Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways
Abstract
:1. Introduction
2. Folding Mechanism of Trpzip2
2.1. Folding Heterogeneity
2.2. Transition State
- The transition state is similar to the native state. For example, Pande’s group [18] found the transition state is similar to the native state except the tryptophan-2 having large fluctuations. Xu et al. [23] found that the transition state ensemble is characterized by a largely formed turn and a compact packing of tryptophanes 2, 4 and 9.
- The transition state is characterized by the formation of the inner hydrogen bonds and the inner pair of hydrophobic residues. For example, Wang’s group [21] found that the transition state is characterized by a largely formed turn, high probabilities of the three inner hydrogen bonds, and the hydrophobic interaction between the inner pair of core residues. Similarly, our unpublished studies of the folding processes of trpzip2 by the united residue (UNRES) model [40] identified that the transition state conformation is characterized by the inner one or two native contacts formed and two tails still having a larger distance.
- The transition state is characterized by the formation of only inner native hydrogen bonds. For example, Yang et al. [36] identified the two types of transition state for trpzip2. One has a conformation with two inner native hydrogen bonds being formed (zip-out pathway). Another has a conformation with two outer native hydrogen bonds being formed (zip-in pathway). There is also a related example: Gai and coworkers [6] compared the folding and unfolding kinetics of trpzip4 and the GB1 β-hairpin differing from each other only in the composition of the hydrophobic cluster and showed that these two β-hairpins have similar folding rate but significantly different unfolding rates. Furthermore, due to the triple tryptophan mutations in the GB1 β-hairpin, the φ value of trpzip4 for folding is about 0.11, suggesting that the two native hydrophobic pairs have not been formed in the transition state.
2.3. Folding Pathways
3. Conclusions
Acknowledgments
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Xiao, Y.; Chen, C.; He, Y. Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways. Int. J. Mol. Sci. 2009, 10, 2838-2848. https://doi.org/10.3390/ijms10062838
Xiao Y, Chen C, He Y. Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways. International Journal of Molecular Sciences. 2009; 10(6):2838-2848. https://doi.org/10.3390/ijms10062838
Chicago/Turabian StyleXiao, Yi, Changjun Chen, and Yi He. 2009. "Folding Mechanism of Beta-Hairpin Trpzip2: Heterogeneity, Transition State and Folding Pathways" International Journal of Molecular Sciences 10, no. 6: 2838-2848. https://doi.org/10.3390/ijms10062838