interacting bZIP proteins are direct targets of COP1-mediated control of lightdependent gene expression in Arabidopsis. Genes Dev 16:1247-1259
21. Yang HQ, Tang RH, Cashmore AR (2001) The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1. Plant Cell 13:2573-2587
22. Holm M, Hardtke CS, Gaudet R, Deng XW (2001) Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 20:118-127
23. Paoli M (2001) Protein folds propelled by diversity. Prog Biophys Mol Biol 76:103-130
24. Fong HK, Hurley JB, Hopkins RS, Miake-Lye R, Johnson MS, Doolittle RF, Simon MI (1986) Repetitive segmental structure of the transducin beta subunit: homology with the CDC4 gene and identification of related mRNAs. Proc Natl Acad Sci USA 83:2162-2166
25. Paroush Z, Finley RL Jr, Kidd T, Wainwright SM, Ingham PW, Brent R, Ish-Horowicz D (1994) Groucho is required for Drosophila neurogenesis, segmentation, and sex determination and interacts directly with hairy-related bHLH proteins. Cell 79:805-815
26. Altschul SF, Madden TL, Schaffer AA, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
27. Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with YASARA NOVA: a selfparameterizing force field. Proteins 47:393-402
28. Song JJ, Kingston RE (2008) WDR5 interacts with mixed lineage leukemia (MLL) protein via the histone H3-binding pocket. J Biol Chem 283:35258-35264
29. Schuetz A, Allali-Hassani A, Martin F, Loppnau P, Vedadi M, Bochkarev A, Plotnikov AN, Arrowsmith CH, Min J (2006) Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J 25:4245-4252
30. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447
31. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T et al (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999-2012
32. York DM, Darden TA, Pedersen LG (1993) The effect of long electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J Chem Phys 99:8345-8348
33. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593
34. Parrinello M, Rahman A (1981) Polymorphic transitions in single-crystals: a new molecular-dynamics method. J Appl Phys 52:7182-7190
35. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463-1472
36. Molecular Operating Environment, MOE 2011.10 (2012) Chemical Computing Group, Montreal, Canada
37. Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulate annealing and Bayesian scoring functions. J Mol Biol 268:209-225
38. Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34:82-95
39. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D (2001) Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins suppl 5:119-126
40. Robetta server: http://robetta.bakerlab.org/
41. Edelsbrunner H (1995) Weighted Alpha Shapes; technical paper of the Department of Computational Science. University of Illinois, Champaign
42. Corbeil CR, Williams CI, Labute P (2012) Variability in docking success rates due to dataset preparation. J Comput Aid Mol Des 26:775-786
43. Valeyev NV, Downing AK, Sondek J, Deane C (2008) Electrostatic and functional analysis of the seven-bladed WD b-propellers. Evol Bioinform 4:203-216
44. Lovell SC, Davis IW, Arendall WB III, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2002) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50:437-450
45. Hardtke CS, Gohda K, Osterlund MT, Oyama T, Okada K, Deng XW (2000) HY5 stability and activity in Arabidopsis is regulated by phosphorylation in its COP1 binding domain. EMBO J 19:4997-5006