Thermodynamics and Kinetics of Protein Folding: A Mean Field Theory K. K. Liang (梁國淦), M. Hayashi (林輪年), Y. J. Shiu (許瑛珍), Y. Mo (莫燕), J. S. Shao (邵久書), Y. J. Yan (嚴以京), and S. H. Lin (林聖賢) Institute of Atomic and Molecular Science, Academia Sinica, Taipei, Taiwan The kinetic Ising model in the mean field approximation is applied to study the equilibrium and kinetic behaviors of protein folding-unfolding. In our model, we regard a protein as a topological collection of interacting peptide bonds (or other protein unites). According to this model, thermodynamics and kinetics of protein folding-unfolding are rated to the elementary process of folding←→unfolding of such interacting units. We shall show that even for the so-called two-state case of protein folding-unfolding, the kinetic behaviors are predicted to be in general non-exponential and that universal curves exist separately for the thermodynamic behaviors and kinetics behaviors of protein folding-unfolding. Our model can treat the effect of temperature and denaturant concentration on the thermodynamics and kinetics of protein folding-unfolding and provide the Chevron plot. It can also be used to calculate the force-extension curve in the atomic force microscopic studies of protein folding-unfolding. Satisfactory demonstrations are presented for treating experimental observations on the thermodynamical and kinetic responses of protein folding-unfolding to the changes in temperature and denaturant concentration and for exhibiting universal plots of protein. References 1 C. B. Anfinsen, Science, 1973, 181, 223.; 2 R. L. Baldwin and G. D. Rose, Trends Biochem. Sci., 1999, 24, 77; R. L. BaldwinG. D. Rose Trends Biochem. Sci.19992426.; 3 S. Akiyama, S. Takahashi, K. Ishimori and I. Morishima, Nature Struct. Biol., 2000, 7, 514.; 4 T. Sivaraman, T. K. S. Kumar, Y. T. Tu, W. Wang, W. Y. Lin, H. M. Chen and C. Yu, Biochem. Biophys. Res. Commun., 1999, 260, 284.; 5 V. R. Agashe, M. C. R. Shastry and J. B. Udganokar, Nature, 1999, 377, 754.; 6 R. Zwanzig, Proc. Natl. Acad. Sci. USA, 1995, 92, 9801.; 7 R. Zwanzig, Proc. Natl. Acad. Sci. USA, 1997, 94, 148.; 8 R. Doyle, K. Simons, H. Qian and D. Baker, Proteins Struct. Funct. Genet., 1997, 29, 282.; 9 K. Iguchi, Int. J. Mod. Phys. B, 2002, 16, 1807.; 10 P. Bruscolini and A. Pelizzola, Phys. Rev. Lett., 2002, 88art. no. 258101.; 11 V. Munõz, P. A. Thompson, J. Hofrichter and W. A. Eaton, Nature, 1997, 390, 196.; 12 V. Munõz and W. A. Eaton, Proc. Natl. Acad. Sci. USA, 1999, 96, 11 311.; 13 E. Alm and D. Baker, Proc. Natl. Acad. Sci. USA, 1999, 96, 11 305.; 14 O. V. Galzitskaya and A. V. Finkelstein, Proc. Natl. Acad. Sci USA, 1999, 96, 11 299.; 15 D. Baker, Nature, 2000, 405, 39.; 16 A. Flammini, J. R. Banavar and A. Maritan, Europhys. Lett., 2002, 58, 623.; 17 M. Carrion-Vazquez, A. F. Oberhauser, T. F. Fisher, P. E. Marszalek, H. Li and J. M. Fernandez, Prog. Biophys. Molec. Biol., 2000, 74, 63.; 18 A. Engel, H. E. Gaub and D. J. Muller, Curr. Biol., 1999, 9, R133–R136.; 19 H. P. Erickson, Science, 1997, 276, 1090.; 20 M. S. Kellermayer, S. B. Smith, H. L. Granzier and C. Bustamante, Science, 1997, 276, 1112.; 21 X. Zhuang, T. Ho, H. D. Kim, T. Centner, S. Labeit and S. Chu, Proc. Natl. Acad. Sci., USA, 2000, 97, 14 241.; 22 A. Boeglin, X.-G. Zhang and S. H. Lin, Physica A, 1986, 137, 439.; 23 T. Kikuchi, Biophys. Chem., 1997, 65, 109.; 24 T. Kikuchi, Biophys. Chem., 2000, 85, 93.; 25 T. L. Hill, Introduction to Statistical Thermodynamics Dover, New York, 1986.; 26 S. H. Lin, R. G. Alden, R. Islampour, H. Ma and A. A. Villaeys, Density Matrix Method and Femtosecond Processes World Scientific, 1991.; 27 W. Colo’n, G. A. Elo‥ ve, L. P. Wakem, F. Shweman and H. Roder, Biochemistry, 1996, 35, 5538.; 28 P. A. Thompson, V. Munoz, G. S. Jas, E. R. Henry, W. A. Eaton and J. Hofrichter, J. Phys. Chem.B, 2000, 104, 378.; 29 B. Gillespie and K. W. Plaxco, Proc. Natl. Acad. Sci. USA, 2000, 97, 12 014.; 30 H. Eyring, D. Henderson, B. J. Stover and E. M. Eyring, Statistical Mechanics and Dynamics Wiley-Interscience, 1964.; 31 A. F. Oberhauser, P. K. Hansma, M. Carrion-Vazquez and J. M. Fernandez, Proc. Natl. Acad. Sci., USA, 2001, 98, 468.; 32 H. Eyring, S. H. Lin and S. M. Lin Basic Chemical Kinetics Wiley-Interscience, New York, 1981, pp. 438–448.