The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site

Rafael Claveria-Gimeno,Sonia Vega,Ignacio Morales-Chueca,Adrian Velazquez-Campoy,Manel Esteller,Pilar M. Lanuza,Olga C. Jorge-Torres,Olga Abian

doi:10.1038/srep41635

Abstract

Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities.

Highlights

Among the thousands of proteins encoded in the human genome 30% of them are completely or partially devoid of stable structure[1,2]
Methyl-CpG binding Protein 2 (MeCP2) is an intrinsically disordered proteins (IDPs) organized into six domains: N-terminal domain (NTD), methyl binding domain (MBD), intervening domain (ID), transcriptional repression domain (TRD), C-terminal domain α(CTDα), and C-terminal domain β(CTDβ) (Supplementary Fig. S1)[8,9]
It has been previously shown that, contrary to the results reported here, the addition of NTD and ID domains lowers the structural stability of MBD12

Summary

Introduction

Among the thousands of proteins encoded in the human genome 30% of them are completely or partially devoid of stable structure[1,2] These intrinsically disordered proteins (IDPs) are characterized by a global or local lack of secondary and tertiary structure, and they may undergo a structural rearrangement upon the interaction with their binding partners. Disordered regions have a priori unknown roles in molecular stability and function While these regions are characterized by a biased residue composition, where polar and charged residues predominate and they exhibit a considerable propensity to be exposed to the solvent[3], they still can make key contacts with structured regions and affect the global stability and the dynamics of the protein, as well as modulate the interaction with a binding partner. It has been proposed to be the core of the protein structure as it would drive interdomain coupling, and mutations on this domain would impact on its own and global stability and function[8]

Methods

Results

Discussion

Conclusion