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Int. J. Mol. Sci. 2018, 19(5), 1515; https://doi.org/10.3390/ijms19051515

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.
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)
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Abstract

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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