The conformational dynamics of H2-H3n and S2-H6 in gating ligand entry into the buried binding cavity of vitamin D receptor.

Wei-Ven Tee,Saharuddin Bin Mohamad,Adiratna Mat Ripen

doi:10.1038/srep35937

Wei-Ven Tee, Saharuddin Bin Mohamad + Show 1 more

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https://doi.org/10.1038/srep35937

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Abstract

Crystal structures of holo vitamin D receptor (VDR) revealed a canonical conformation in which the ligand is entrapped in a hydrophobic cavity buried in the ligand-binding domain (LBD). The mousetrap model postulates that helix 12 is positioned away from the domain to expose the interior cavity. However, the extended form of helix 12 is likely due to artifacts during crystallization. In this study, we set out to investigate conformational dynamics of apo VDR using molecular dynamics simulation on microsecond timescale. Here we show the neighboring backbones of helix 2-helix 3n and beta strand 2-helix 6 of LBD, instead of the helix 12, undergo large-scale motion, possibly gating the entrance of ligand to the ligand binding domain. Docking analysis to the simulated open structure of VDR with the estimated free energy of −37.0 kJ/mol, would emphasise the role of H2-H3n and S2-H6 in facilitating the entrance of calcitriol to the LBD of VDR.

Highlights

The human vitamin D receptor is a ligand-dependent transcription factor that belongs to the nuclear receptor (NR) superfamily[1]
In other NRs, helix 12 (H12) of apo retinoid X receptor alpha (RXRα) is extended away from the LBD4,5 but folded against the ligand-binding domain (LBD) of holo retinoic acid receptor gamma (RARγ)[6]. These observations led to the mouse-trap model[6] which proposes that large scale re-positioning of H12 seals the exposed binding cavity and stabilized by bound ligand to form a hydrophobic cleft known as activation function 2 (AF-2) for recruitment of coactivator[7]
This is consistent with the view that apo LBD of NRs exhibits some properties of molten globule[8,18], especially in the lower portion, probably due to an empty cavity in the hydrophobic core

Summary

Introduction

The human vitamin D receptor (hVDR) is a ligand-dependent transcription factor that belongs to the nuclear receptor (NR) superfamily[1]. Crystal structure of hVDR in apo state still remains elusive after 16 years. In other NRs, helix 12 (H12) of apo retinoid X receptor alpha (RXRα) is extended away from the LBD4,5 but folded against the LBD of holo retinoic acid receptor gamma (RARγ)[6]. These observations led to the mouse-trap model[6] which proposes that large scale re-positioning of H12 seals the exposed binding cavity and stabilized by bound ligand to form a hydrophobic cleft known as activation function 2 (AF-2) for recruitment of coactivator[7]. As crystal structures represent only a transient conformation of biomolecules in their lowest states of energy, X-ray crystallography is limited in elucidating dynamic conformational changes

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