Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

Alejandro Estaña 1 Nathalie Sibille 2 Elise Delaforge 3 Marc Vaisset 4 Juan Cortés 5 Pau Bernadó 1
1 CBS - Centre de Biochimie Structurale [Montpellier]
2 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576
3 IBS - UMR 5075 - Institut de biologie structurale
4 LAAS-IDEA - Service Informatique : Développement, Exploitation et Assistance
LAAS - Laboratoire d'analyse et d'architecture des systèmes
5 LAAS-RIS - Équipe Robotique et InteractionS
LAAS - Laboratoire d'analyse et d'architecture des systèmes
Abstract : Intrinsically Disordered Proteins (IDPs) play fundamental roles in signaling, regulation and cell homeostasis by specifically interacting with their partners. The structural characterization of these interacting regions remains challenging and requires the integration of extensive experimental information. Here we present an approach that exploits the structural information encoded in tripeptide fragments from coil regions of high-resolution structures. Our results indicate that a simple building approach that disregards the sequence context provides a good structural representation of fully disordered regions. Conversely, the description of partially structured motifs calls for the consideration of sequence-dependent structural preferences. By using NMR Residual Dipolar Couplings and SAXS data for multiple IDPs we demonstrate that the appropriate combination of these two building strategies produces ensemble models that correctly describe the secondary structural classes and the population of partially structured regions. This study paves the way for the extension of structure prediction and protein design to disordered proteins.
Keywords : Residual dipolar couplings Protein fragment database Intrinsically disordered proteins Conformational sampling
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https://hal.laas.fr/hal-01954977
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Submitted on : Friday, December 14, 2018 - 10:27:00 AM
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Alejandro Estaña, Nathalie Sibille, Elise Delaforge, Marc Vaisset, Juan Cortés, et al.. Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database. Structure, Elsevier (Cell Press), In press, ⟨10.1016/j.str.2018.10.016⟩. ⟨hal-01954977⟩

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