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

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.

Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations

“…31 During simulations of several tens of nanoseconds, 24−26 the VDR-LBD/antagonist complex fluctuated around the crystal structure (i.e., the active conformation), and a large conformational change around H12 was not observed. Even in microsecond-scale all-atom or coarse-grained MD simulations of VDR-LBD without ligand, 29 the position of H12 was not significantly different from that in the active conformation.…”

“…21,22 In contrast, in the antagonist-bound state, the H11-H12 region is disordered, 23 suggesting that the flexibility around H12 prevents the active conformation of H12. Molecular dynamics (MD) simulations have been applied to study the structural fluctuation of H12 in agonist-and/or antagonist-bound VDR-LBD, 24−26 VDR-LBD with coactivator, 27 drug design, 28 conformational changes in the apo state, 29 and pathway analysis of ligand dissociation from VDR-LBD 30 and NRs. 31 During simulations of several tens of nanoseconds, 24−26 the VDR-LBD/antagonist complex fluctuated around the crystal structure (i.e., the active conformation), and a large conformational change around H12 was not observed.…”

“…According to experimental studies using small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange coupled with mass spectrometry, , and nuclear magnetic resonance, natural hormone (agonist)-bound VDR adopts an active conformation even in solution, whereas structural fluctuations in the H11-H12 region were observed in the apo state. , In contrast, in the antagonist-bound state, the H11-H12 region is disordered, suggesting that the flexibility around H12 prevents the active conformation of H12. Molecular dynamics (MD) simulations have been applied to study the structural fluctuation of H12 in agonist- and/or antagonist-bound VDR-LBD, − VDR-LBD with coactivator, drug design, conformational changes in the apo state, and pathway analysis of ligand dissociation from VDR-LBD and NRs . During simulations of several tens of nanoseconds, − the VDR-LBD/antagonist complex fluctuated around the crystal structure (i.e., the active conformation), and a large conformational change around H12 was not observed.…”