Abstract
Structural fluctuation of protein is not just an mechanical “oscillation,” but an event induced by an interplay of mechanical and thermodynamic processes in which water plays crucial role. The chapter is devoted to provide a theoretical description concerning the concept of structural fluctuation of protein, based on methods of the statistical mechanics.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akasaka K (2003) Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance. Biochemistry 42:10877–10885
Akasaka K (2006) Probing conformational fluctuation of proteins by pressure perturbation. Chem Rev 106:1814–1835
Akasaka K, Li H, Yamada H, Li R, Thoresen T, Woodward CK (1999) Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI. Protein Sci 8:1946–1953
Bihan DL, Fukuyama H (eds) (2010) Water: The forgotten biological molecule. Pan Stanford Publishing, Singapore
Brooks B, Karplus M (1983) Harmonic dynamics of protein: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A 80:6571–6575
Burghardt TP, Josephson MP, Ajtai K (2011) Single myosin cross-bridge orientation in cardiac papillary muscle detects lever-arm shear strain in transduction. Biochemistry 50:7809–7821
Chandrasekhar S (1943) Stochastic problems in physics and astronomy. Rev Mod Phys 15:1–89
Chong SH, Hirata F (1997) Nonlinear electrical potential fluctuations of solvent around solutes: an integral equation study. J Chem Phys 106:5225–5238
Chong SH, Miura S, Bsasu G, Hirata F (1995) Molecular theory for the non-equilibrium free energy profile in electron transfer reaction. J Phys Chem 99:10526–10529
Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352–1360
Fourme R, Girard E, Akasaka K (2012) High-pressure macromolecular crystallography and NMR: status, achievements and prospects. Current Opinion in Struct Biol 22:1–7
Go N, Noguchi T, Nishikawa T (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci U S A 80:3696–3700
Hayward S, Kitao A, Hirata F, Go N (1993) Effect of solvent on collective motions in BPTI. J Mol Biol 234:1207–1217
Hirata F (1992) Interaction-site representation of the Smoluchowski-Vlasov equation – the space-time correlation-functions in a molecular-liquid. J Chem Phys 96:4619–4624
Hirata F (ed) (2003) Molecular theory of solvation. Kluwer Academic Publishers, Dordrecht
Hirata F, Akasaka K (2015) Structural fluctuation of protein induced by thermodynamic perturbation. J Chem Phys 142:044110–044118
Horiuchi T, Go N (1991) Investigating protein dynamics in collective coordinate space. Proteins 10:106–116
Ikeguchi M, Ueno J, Sato M, Kidera A (2005) Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 94:078102–078104
Imai T, Kinoshita M, Hirata F (2000) Theoretical study for partial molar volume of amino acids in aqueous solution: implication of ideal fluctuation volume. J Chem Phys 112:9469–9478
Imai T, Kovalenko A, Hirata F (2004) Solvation thermodynamics of protein studied by the 3D-RISM theory. Chem Phys Lett 395:1–6
Imai T, Ohyama S, Kovalenko A, Hirata F (2007) Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin. Protein Sci 16:1927–1933
Kim B, Hirata F (2013) Structural fluctuation of protein in water around its native state: a new statistical mechanics formulation. J Chem Phys 138:054108–054119
Kirkwood JG, Buff FP (1951) The statistical mechanical theory of solutions. J Chem Phys 19:774–777
Kitahara R, Yokoyama S, Akasaka K (2005) NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar. J Mol Biol 347:277–285
Kitao A, Hirata F, Go N (1991) The effect of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum. Chem Phys 158:447–472
Kubo R, Toda M, Hashitsume N (1991) Statistical physics II, nonequilibrium statistical mechanics. Springer, Berlin
Kuwajima K, Goto Y, Hirata F, Terazima M, Kataoka M (eds) (2009) Water and biomolecules. Springer, Berlin/Heidelberg
Lamm G, Szabo A (1986) Langevin modes of macromolecules. J Chem Phys 85:7334–7348
Landau LD, Lifshitz EM (1964) Statistical physics (Japanese translation). Iwanami, Tokyo
Makowski L, Rodi DJ, Mandava S, Minh D, Gore DB, Fischetti RF (2008) Molecular crowding inhibits intramolecular breathing motions in proteins. J Mol Biol 375:529–546
Marcus R (1956) On the theory of oxidation–reduction reactions involving electron transfer. I. J Chem Phys 24:966–979
Mchaourab HS, Oh KJ, Fang CJ, Hubbell WL (1997) T4 lysozyme and mutants thereof crystallize in different conformations that are related to each other by a bend about a hinge in the molecule. Biochemistry 36:307–316
McQuarrie DA (1976) Statistical mechanics. Harper and Row Publishers, New York
Mori H (1962) Collective motion of particles at finite temperatures. Prog Theor Phys 28:763–783
Wang MC, Uhlenbeck GE (1945) On the theory of the Brownian motion II. Rev Mod Phys 17:323–342
Yoshida N, Imai T, Phongphanphanee S, Kovalenko A, Hirata F (2009) Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids. J Phys Chem B 113:873–886
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Hirata, F. (2015). Water Turns the “Non-biological” Fluctuation of Protein into “Biological” One. In: Akasaka, K., Matsuki, H. (eds) High Pressure Bioscience. Subcellular Biochemistry, vol 72. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9918-8_7
Download citation
DOI: https://doi.org/10.1007/978-94-017-9918-8_7
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-017-9917-1
Online ISBN: 978-94-017-9918-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)