A structural entropy index to analyse local conformations in intrinsically disordered proteins

[Display omitted] •Analyses of ensemble of Intrinsic Disorder Proteins.•Use of a protein structural alphabet to analyze the IDP ensemble.•Local protein conformation entropy to distinguish rigidity, flexibility and disorder zones.•Some IDPs have highly rigid (mobile) regions. Sequence – structure – f...

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Published in:Journal of structural biology 2020-04, Vol.210 (1), p.107464-107464, Article 107464
Main Authors: Akhila, Melarkode Vattekatte, Narwani, Tarun Jairaj, Floch, Aline, Maljković, Mirjana, Bisoo, Soubika, Shinada, Nicolas K., Kranjc, Agata, Gelly, Jean-Christophe, Srinivasan, Narayanaswamy, Mitić, Nenad, de Brevern, Alexandre G.
Format: Article
Language:English
Subjects:
Entropy
Flexibility
Protein structures
Rigidity
Structural alphabet
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Summary:[Display omitted] •Analyses of ensemble of Intrinsic Disorder Proteins.•Use of a protein structural alphabet to analyze the IDP ensemble.•Local protein conformation entropy to distinguish rigidity, flexibility and disorder zones.•Some IDPs have highly rigid (mobile) regions. Sequence – structure – function paradigm has been revolutionized by the discovery of disordered regions and disordered proteins more than two decades ago. While the definition of rigidity is simple with X-ray structures, the notion of flexibility is linked to high experimental B-factors. The definition of disordered regions is more complex as in these same X-ray structures; it is associated to the position of missing residues. Thus a continuum so seems to exist between rigidity, flexibility and disorder. However, it had not been precisely described. In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disordered proteins in our study.
ISSN:1047-8477
1095-8657
DOI:10.1016/j.jsb.2020.107464