Solvation dynamics of biomolecules: Modeling and terahertz experiments

HFSP Journal

Volumn 2, Issue 6, 2008, Pages 314-323

  Leitner, David M ^a   Gruebele, Martin ^b   Havenith, Martina ^c  

^a UNIVERSITY OF NEVADA   (United States)

^b University of Illinois at Urbana Champaign   (United States)

^c RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70349746078     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.2976661     Document Type: Article

References (44)

1. Bagchi, B (2005). "Water dynamics in the hydration layer around proteins and miscelles." Chem. Rev. (Washington, D.C.) 105, 3197-3219.
2. Bergner, A, et al. (2005). "New p-Ge THz laser spectrometer for the study of solutions: THz absorption spectroscopy of water." Rev. Sci. Instrum. 76, 063110.
3. Block, W (2003). "Water or ice? The challenge for invertebrate cold survival." Sci. Prog. 86, 77-101.
4. Born, B, Kim, SJ, Ebbinghaus, S, Gruebele, M, and Havenith, M (2008). Faraday Discuss. (submitted).
5. Cameron, IL, and Fullerton, GD (2006). "Non-bulk-like water on cellular interfaces." In Water and the cell, Pollack, G, ed., pp. 315-323, Springer, Heidelberg.
6. Chen, J-Y, Knab, JR, Cerne, J, and Markelz, AG (2005). "Large oxidation dependence observed in terahertz dielectric response for cytochrome c." Phys. Rev. E 72, 040901-040904.
7. Crowe, JH, Crowe, LM, and Chapman, D (1984). "Preservation of membranes in anhydrobiotic organisms: the role of trehalose." Science 223, 701-703.
8. Dexheimer, S (2007). Terahertz spectroscopy: principles and applications, Taylor & Francis, London.
9. Ebbinghaus, S, et al. (2007). "An extended dynamical solvation shell around proteins." Proc. Natl. Acad. Sci. U.S.A. 104, 20749-20752.
10. Ebbinghaus, S, et al. (2008). "Protein sequence- and pH-dependent hydration probed by terahertz spectroscopy." J. Am. Chem. Soc. 130, 2374-2375.
11. Elber, R, and Karplus, M (1986). "Low-frequency modes in proteins: use of effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements." Phys. Rev. Lett. 56, 394-397.
12. Ervin, J, Larios, E, Osvath, S, Schulten, K, and Gruebele, M (2002). "What causes hyperfluorescence: folding intermediates or conformationally flexible native states?" Biophys. J. 83, 473-483.
13. Evans, SV, and Brayer, GD (1990). "High-resolution study of the threedimensional structure of horse heart metmyoglobin." J. Mol. Biol. 213, 885-897.
14. Fenimore, PW, Frauenfelder, H, McMahon, BH, and Parak, FG (2002). "Slaving: solvent fluctuations dominate protein dynamics and functions." Proc. Natl. Acad. Sci. U.S.A. 99, 16047-16051.
15. Gallagher, T, Alexander, P, Bryan, P, and Gilliland, GL (1994). "Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR." Biochemistry 33, 4721-4729.
16. Halle, B (2004). "Protein hydration dynamics in solution: a critical survey." Philos. Trans. R. Soc. London 359, 1207-1224.
17. Head-Gordon, T (1995). "Is water structure around hydrophobic groups clathrate-like?" Proc. Natl. Acad. Sci. U.S.A. 92, 8308-8312.
18. Herrick, RC, and Stapleton, HJ (1976). "Anomalous T7 Raman spinlattice relaxation rate of low spin cytochrome P-450 from Pseudomonas putida." J. Chem. Phys. 65, 4778-4785.
19. Heugen, U et al. (2006). "Solute induced retardation of water dynamics: hydration water probed directly by THz spectroscopy." Proc. Natl. Acad. Sci. U.S.A. 103, 12301-12306.
20. Heyden, M, et al. (2008). "Long-range influence of carbohydrates on the solvation dynamics of water-answers from terahertz absorption measurements and molecular modelling simulations." J. Am. Chem. Soc. 130, 5773-5779.
21. Kim, SJ, Born, B, Havenith, M, and Gruebele, M (2008). "Real-time detection of protein-water dynamics upon protein folding by terahertz absorption." Angew. Chem., Int. Ed. 47(34), 6486-6489.
22. Knab, J, Chen, JY, and Markelz, AG (2006). "Hydration dependence of conformational dielectric relaxation of lysozyme." Biophys. J. 90, 2576-2581.
23. Kumar, R, Schmidt, JR, and Skinner, JL (2007). "Hydrogen bonding definitions and dynamics in liquid water." J. Chem. Phys. 126, 204107-204112.
24. Lee, SL, Debenedetti, PG, and Errington, JR (2005). "A computational study of hydration, solution structure." J. Chem. Phys. 122, 204510-204511.
25. Leitner, DM (2008). "Energy flow in proteins." Annu. Rev. Phys. Chem. 59, 233-259.
26. Leitner, DM, Havenith, M, and Gruebele, M (2006). "Biomolecule largeamplitude motion and solvation dynamics: modeling and probes from THz to x-rays." J. Radiol. Prot. 25, 553-582.
27. Markelz, AG. J. R. K, and Chen, JY (2007). Chem. Phys. Lett. 442(4-6),413-417
28. Murarka, RK, and Head-Gordon, T (2008). "Dielectric relaxation of aqueous solutions of hydrophilic vs. amphiphilic peptides." J. Phys. Chem. B 112, 179-186.
29. Nandi, N, Bhattacharyya, K, and Bagchi, B (2000). "Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems." Chem. Rev. (Washington, D.C.) 100, 2013-2045.
30. Otting, G, and Wüthrich, K (1989). "Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules." Biochemistry 111, 1871-1875.
31. Persson, E, and Halle, B (2008). "Cell water dynamics on multiple time scales." Proc. Natl. Acad. Sci. U.S.A. 105, 6266-6271.
32. Pertsemlidis, A, Saxena, AM, Soper, AK, Head-Gordon, T, and Glaeser, RM (1996). "Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid." Proc. Natl. Acad. Sci. U.S.A. 93, 10769-10774.
33. Plusquellic, DF, Siegrist, K, Heilweil, EJ, and Esenturk, O (2007). "Applications of terahertz spectroscopy in biosystems." ChemPhysChem 8, 2412-2431.
34. Ronne, C, et al. (1997). J. Chem. Phys. 107, 5319-5330.
35. Rosenfeld, DE, and Schmuttenmaer, CA (2007). "Dynamics of water confined within reverse miscelles." J. Phys. Chem. B 110, 14304-14312.
36. Tarek, M, and Tobias, DJ (2002). "Role of protein-water hydrogen bond dynamics in the protein dynamical transition." Phys. Rev. Lett. 88, 138101-138104.
37. Tehei, M, et al. (2007). "Neutron scattering reveals extremely slow cell water in a Dead Sea organism." Proc. Natl. Acad. Sci. U.S.A. 104, 766-771.
38. Tonouchi, M (2007). Nat. Photonics 1, 97.
39. Whitmire, SE, et al. (2003). "Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin." Biophys. J. 85, 1269-1277.
40. Wood, K, et al. (2008). "Coincidence of dynamical transitions in a soluble protein and its hydration water: direct measurements by neutron scattering and MD simulations." J. Am. Chem. Soc. 130, 4586-4587.
41. Xu, J, Plaxco, KW, and Allen, SJ (2006). "Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy." Protein Sci. 15, 1175-1181.
42. Yang, WY, and Gruebele, M (2004). "Rate-temperature relationships in lambda repressor fragment 6-85 folding." Biophys. J. 43, 13018-13025.
43. Zhang, CF, and Durbin, SM (2006). "Hydration-induced far-infrared absorption increase in myoglobin." J. Phys. Chem. B 110, 23607-23613.
44. Zhong, DP, Pal, SK, Zhang, DQ, Chan, SI, and Zewail, AH (2002). "Femtoseond dynamics of rubredoxin: tryptophan salvation and resonance energy transfer in the protein." Proc. Natl. Acad. Sci. U.S.A. 99, 13-18.