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. 2013 Oct;81(10):1686-98.
doi: 10.1002/prot.24303. Epub 2013 Jul 23.

Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins

Wade Borcherds  1 , Stepan Kashtanov, Hongwei Wu, Gary W Daughdrill
Affiliations

Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins

Wade Borcherds et al. Proteins. 2013 Oct.

Abstract

The p53 transactivation domain (p53TAD) is an intrinsically disordered protein (IDP) domain that undergoes coupled folding and binding when interacting with partner proteins like the E3 ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70. The secondary structure and dynamics of six closely related mammalian homologues of p53TAD were investigated using nuclear magnetic resonance (NMR) spectroscopy. Differences in both transient secondary structure and backbone dynamics were observed for the homologues. Many of these differences were localized to the binding sites for MDM2 and RPA70. The amount of transient helical secondary structure observed for the MDM2 binding site was lower for the dog and mouse homologues, compared with human, and the amount of transient helical secondary structure observed for the RPA70 binding site was higher for guinea pig and rabbit, compared with human. Differences in the amount of transient helical secondary structure observed for the MDM2 binding site were directly related to amino acid substitutions occurring on the solvent exposed side of the amphipathic helix that forms during the p53TAD/MDM2 interaction. Differences in the amount of transient helical secondary structure were not as easily explained for the RPA70 binding site because of its extensive sequence divergence. Clustering analysis shows that the divergence in the transient secondary structure of the p53TAD homologues exceeds the amino acid sequence divergence. In contrast, strong correlations were observed between the backbone dynamics of the homologues and the sequence identity matrix, suggesting that the dynamic behavior of IDPs is a conserved evolutionary feature.

Keywords: intrinsically disordered proteins; protein dynamics; structural divergence; structural evolution.

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