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- The Complex Kinetics of Protein Folding in Wide Temperature Ranges

Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052–6062.

Bryngelson, J. D., and P. G. Wolynes. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:6902–6915.

Bryngelson, J. D., J. O. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein-folding—a synthesis. Proteins Struct. Funct. Genet. 21:167–195.

Chan, H. S., and K. A. Dill. 1994. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238–9257.

Chan, H. S., S. Shimizu, and H. Kaya. 2004. Cooperativity principles in protein folding. Meth. Enzymol. 380:350–379.

Cieplak, M., T. X. Hoang, and M. S. Li. 1999. Scaling of folding properties in simple models of proteins. Phys. Rev. Lett. 83:1684–1687.

Derrida, B. 1981. Random-energy model: an exactly solvable model of disordered systems. Phys. Rev. B. 24:2613–2626.

Frauenfelder, H., F. Parak, and R. D. Young. 1988. Conformational substrates in proteins. Annu. Rev. Biophys. Biophys. Chem. 17:451–479.

Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598–1603.

Gutin, A. M., V. I. Abkevich, and E. I. Shakhnovich. 1996. Chain-length scaling of protein folding time. Phys. Rev. Lett. 77:5433–5436.

Itzhaki, L. S., D. E. Otzen, and A. R. Fersht. 1995. The structure of the transition state for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods—evidence for a nucleation-condensation mechanism for protein-folding. J. Mol. Biol. 254:260–288.

Jia, Y. W., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69–83.

Kaya, H., and H. S. Chan. 2000. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85:4823–4826.

Kaya, H., and H. S. Chan. 2002. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding? J. Mol. Biol. 315:899–909.

Kaya, H., and H. S. Chan. 2003. Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins. 52:524–533.

Kirkpatrick, T. R., and P. G. Wolynes. 1987. Stable and metastable states in mean-field Potts and structural glasses. Phys. Rev. B. 36:8552–8564.

Kirkpatrick, T. R., D. Thirumalai, and P. G. Wolynes. 1989. Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. Phys. Rev. A. 40:1045–1054.

Klimov, D. K., and D. Thirumalai. 1998. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J. Chem. Phys. 109:4119–4125.

Lee, C. L., C. T. Lin, G. Stell, and J. Wang. 2003. Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules. Phys. Rev. E. 67:041905.

Lee, C. L., G. Stell, and J. Wang. 2003. First-passage time distribution and non-Markovian diffusion dynamics of protein folding. J. Chem. Phys. 118:959–968.

Levinthal, C. 1969. Proceedings in Mössbauer Spectroscopy in Biological Systems. P. DeBrunner, J. Tsibris, and E. Munck, editors. University of Illinois Press, Urbana, IL. p22.

Lipman, E. A., B. Schuler, O. Bakajin, and W. A. Eaton. 2003. Single-molecule measurement of protein folding kinetics. Science. 301:1233–1235.

Lu, H. P., L. Y. Xun, and X. S. Xie. 1998. Single-molecule enzymatic dynamics. Science. 282:1877–1882.

Moerner, W. E. 1996. High-resolution optical spectroscopy of single molecules in solids. Acc. Chem. Res. 29:563–571.

Miller, R., C. A. Danko, M. J. Fasolka, A. C. Balazs, H. S. Chan, and K. A. Dill. 1992. Folding kinetics of proteins and copolymers. J. Chem. Phys. 96:768–780.

Nguyen, H., M. Jäger, A. Moretto, M. Gruebele, and J. W. Kelly. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. USA. 100:3948–3953.

Onuchic, J. N., J. Wang, and P. G. Wolynes. 1999. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions. Chem. Phys. 247:175–184.

Plotkin, S. S., and P. G. Wolynes. 1998. Non-Markovian configurational diffusion and reaction coordinates for protein folding. Phys. Rev. Lett. 80:5015–5018.

Plotkin, S. S., and J. N. Onuchic. 2002a. Understanding protein folding with energy landscape theory. I. Basic concepts. Quar. Rev. Biophys. 35:111–167.

Plotkin, S. S., and J. N. Onuchic. 2002b. Understanding protein folding with energy landscape theory. II. Quantitative aspects. Quar. Rev. Biophys. 35:205–286.

Sabelko, J., J. Ervin, and M. Gruebele. 1999. Stretching lattice models of protein folding. Proc. Natl. Acad. Sci. USA. 96:6031–6036.

Saven, J. G., J. Wang, and P. G. Wolynes. 1994. Kinetics of protein folding: the dynamics of globally connected rough energy landscapes with biases. J. Chem. Phys. 101:11037–11043.

Seno, F., C. Micheletti, A. Maritan, and J. R. Banavar. 1998. Variational approach to protein design and extraction of interaction potentials. Phys. Rev. Lett. 81:2172–2175.

Schenter, G. K., H. P. Lu, and X. S. Xie. 1999. Statistical analyses and theoretical models of single-molecule enzymatic dynamics. J. Phys. Chem. A. 103:10477–10488.

Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743–747.

Socci, N. D., and J. N. Onuchic. 1994. Folding kinetics of proteinlike heteropolymers. J. Chem. Phys. 101:1519–1528.

Socci, N. D., and J. N. Onuchic. 1995. Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732–4744.

Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1996. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104:5860–5868.

Wang, J., and P. G. Wolynes. 1995. Intermittency of single molecule reaction dynamics in fluctuating environments. Phys. Rev. Lett. 74:4317–4320.

Wang, J., J. Onuchic, and P. Wolynes. 1996a. Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding. Phys. Rev. Lett. 76:4861–4864.

Wang, J., J. G. Saven, and P. G. Wolynes. 1996b. Kinetics in a globally connected, correlated random energy model. J. Chem. Phys. 105:11276–11284.

Wang, J., and P. G. Wolynes. 1999. Intermittency of activated events in single molecules: the reaction diffusion description. J. Chem. Phys. 110:4812–4819.

Wang, J. 2003. Statistics, pathways and dynamics of single molecule protein folding. J. Chem. Phys. 118:952–958.

Yang, H., and X. S. Xie. 2002a. Statistical approaches for probing single-molecule dynamics photon by photon. Chem. Phys. 284:423–437.

Yang, H., and X. S. Xie. 2002b. Probing single-molecule dynamics photon-by-photon. J. Chem. Phys. 117:10965–10979.

Zhou, Y., C. Zhang, G. Stell, and J. Wang. 2003. Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second-hairpin fragment of protein G. J. Am. Chem. Soc. 125:6300–6305.

Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048–2051.

Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473–1476.

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