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

作者：Sun, Yunxiang; Ding, Feng; Ming, Dengming^*

来源：International Journal of Molecular Sciences, 2018, 19(5): 1515.

DOI：10.3390/ijms19051515

• nonnative energetic frustration
• non-native contact
• frustrated G-like model
• -sandwich protein
• hydrophilic-hydrophobic mutation

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- 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) beta-sandwich proteins, and examined nonnative-contact-based energetic frustrations G-like model. Our calculations showed that nonnative-interaction-based energetic frustrations in beta-sandwich proteins are much more complicated than those in all-alpha 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 beta-sandwich proteins. Taken together, a strong interplay might exist between nonnative-interaction energetic frustrations and the protein native-contact networks, which ensures that beta-sandwich domains adopt a common folding mechanism.

• 出版日期2018-5
• 单位南京工业大学