Protein folding mechanisms unfolding rates

Fig. 7. Conservation of the unfolding/folding mechanism of cold-shock proteins (Csp) from B. subtilis (Bs), B. caldolyticus (fid), and Thermotoga maritima (Tm). (a) Equilibrium unfolding transitions of Csp from Bs (A), Be ( ), and Tm ( ) induced by GdmCI at 25° and monitored by intrinsic fluorescence. Least-squares fit analyses based on the two-state model yield stabilization energies AGstab = 11.3,20.1, and 26.2 kJ/mol for Csp from Bs, Be, and Tm, respectively, (b) Kinetics of unfolding (open symbols) and refolding (closed symbols) of Bs (A, A), Be ( , ) and T Csp (O, ), respectively. The apparent rate constants, X, are plotted against the GdmCI concentration. The fits are on the basis of the linear two-state model. ...

Isotope patterns produced by EXl mechanism can be recognized by peak width analysis [39]. The majority of proteins display EX2 mechanism in native conditions. However, EXl can often be achieved by either increasing (e.g., higher pH) or decreasing (e.g., adding denaturant to destabilize the folded stracture). EXl phenomenon is particularly valuable in the study of protein dynamics because the local unfolding rate can be determined directly from the spectra of deuterated... 

An example of this effect is provided by ribonuclease A (RNase A). At pH 8 and 37°, the rate of deamidation of Asn67 was more than 30-fold lower in the native than in the unfolded protein [111]. Deamidation of the native RNase A was also ca. 30-fold slower than of an octapeptide whose sequence is similar to that of the deamidation site, although the reaction mechanisms were similar [108][123],... 

Although there are exceptions, many of the smaller proteins studied to date fold by a two-state mechanism with a single rate-limiting transition state. The transition state is a crucial but unstable stage along a folding pathway traversal back to the native state has equal probability to that of the system progressing to the unfolded state. Transition states are often a less compact version... 

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