Light-induced differences in conformational dynamics of the circadian clock regulator VIVID

Journal of Molecular Biology

Volumn 426, Issue 3, 2014, Pages 601-610

  Lee, Chung Tien ^a,c   Malzahn, Erik ^b   Brunner, Michael ^b   Mayer, Matthias P ^a  

^a GERMAN CANCER RESEARCH CENTER   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

circadian regulator; conformational equilibrium; dynamics; EX1

Indexed keywords

AMIDE; DIMER; LIGHT OXYGEN VOLTAGE DOMAIN PROTEIN; MONOMER; PHOTOACTIVE YELLOW PROTEIN; PROTON; SOLVENT; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; PROTEIN; PROTEIN VIVID;

ARTICLE; BLUE LIGHT; CIRCADIAN RHYTHM; CONFORMATIONAL TRANSITION; DIMERIZATION; LIGHT DARK CYCLE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN REFOLDING; PROTEIN UNFOLDING; AMINO ACID SEQUENCE; CIRCULAR DICHROISM; CONTROLLED STUDY; EX1 MECHANISM; HYDROGEN EXCHANGE MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN LOCALIZATION;

NEUROSPORA;

CIRCADIAN REGULATOR; CONFORMATIONAL EQUILIBRIUM; DYNAMICS; EX1; HX; HYDROGEN ((1)H/(2)H) EXCHANGE; MASS SPECTROMETRY; MS; PHOTOACTIVE YELLOW PROTEIN; PYP;

AMINO ACID SEQUENCE; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; FUNGAL PROTEINS; LIGHT; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUROSPORA CRASSA; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY;

EID: 84892498764     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.10.035     Document Type: Article

References (36)

1. B.L. Taylor, and I.B. Zhulin PAS domains: internal sensors of oxygen, redox potential, and light Microbiol Mol Biol Rev 63 1999 479 506
2. R.A. Ayers, and K. Moffat Changes in quaternary structure in the signaling mechanisms of PAS domains Biochemistry 47 2008 12078 12086
3. A. Möglich, R.A. Ayers, and K. Moffat Structure and signaling mechanism of Per-ARNT-Sim domains Structure 17 2009 1282 1294
4. S. Crosson, and K. Moffat Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch Plant Cell 14 2002 1067 1075
5. J.M. Christie Phototropin blue-light receptors Annu Rev Plant Biol 58 2007 21 45
6. B.D. Zoltowski, A.I. Nash, and K.H. Gardner Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay Biochemistry 50 2011 8771 8779
7. J.L. Pellequer, K.A. Wager-Smith, S.A. Kay, and E.D. Getzoff Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily Proc Natl Acad Sci USA 95 1998 5884 5890
8. P. Ballario, C. Talora, D. Galli, H. Linden, and G. Macino Roles in dimerization and blue light photoresponse of the PAS and LOV domains of Neurospora crassa white collar proteins Mol Microbiol 29 1998 719 729
9. C. Schwerdtfeger, and H. Linden Blue light adaptation and desensitization of light signal transduction in Neurospora crassa Mol Microbiol 39 2001 1080 1087
10. C. Schwerdtfeger, and H. Linden VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation EMBO J 22 2003 4846 4855
11. C. Heintzen, J.J. Loros, and J.C. Dunlap The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting Cell 104 2001 453 464
12. P. Cheng, Q. He, Y. Yang, L. Wang, and Y. Liu Functional conservation of light, oxygen, or voltage domains in light sensing Proc Natl Acad Sci USA 100 2003 5938 5943
13. E. Malzahn, S. Ciprianidis, K. Káldi, T. Schafmeier, and M. Brunner Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains Cell 142 2010 762 772
14. B.D. Zoltowski, and B.R. Crane Light activation of the LOV protein vivid generates a rapidly exchanging dimer Biochemistry 47 2008 7012 7019
15. B.D. Zoltowski, C. Schwerdtfeger, J. Widom, J.J. Loros, A.M. Bilwes, and J.C. Dunlap et al. Conformational switching in the fungal light sensor Vivid Science 316 2007 1054 1057
16. A.T. Vaidya, C.-H. Chen, J.C. Dunlap, J.J. Loros, and B.R. Crane Structure of a light-activated LOV protein dimer that regulates transcription Sci Signaling 4 2011 ra50
17. J.S. Lamb, B.D. Zoltowski, S.A. Pabit, B.R. Crane, and L. Pollack Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle X-ray scattering J Am Chem Soc 130 2008 12226 12227
18. J.S. Lamb, B.D. Zoltowski, S.A. Pabit, L. Li, B.R. Crane, and L. Pollack Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering J Mol Biol 393 2009 909 919
19. T.E. Wales, and J.R. Engen Hydrogen exchange mass spectrometry for the analysis of protein dynamics Mass Spectrom Rev 25 2006 158 170
20. A.N. Hoofnagle, K.A. Resing, and N.G. Ahn Protein analysis by hydrogen exchange mass spectrometry Annu Rev Biophys Biomol Struct 32 2003 1 25
21. R. Brudler, C.R. Gessner, S. Li, S. Tyndall, E.D. Getzoff, and V.L. Woods PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry J Mol Biol 363 2006 148 160
22. W. Rist, T.J.D. Jørgensen, P. Roepstorff, B. Bukau, and M.P. Mayer Mapping temperature-induced conformational changes in the Escherichia coli heat shock transcription factor sigma 32 by amide hydrogen exchange J Biol Chem 278 2003 51415 51421
23. W. Rist, M.P. Mayer, J.S. Andersen, P. Roepstorff, and T.J.D. Jørgensen Rapid desalting of protein samples for on-line microflow electrospray ionization mass spectrometry Anal Biochem 342 2005 160 162
24. B.A. Krantz, L.B. Moran, A. Kentsis, and T.R. Sosnick D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding Nat Struct Biol 7 2000 62 71
25. M.J. Parker, and A.R. Clarke Amide backbone and water-related H/D isotope effects on the dynamics of a protein folding reaction Biochemistry 36 1997 5786 5794
26. D.D. Weis, T.E. Wales, J.R. Engen, M. Hotchko, and L.F. Eyck Ten Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis J Am Soc Mass Spectrom 17 2006 1498 1509
27. A. Kreshuk, M. Stankiewicz, X. Lou, M. Kirchner, F.A. Hamprecht, and M.P. Mayer Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon Int J Mass Spectrom 302 2011 125 131
28. I.A. Kaltashov, and S.J. Eyles Mass spectrometry in biophysics: conformation and dynamics of biomolecules 2005 John Wiley & Sons, Inc. New Jersey
29. S.M. Hunt, M. Elvin, S.K. Crosthwaite, and C. Heintzen The PAS/LOV protein VIVID controls temperature compensation of circadian clock phase and development in Neurospora crassa Genes Dev 21 2007 1964 1974
30. M. Vendruscolo, T.P.J. Knowles, and C.M. Dobson Protein solubility and protein homeostasis: a generic view of protein misfolding disorders Cold Spring Harbor Perspect Biol 3 2011 10.1101/cshperspect.a010454
31. F.U. Hartl, A. Bracher, and M. Hayer-Hartl Molecular chaperones in protein folding and proteostasis Nature 475 2011 324 332
32. G. Rubinstenn, G.W. Vuister, F.A. Mulder, P.E. Düx, R. Boelens, and K.J. Hellingwerf et al. Structural and dynamic changes of photoactive yellow protein during its photocycle in solution Nat Struct Biol 5 1998 568 570
33. S.M. Harper, L.C. Neil, and K.H. Gardner Structural basis of a phototropin light switch Science 301 2003 1541 1544
34. A.I. Nash, R. McNulty, M.E. Shillito, T.E. Swartz, R.A. Bogomolni, and H. Luecke et al. Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein Proc Natl Acad Sci 108 2011 9449 9454
35. W. Rist, C. Graf, B. Bukau, and M.P. Mayer Amide hydrogen exchange reveals conformational changes in hsp70 chaperones important for allosteric regulation J Biol Chem 281 2006 16493 16501
36. C. Graf, M. Stankiewicz, G. Kramer, and M.P. Mayer Spatially and kinetically resolved changes in the conformational dynamics of the Hsp90 chaperone machine EMBO J 28 2009 602 613