Thermal unfolding pathway

Chen, B.-L., and King, J. (1991). Thermal unfolding pathway for the thermostable P22 tailspike endorhamnosidase. Biochemistry 30, 6260-6269. 

During the forward folding pathway the newly synthesized chain forms a partially folded single chain intermediate (5435). This folds further to a species with sufficient structure for chain recognition. Three of these intermediates associate into a protrimer in which the chains are associated but not fully folded (36). This species then folds further to the thermostable detergent and protease resistant native trimer. There are no known covalent modifications in the process. A similar process occurs in refolding urea denatured chains in vitro (37). Thermal Unfolding Pathway of Tailspike... 

Thermal Unfolding Pathway Differs from the in vivo Folding Pathway... 

In any case, the difference between the in vivo folding pathway and the in vitro thermal unfolding pathway indicates the importance of kinetic aspects in controlling the folding and unfolding of this protein. 

Pathway for the Thermal Unfolding of Wild Type and Mutant Forms of the Thermostable P22 Tailspike Endorhamnosidase... 

Thermal denaturation simulations "" were designed to simulate the unfolding pathway and provide explicit structural models for the transition state. Four thermal denaturation simulations were run in water at 498 K, using the correct density, for at least 1 ns to ensure consistency of the simulation results. The transition states were characterized in terms of the rate of change of the rmsd(Ca) for every structure against every other structure from the trajectory. Since one expects a rapid change in the protein structure once the transition state has been passed, Ae transition state was identified as... 

Bamase, like CI2, has been the subject of extensive studies, using the protein engineering method combined with kinetic and equilibrium experiments, to investigate its fold-ing/unfolding pathway." Molecular dynamics simulations of thermal denaturation of the wild-type and two mutant proteins (Tyr 17 —> Gly and He 88 —> Val) have been performed to investigate the effect of mutations on the unfolding pathway and transition state." ... 

Y. Y. Sham, B. Ma, C.-J. Tsai, and R. Nussinov, Proteins Struct., Punct., Bioinf., 46, 308 (2002). Thermal Unfolding Molecular Dynamics Simulation of Escherichia Coli Dihydrofolate Reductase Thermal Stability of Protein Domains and Unfolding Pathway. 

Fig. 8.11. Pathway of thermal unfolding of unreduced RNase (according to Burgess and Scheraga, 1975a) (see text).

The single funnel hypothesis also provides a mechanism for folding. Indeed, if the free energy landscape of proteins has the form of a single funnel, a trajectory driven solely by thermal fluctuations, will always take an unfolded protein, through many possible pathways down the funnel, to the native structure that is located at the bottom. This new view (of many pathways) was later reconciled with Levinthal s old view (of one specific pathway for folding ), by considering that in some cases one pathway may be dominant. ... 

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