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Open AccessArticle

Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins

1
College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, China
2
Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(5), 1515; https://doi.org/10.3390/ijms19051515
Received: 18 April 2018 / Revised: 8 May 2018 / Accepted: 9 May 2018 / Published: 18 May 2018
(This article belongs to the Special Issue Protein Structural Dynamics)
Nonnative interactions cause energetic frustrations in protein folding and were found to dominate key events in folding intermediates. However, systematically characterizing energetic frustrations that are caused by nonnative intra-residue interactions at residual resolution is still lacking. Recently, we studied the folding of a set of homologous all-α proteins and found that nonnative-contact-based energetic frustrations are highly correlated to topology of the protein native-contact network. Here, we studied the folding of nine homologous immunoglobulin-like (Ig-like) β-sandwich proteins, and examined nonnative-contact-based energetic frustrations Gō-like model. Our calculations showed that nonnative-interaction-based energetic frustrations in β-sandwich proteins are much more complicated than those in all- α proteins, and they exhibit highly heterogeneous effects on the folding of secondary structures. Further, the nonnative interactions introduced distinct correlations in the folding of different folding-patches of β-sandwich proteins. Taken together, a strong interplay might exist between nonnative-interaction energetic frustrations and the protein native-contact networks, which ensures that β-sandwich domains adopt a common folding mechanism. View Full-Text
Keywords: nonnative energetic frustration; non-native contact; frustrated Gō-like model; β-sandwich protein; hydrophilic-hydrophobic mutation nonnative energetic frustration; non-native contact; frustrated Gō-like model; β-sandwich protein; hydrophilic-hydrophobic mutation
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Sun, Y.; Ding, F.; Ming, D. Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins. Int. J. Mol. Sci. 2018, 19, 1515.

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