Unfolding transition states

Li A. and Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 

Daggett, V., Validation of protein-unfolding transition states identified in molecular dynamics simulations. Biochem Soc Symp, 2001(68) 83-93. 

Lampa-Pastirk S, Beck WE. 2006. Intramolecular vibrational preparation of unfolding transition state of Znll-substimted cytochrome c. J. Phys. Chem. B 110 22971-22974. 

Dougan L, Genchev GZ, Lu H, Fernandez JM (2011) Probing osmolyte participation in the unfolding transition state of a protein. Proc Natl Acad Sci USA 108 9759-9764... 

To contrast the denaturation pathways with and without urea as a co-solvent, preliminary simulations were done at 353 K, one in pure water and one in 8 M urea. The 8 M urea solution rapidly expanded, reaching an rmsd of 4.4 A in 750 ps. The water simulation maintained near-native structure, with the secondary structure largely intact and a slightly disrupted, albeit compact, core. In urea the molecule is much more expanded. The secondary structure is still mostly intact, but the core is greatly expanded, in a manner similar to the unfolding transition state (vide supra). 

R. Day and V. Daggett, Protein Sci., 14, 1242 (2005). Sensitivity of the Folding/Unfolding Transition State Ensemble of Chymotrypsin Inhibitor 2 to Changes in Temperature and Solvent. 

A. Li and V. Daggett, /. Mol. Biol., 257, 412 (1996). Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics... 

Given that a sequence folds to a known native stmcture, what are the mechanisms in the transition from the unfolded confonnation to the folded state This is a kinetics problem, the solution of which requires elucidation of the pathways and transition states in the folding process. 

A Li, V Daggett. Characterization of the transition state of protein unfolding by use of molecular dynamics Chymotrypsm inhibitor 2. Proc Natl Acad Sci USA 91 10430-10434, 1994. 

Fig. 8. Dependence of (A) corrected diffusion coefficient (D), (B) steady-state fluorescence intensity, and (C) corrected number of particles in the observation volume (N) of Alexa488-coupled IFABP with urea concentration. The diffusion coefficient and number of particles data shown here are corrected for the effect of viscosity and refractive indices of the urea solutions as described in text. For steady-state fluorescence data the protein was excited at 488 nm using a PTI Alphascan fluorometer (Photon Technology International, South Brunswick, New Jersey). Emission spectra at different urea concentrations were recorded between 500 and 600 nm. A baseline control containing only buffer was subtracted from each spectrum. The area of the corrected spectrum was then plotted against denaturant concentrations to obtain the unfolding transition of the protein. Urea data monitored by steady-state fluorescence were fitted to a simple two-state model. Other experimental conditions are the same as in Figure 6.

Figure 13.1 Microcalorimetry scans displaying Tm values for interleukin-1 receptor (IL-1R type I). The inlay displays the unfolding of IL-1R (I) showing the ACp measured as the baseline difference between the native (N) and denatured (D) states for two independent scans. Thermal unfolding of IL-1R (I) is composed of three cooperative unfolding transitions, labeled 1, 2, and 3.

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