We studied the refolding free energy landscape of 26 proteins using the Go-like model. The distance between the denaturated state and the transition state, XF, was calculated using the Bell theory and the nonlinear Dudko-Hummer-Szabo theory, and its relation to the geometrical properties of the native state was considered in detail. We showed that none of the structural parameters, such as the contact order, protein length, and radius of cross section, correlate with XF for all classes of proteins. To overcome this problem, we have introduced the nematic order parameter P02, which describes the ordering of the structured elements of the native state. Due to its topologically global nature, P02 is better than other structural parameters in describing the folding free energy landscape. In particular, P02 displays a good correlation with XF extracted from the nonlinear theory for all three classes of proteins. Therefore, this parameter can be used to predict XF for any protein, if its native structure is known.
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7 November 2018
Research Article|
November 02 2018
A topological order parameter for describing folding free energy landscapes of proteins Available to Purchase
Maksim Kouza
Mai Suan Li
a)
P. D. Lan and M. Kouza contributed equally to this work.
b)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 149, 175101 (2018)
Article history
Received:
July 31 2018
Accepted:
October 11 2018
Citation
Pham Dang LanMaksim KouzaAndrzej KloczkowskiMai Suan Li; A topological order parameter for describing folding free energy landscapes of proteins. J. Chem. Phys. 7 November 2018; 149 (17): 175101. https://doi.org/10.1063/1.5050483
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