Photoactive yellow protein terahertz response: Hydration, heating and intermediate states

IEEE Transactions on Terahertz Science and Technology

Volumn 3, Issue 3, 2013, Pages 288-294

  George, Deepu K ^a   Knab, Joseph R ^a,b   He, Yunfen ^a,c   Kumauchi, Masato ^d   Birge, Robert R ^e   Hoff, Wouter D ^d   Markelz, Andrea G ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^c Shanghai ChemPartner Co Ltd   (China)

^d OKLAHOMA STATE UNIVERSITY   (United States)

^e UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Conformational change; hydration; normal mode analysis; photo cycling; photoactive yellow protein (PYP); principal component analysis; protein dynamics; protein structure; terahertz (THz)

Indexed keywords

CONFORMATIONAL CHANGE; NORMAL MODE ANALYSIS; PHOTO CYCLING; PHOTOACTIVE YELLOW PROTEINS; PROTEIN DYNAMICS; PROTEIN STRUCTURES; TERAHERTZ;

DEHYDRATION; EXCITED STATES; HYDRATION; PRINCIPAL COMPONENT ANALYSIS;

PROTEINS;

EID: 84877583350     PISSN: 2156342X     EISSN: None     Source Type: Journal    
DOI: 10.1109/TTHZ.2013.2256233     Document Type: Article

References (34)

1. H. J. Berendsen and S. Hayward, "Collective protein dynamics in relation to function," CurrentOpinion in Struct. Biol., vol. 10, pp. 165-169, 2000. (Pubitemid 30198942)
2. F. G. Parak, "Physical aspects of protein dynamics," Rep. Prog. Phys., vol. 66, pp. 103-129, 2003. (Pubitemid 36290403)
3. E. Balog, T. Becker,M. Oettl, R. Lechner, R. Daniel, J. Finney, and J. C. Smith, "Direct determination of vibrational density of states change on ligand binding to a protein," Phys. Rev. Lett., vol. 93, p. 28103, 2004.
4. E. Balog, D. Perahia, J. C. Smith, and F. Merzel, "Vibrational softening of a protein on ligand binding," J. Phys. Chem. B, vol. 115, pp. 6811-6817, 2011.
5. A. H. Xie, A. F.G.V.D. Meer, and R. H. Austin, "Excited-state lifetimes of far-infrared collective modes in proteins," Phys. Rev. Lett., vol. 88, p. 018102, 2002.
6. I. Bahar and A. J. Rader, "Coarse-grained normal mode analysis in structural biology," Current Opinion in Structural Biology, vol. 15, pp. 586-592, 2005. (Pubitemid 41393491)
7. F. Gabel, M. Weik, P. Masson, F. Renault, D. Fournier, L. Brochier, B. P. Doctor, A. Saxena, I. Silman, and G. Zaccai, "Effects of Soman Inhibition and of structural differences on cholinesterase molecular dynamics: A neutron scattering study," Biophys. J., vol. 89, pp. 3303-3311, 2005. (Pubitemid 41636085)
8. M. Brucherseifer,M. Nagel, P. H. Bolivar, H. Kurz,A.Bosserhoff, and R. Buttner, "Label-free probing of the binding state of DNA by timedomain terahertz sensing," Appl. Phys. Lett., vol. 77, pp. 4049-4051, 2000.
9. A. Menikh, S. P. Mickan, H. Liu, R. MacColl, and X.-C. Zhang, "Label-free amplified bioaffinity detection using terahertz wave technology," Biosensors & Bioelectron., vol. 20, pp. 658-662, 2004. (Pubitemid 39445782)
10. J.-Y. Chen, J. R. Knab, S. Ye, Y. He, and A. G. Markelz, "Terahertz Dielectric Assay of Solution Phase Protein Binding," Appl. Phys. Lett., vol. 90, p. 243901, 2007.
11. S. E. Whitmire, D. Wolpert, A. G. Markelz, J. R. Hillebrecht, J. Galan, and R. R. Birge, "Protein flexibility and conformational state: A comparison of collective vibrational modes of WT and D96N bacteriorhodopsin, " Biophys. J., vol. 85, pp. 1269-1277, 2003. (Pubitemid 36909687)
12. J. Knab, J.-Y. Chen, and A. Markelz, "Hydration dependence of conformational dielectric relaxation of lysozyme," Biophys. J., vol. 90, pp. 2576-2581, 2006.
13. T. E. Meyer, E. Yakali, M. A. Cusanovich, and G. Tollin, "Properties of a water soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin," Biochemistry, vol. 26, pp. 418-23, 1987. (Pubitemid 17022111)
14. W. W. Sprenger, W. D. Hoff, J. P. Armitage, and K. J. Hellingwerf, "The Eubacterium Ectothiorhodospira-Halophila Is Negatively Phototactic, with a Wavelength Dependence That Fits the Absorption-Spectrum of the Photoactive Yellow Protein," J. Bacteriol., vol. 175, pp. 3096-3104, May 1993. (Pubitemid 23148746)
15. A. H. Xie, W. D. Hoff, A. R. Kroon, and K. J. Hellingwerf, "Glu46 donates a proton to the 4-hydroxycinnamate anion chromophore during the photocycle of photoactive yellow protein," Biochem., vol. 35, pp. 14671-14678, Nov 26, 1996. (Pubitemid 26423797)
16. B.-C. Lee, A. Pandit, P. A. Croonquist, and W. D. Hoff, "Folding and signaling share the same pathway in a photoreceptor," Proc. Nat. Acad Sci. U.S.A., vol. 98, pp. 9062-67, 2001. (Pubitemid 32743869)
17. B.-C. Lee, P. A. Croonquist, T. R. Sosnick, and W. D. Hoff, "PAS Domain Receptor Photoactive Yellow Protein Is Converted to a Molten Globule State upon Activation," J. Biol. Chem., vol. 276, pp. 20821-20823, 2001.
18. M. A. van der Horst, I. H. M. van Stokkum, N. A. Dencher, and K. J. Hellingwerf, "Controlled reduction of the humidity induces a shortcut recovery reaction in the photocycle of photoactive yellow protein," Biochemistry, vol. 44, pp. 9160-9167, 2005\. (Pubitemid 40943230)
19. E. Castro-Camus and M. B. Johnston, "Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy," Chem. Phys. Lett., vol. 455, pp. 289-292, 2008.
20. D. Grischkowsky, S. Keiding, M. van Exter, and C. Fattinger, "Far-infrared time-domain spectroscopy with terahertz beams of dielectrics and semiconductors," J. Opt. Soc. Amer. B: Opt. Phys., vol. 7, pp. 2006-2015, 1990.
21. Q. Wu and X.-C. Zhang, "Free-space electro-optic sampling of terahertz beams," Appl. Phys. Lett., vol. 67, pp. 3523-3525, 1995.
22. J.-Y. Chen, J. R. Knab, J. Cerne, and A. G. Markelz, "Large oxidation dependence Observed in Terahertz Dielectric Response for Cytochrome C," Phys. Rev. E. Rapid, vol. 72, p. 040901, 2005.
23. J.Y.Chen, J. R. Knab,S. J.Ye, Y. F.He, andA.G.Markelz, "Terahertz dielectric assay of solution phase protein binding," Appl. Phys. Lett., vol. 90, Jun 2007.
24. , S. A. Doyle, Ed., "High throughput protein expression and purification: Methods and protocols," in Methods in Molecular Biology. Totowa, NJ, USA: Humana Press, 2008, pp. Pages.
25. A. G. Markelz, J. R. Knab, J. Y. Chen, and Y. He, "Protein dynamical transition in terahertz dielectric response," Chem. Phys. Lett., vol. 442, pp. 413-417, 2007. (Pubitemid 47022988)
26. E. Castro-Camus personal communication.
27. Y. F.He, J.Y. Chen, J.R.Knab,W. J. Zheng, andA.G. Markelz, "Evidence of Protein Collective Motions on the Picosecond Timescale," Biophys. J., vol. 100, pp. 1058-1065, Feb 2011.
28. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations," J. Comput. Chem., vol. 4, pp. 187-217, 1983.
29. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J.Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, "All-atom empirical potential for molecular modeling and dynamics studies of proteins," J. Phys. Chem. B, vol. 102, pp. 3586-3616, 1998. (Pubitemid 128576688)
30. M. Boggio-Pasqua and G. Groenhof, "Controlling the Photoreactivity of the Photoactive Yellow Protein Chromophore by Substituting at the p-Coumaric Acid Group," J. Phys. Chem. B, vol. 115, pp. 7021-7028, Jun 2011.
31. G. G. Maisuradze, X. Yu, and D. M. Leitner, "Normal mode analysis and calculation of the cooling rates of the chromophore vibrations during isomerization of photoactive yellow protein," J. Biol. Phys. Chem., vol. 7, pp. 25-29, 2007.
32. W. D. Hoff, A. Xie, I. H. M. van Stokkum, X.-J. Tang, J. Gural, A. R. Kroon, and K. J. Hellingwerf, "Global conformational changes upon receptor stimulation in photoactive yellow protein," Biochemistry, vol. 38, pp. 1009-1017, 1999.
33. P. W. Fenimore, H. Frauenfelder, B. H. McMahon, and R. D. Young, "Bulk-solvent and hydration-shell fluctuations, similar to alpha-and beta-fluctuations in glasses, control protein motions and functions," Proc. Nat. Acad Sci. U.S.A., vol. 101, pp. 14408-14413, 2004. (Pubitemid 39346762)
34. J. Robert, F. Tilton, J. C. Dewan, and G.A. Petsko, "Effects of temperature on protein structure and dynamics: X-ray crystallographic Studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K," Biochem., vol. 31, pp. 2469-2481, 1992.