Dr Seishi Shimizu - Scientific Publications

  1. S. Shimizu, W.L. McLaren and N. Matubayasi (2006). The Hofmeister effect and protein-salt interactions. Journal of Chemical Physics 129 234905.

  2. S. Shimizu (2006). A statistical-mechanical approach to the cosolvent effects on protein stability (Review). Ensemble (Journal of Molecular Simulation Society of Japan) 8, 29 - 32.

  3. S. Shimizu and N. Matubayasi (2006). Preferential hydration of proteins: A Kirkwood-Buff approach. Chemical Physics Letters 420, 518 - 522.

  4. A.H. Keeble, N. Kirkpatrick, S. Shimizu, and C. Kleanthous (2006). Thermodynamic basis for specificity within a family of conserved, cross-reactive protein-protein complexes. Biochemistry 45, 3243 - 3245

  5. S. Shimizu, M.S. Moghaddam, and H.S. Chan (2005). Comment on "Molecular Origin of Anticooperativity in Hydrophobic Association". Journal of Physical Chemistry B 109, 21220 - 21221.

  6. M.S. Moghaddam, S. Shimizu, and H.S. Chan (2005). Temperature dependence of three-body hydrophobic interactions: Potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity. Journal of the American Chemical Society, 127, 303 - 316. [pdf file] Correction: 127, 2363 (2005).[pdf file]

  7. S. Shimizu and C.L. Boon (2004). The Kirkwood-Buff theory and the effect of cosolvents on biochemical reactions. Journal of Chemical Physics 121, 9147 - 9155.[pdf file] Errata: 122, 049901 (2005) [pdf file]; 188901 (2005) [pdf file]

  8. S. Shimizu and D.J. Smith (2004). Preferential hydration and the exclusion of cosolvents from protein surfaces. Journal of Chemical Physics 121, 1148 - 1154. [pdf file]

  9. S. Shimizu (2004). The hydrophobic effect and the excess free energy of solvation. Chemical Physics Letters 392, 456 - 459. [pdf file]

  10. S. Shimizu (2004). Estimation of excess solvation numbers of water from preferential interaction and volumetric experiments. Journal of Chemical Physics 120, 4989 - 4990. [pdf file]

  11. S. Shimizu (2004). Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments. Proceedings of the National Academy of Sciences (USA) 101, 1195 - 1199.[pdf file]

  12. H.S. Chan, S. Shimizu, and H. Kaya (2004). Cooperativity Principles in Protein Folding. Methods in Enzymology 380, 350 - 379. [pdf file]

  13. S. Shimizu and H.S. Chan (2002). Origins of Protein Denatured States Compactness and Hydrophobic Clustering in Aqueous Urea: Inferences from Nonpolar Potentials of Mean Force. Proteins: Structure, Function, and Genetics 49, 560-566.[pdf file]

  14. S. Shimizu and H.S. Chan (2002). Anti-Cooperativity and Cooperativity in Hydrophobic Interactions: Three-Body Free Energy Landscape and Comparison with Implicit-Solvent Potential Functions for Proteins. Proteins: Structure, Function, and Genetics 48, 15-30.[pdf file] Erratum: 49, 294 (2002).[pdf file]

  15. S. Shimizu and H.S. Chan (2002). Reply to "Comment on 'Anti-Cooperativity in Hydrophobic Interactions: A Simulation Study of Spatial Dependence of Three-Body Effects and Beyond' [J. Chem. Phys. 116, 2665 (2002)]." Journal of Chemical Physics 116, 2668-2669.[pdf file]

  16. H.S. Chan, H. Kaya, and S. Shimizu (2002). Computational Methods for Protein Folding: Scaling a Hierarchy of Complexities", in Current Topics in Computational Biology T. Jiang, T. Smith, Y. Yu, M.Q. Zhang, eds., MIT Press, Boston, USA. Chapter 16, pp. 403-447.[Publisher]

  17. T. Ooi and S. Shimizu (2002). Molecular Life of Proteins: Folding and Stability. in Recent Research Developments in Protein Folding, Stability, and Design M.M. Gromiha and S. Selvaraj eds., Research Signpost, Kerala, India. Chapter 17, pp. 243-264.[Publisher]

  18. S. Shimizu and H.S. Chan (2001). Statistical Mechanics of Solvophobic Effects: Additive and Cooperative Effects. Journal of Chemical Physics 115, 3424-3431.[pdf file]

  19. S. Shimizu and H.S. Chan (2001). Anti-Cooperativity in Hydrophobic Interactions: A Simulation Study of Spatial Dependence of Three-Body Effects and Beyond. Journal of Chemical Physics 115, 1414-1421.[pdf file]

  20. S. Shimizu and H.S. Chan (2001). Configuration-Dependent Heat Capacity of Pairwise Hydrophobic Interactions. Journal of the American Chemical Society 121, 2083-2084.[pdf file]

  21. S. Shimizu and H.S. Chan (2000). Temperature Dependence of Hydrophobic Interactions: A Mean Force Perspective, Effects of Water Density, and Non-Additivity of Thermodynamic Signatures. Journal of Chemical Physics 113, 4683-4700.[pdf file.] Erratum: 116, 8636 (2002).[pdf file]

  22. S. Shimizu (2000). Controversies over Hydration and Surface Area. in Water and Life: from Thermodynamics to Physiology K. Nagayama, ed., Kyoritsu Shuppan, Tokyo, Japan (in Japanese) Chapter 2, pp. 15-32.[Publisher]

  23. S. Shimizu and K. Shimizu (1999). Alcohol Denaturation: Thermodynamic Theory of Peptide Unit Solvation. Journal of the American Chemical Society 121, 2387-2392.[pdf file]

  24. S. Shimizu, M. Ikeguchi, S. Nakamura, and K. Shimizu (1999). Size Dependence of Transfer Free Energies: A Hard-Sphere-Chain-Based Formalism. Journal of Chemical Physics 110, 2971-2982.[pdf file]

  25. M. Ikeguchi, S. Shimizu, S. Nakamura, and K. Shimizu (1998). Roles of Hydrogen Bonding and the Hard Core of Water on Hydrophobic Hydration. Journal of Physical Chemistry B 102, 5891-5898.[pdf file]

  26. M. Ikeguchi, S. Shimizu, S. Nakamura, and K. Shimizu (1998). Calculation of Temperature Dependence of Free Energy Caused by Potential Function Changes. Chemical Physics Letters 288, 333-337.[pdf file]

  27. J.-I. Sagara, S. Shimizu, T. Kawabata, S. Nakamura, M. Ikeguchi and K. Shimizu (1998). A Novel Method to Detect Identities in tRNAs. Nucleic Acid Research 26, 1974-1979.[pdf file]

  28. S. Shimizu, M. Ikeguchi, S. Nakamura, and K. Shimizu (1998). Molecular Volume, Surface Area, and Curvature Dependence of the Configurational Entropy Change upon Solvation: Effects of Molecular Bonding. Chemical Physics Letters 284, 235-246.[pdf file]

  29. S. Shimizu, M. Ikeguchi, and K. Shimizu (1998). An Off-lattice Theory of Solvation: Extension of the Flory chi Parameter into Continuum Space. Chemical Physics Letters 282, 79-90.[pdf file]

  30. S. Shimizu, M. Ikeguchi, and K. Shimizu (1997). Extracting Contact Free Energy from Solubility: Excluded Volume Effects of Polymers in Continuum Space. Chemical Physics Letters 268, 93-100.[pdf file]