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The principle of compromise in competition: exploring stability condition of protein folding

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Abstract

Thermodynamic hypothesis and kinetic stability are currently used to understand protein folding. The former assumes that free energy minimum is the exclusive dominant mechanism in most cases, while the latter shows that some proteins have even lower free energy in intermediate states and their native states are kinetically trapped in the higher free energy region. This article explores the stability condition of protein structures on the basis of our study of complex chemical systems. We believe that separating one from another is not reasonable since they should be coupled, and protein structures should be dominated by at least two mechanisms resulting in different characteristic states. It is concluded that: (1) Structures of proteins are dynamic, showing multiple characteristic states emerging alternately and each dominated by a respective mechanism. (2) Compromise in competition of multiple dominant mechanisms might be the key to understanding the stability of protein structures. (3) The dynamic process of protein folding should be depicted through the time series of both its energetic and structural changes, which is much meaningful and applicable than the free energy landscape.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (21103195) and the Knowledge Innovation Program of Chinese Academy of Sciences (KGCX2-YW-124). We especially thank Profs. Chih-chen Wang and Ruiming Xu (Institute of Biophysics, Chinese Academy of Sciences, China) for their fruitful discussions and helpful comments.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Correspondence to Ying Ren.

Electronic supplementary material

Below is the link to the electronic supplementary material.

The trajectory transformations from the starting structure to C3. Color scheme is the same as Fig. 2(b). (MP4 8312 kb)

The trajectory transformations from C3 to C2. Color scheme is the same as Fig. 2(b). (MP4 5773 kb)

The trajectory transformations from C2 to C1. Color scheme is the same as Fig. 2(b). (MP4 10956 kb)

Supplementary Video 1

The trajectory transformations from the starting structure to C3. Color scheme is the same as Fig. 2(b). (MP4 8312 kb)

Supplementary Video 2

The trajectory transformations from C3 to C2. Color scheme is the same as Fig. 2(b). (MP4 5773 kb)

Supplementary Video 3

The trajectory transformations from C2 to C1. Color scheme is the same as Fig. 2(b). (MP4 10956 kb)

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Cite this article

Xu, J., Han, M., Ren, Y. et al. The principle of compromise in competition: exploring stability condition of protein folding. Sci. Bull. 60, 76–85 (2015). https://doi.org/10.1007/s11434-014-0718-3

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Keywords

  • Protein folding
  • Dynamic structure
  • Multiple mechanisms
  • Compromise in competition
  • Mesoscale
  • Stability