Transition states for folding of circular‐permuted proteins

Jie Chen; Jun Wang; Wei Wang

doi:10.1002/prot.20175

journal article Jun 11, 2004

Transition states for folding of circular‐permuted proteins

Jie Chen

Jun Wang

Wei Wang

Proteins: Structure, Function, and Bioinformatics Vol. 57 No. 1 pp. 153-171 · Wiley

View at Publisher Save 10.1002/prot.20175

Abstract

AbstractTo explore the role of entropy and chain connectivity in protein folding, a particularly interesting scheme, namely, the circular permutation, has been used. Recently, experimental observations showed that there are large differences in the folding mechanisms between the wild‐type proteins and their circular permutants. These differences are strongly related to the change in the intrachain connectivity. Some results obtained by molecular dynamics simulations also showed a good agreement with the experimental findings. Here, we use a topology‐based free‐energy functional method to study the role of the chain connectivity in folding by comparing features of transition states of the wild‐type proteins with those of their circular permutants. We concentrate our study on 3 small globular proteins, namely, the α‐spectrin SH3 domain (SH3), the chymotrypsin inhibitor 2 (CI2), and the ribosomal protein S6, and obtain exciting results that are consistent with the available experimental and simulation results. A heterogeneity of the interaction energies between contacts for protein CI2 and for protein S6 is also introduced, which characterizes the strong interactions between contacts with long loops, as speculated from experiments for protein S6. The comparison between the folding nucleus of the wild‐type proteins and those of their circular permutants indicates that chain connectivity affects remarkably the shapes of the energy profiles and thus the folding mechanism. Further comparisons between our theoretical calculated ϕth values and the experimental observed ϕexp values for the 3 proteins and their permutants show that our results are in good agreement with experimental ones and that correlations between them are high. These indicate that the free‐energy functional method really provides a way to analyze the folding behavior of the circular‐permuted proteins and therefore the folding mechanism of the wild‐type proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.

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References

Details

Published: Jun 11, 2004
Vol/Issue: 57(1)
Pages: 153-171
License: View

Authors

J

Jie Chen

Guangdong Academy of Medical Sciences

J

Jun Wang

Shenyang Pharmaceutical University

W

Wei Wang

Hong Kong University of Science and Technology

Cite This Article

Jie Chen, Jun Wang, Wei Wang (2004). Transition states for folding of circular‐permuted proteins. Proteins: Structure, Function, and Bioinformatics, 57(1), 153-171. https://doi.org/10.1002/prot.20175

Transition states for folding of circular‐permuted proteins

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