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Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications.

Yaghmaei S, Roberts C, Ai R, Mizwicki MT, Chang CE - In Silico Pharmacol (2013)

Bottom Line: This differs from the x-ray, kinked geometry, where the side-chain forms an H-bond with the 1α-OH group.Furthermore, 1,25D3, but not MK was observed to stabilize the x-ray geometry of R274 during the > 30 ns MD runs.The MD methodology applied herein provides an in silico foundation to be expanded upon to better understand the intrinsic flexibility of the VDR and better understand key side-chain and backbone movements involved in the bimolecular interaction between the VDR and its' ligands.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of California, Riverside, California.

ABSTRACT

Purpose: The thermodynamically favored complex between the nuclear vitamin D receptor (VDR) and 1α,25(OH)2-vitamin D3 (1,25D3) triggers a shift in equilibrium to favor VDR binding to DNA, heterodimerization with the nuclear retinoid x receptor (RXR) and subsequent regulation of gene transcription. The key amino acids and structural requirements governing VDR binding to nuclear coactivators (NCoA) are well defined. Yet very little is understood about the internal changes in amino acid flexibility underpinning the control of ligand affinity, helix 12 conformation and function. Herein, we use molecular dynamics (MD) to study how the backbone and side-chain flexibility of the VDR differs when a) complexed to 1α,25(OH)2-vitamin D3 (1,25D3, agonist) and (23S),25-dehydro-1α(OH)-vitamin D3-26,23-lactone (MK, antagonist); b) residues that form hydrogen bonds with the C25-OH (H305 and H397) of 1,25D3 are mutated to phenylalanine; c) helix 12 conformation is changed and ligand is removed; and d) x-ray water near the C1- and C3-OH groups of 1,25D3 are present or replaced with explicit solvent.

Methods: We performed molecular dynamic simulations on the apo- and holo-VDRs and used T-Analyst to monitor the changes in the backbone and side-chain flexibility of residues that form regions of the VDR ligand binding pocket (LBP), NCoA surface and control helix 12 conformation.

Results: The VDR-1,25D3 and VDR-MK MD simulations demonstrate that 1,25D3 and MK induce highly similar changes in backbone and side-chain flexibility in residues that form the LBP. MK however did increase the backbone and side-chain flexibility of L404 and R274 respectively. MK also induced expansion of the VDR charge clamp (i.e. NCoA surface) and weakened the intramolecular interaction between H305---V418 (helix 12) and TYR401 (helix 11). In VDR_FF, MK induced a generally more rigid LBP and stronger interaction between F397 and F422 than 1,25D3, and reduced the flexibility of the R274 side-chain. Lastly the VDR MD simulations indicate that R274 can sample multiple conformations in the presence of ligand. When the R274 is extended, the β-OH group of 1,25D3 lies proximal to the backbone carbonyl oxygen of R274 and the side-chain forms H-bonds with hinge domain residues. This differs from the x-ray, kinked geometry, where the side-chain forms an H-bond with the 1α-OH group. Furthermore, 1,25D3, but not MK was observed to stabilize the x-ray geometry of R274 during the > 30 ns MD runs.

Conclusions: The MD methodology applied herein provides an in silico foundation to be expanded upon to better understand the intrinsic flexibility of the VDR and better understand key side-chain and backbone movements involved in the bimolecular interaction between the VDR and its' ligands.

No MeSH data available.


Related in: MedlinePlus

Changes in the backbone and side-chain molecular dynamics (MD) of apoVDR complexes. In the figure panels helix 12 is colored yellow; increased (green ribbon) or reduced (magenta ribbon) backbone flexibility; and increased (red tube structure) or reduced (blue tube structure) side-chain flexibility are highlighted and labeled. A) Changes in the MD when helix 12 is closed and the 1,25D3 ligand removed (apoVDR) when compared to VDR-1,25D3. B) Changes in the flexibility of the homology modeled helix 12 opened apoVDR moleclule backbone and side-chain residues when compared to the helix 12 closed apoVDR molecule. C) Changes in the flexibility of the backbone and side-chain atoms of the closed helix 12 apoVDR_FF conformation when compared to the helix 12 closed, apoVDR conformer. D) Changes in the backbone and side-chain flexibility of the helix 12 opened, apoVDR_FF conformation when compared to helix 12 opened apoVDR conformer. As in Figure 2, only changes in the backbone flexibility of residues with an entropy difference > 0.14 kcal/mol are labeled in the figure. Flexibility changes of LBP side-chain residues are labeled if the entropy difference was > 0.3 kcal/mol in the comparsion. Only the lower portion of the VDR is shown for simplicity (compare to Figure 1).
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Fig5: Changes in the backbone and side-chain molecular dynamics (MD) of apoVDR complexes. In the figure panels helix 12 is colored yellow; increased (green ribbon) or reduced (magenta ribbon) backbone flexibility; and increased (red tube structure) or reduced (blue tube structure) side-chain flexibility are highlighted and labeled. A) Changes in the MD when helix 12 is closed and the 1,25D3 ligand removed (apoVDR) when compared to VDR-1,25D3. B) Changes in the flexibility of the homology modeled helix 12 opened apoVDR moleclule backbone and side-chain residues when compared to the helix 12 closed apoVDR molecule. C) Changes in the flexibility of the backbone and side-chain atoms of the closed helix 12 apoVDR_FF conformation when compared to the helix 12 closed, apoVDR conformer. D) Changes in the backbone and side-chain flexibility of the helix 12 opened, apoVDR_FF conformation when compared to helix 12 opened apoVDR conformer. As in Figure 2, only changes in the backbone flexibility of residues with an entropy difference > 0.14 kcal/mol are labeled in the figure. Flexibility changes of LBP side-chain residues are labeled if the entropy difference was > 0.3 kcal/mol in the comparsion. Only the lower portion of the VDR is shown for simplicity (compare to Figure 1).

Mentions: Removal of 1,25D3 from VDRwt resulted in no major overall change in the ligand binding pocket (LBP) backbone entropy. Perhaps most importantly, helix 12 did not show a significant change in backbone motion in the absence of ligand when compared to VDR-1,25D3 (Figure 5A). Overall, not many changes in the VDR side-chain flexibility was observed; however, H305 did become more flexible and L230 more rigid during the run (Figure 5A).Figure 5


Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications.

Yaghmaei S, Roberts C, Ai R, Mizwicki MT, Chang CE - In Silico Pharmacol (2013)

Changes in the backbone and side-chain molecular dynamics (MD) of apoVDR complexes. In the figure panels helix 12 is colored yellow; increased (green ribbon) or reduced (magenta ribbon) backbone flexibility; and increased (red tube structure) or reduced (blue tube structure) side-chain flexibility are highlighted and labeled. A) Changes in the MD when helix 12 is closed and the 1,25D3 ligand removed (apoVDR) when compared to VDR-1,25D3. B) Changes in the flexibility of the homology modeled helix 12 opened apoVDR moleclule backbone and side-chain residues when compared to the helix 12 closed apoVDR molecule. C) Changes in the flexibility of the backbone and side-chain atoms of the closed helix 12 apoVDR_FF conformation when compared to the helix 12 closed, apoVDR conformer. D) Changes in the backbone and side-chain flexibility of the helix 12 opened, apoVDR_FF conformation when compared to helix 12 opened apoVDR conformer. As in Figure 2, only changes in the backbone flexibility of residues with an entropy difference > 0.14 kcal/mol are labeled in the figure. Flexibility changes of LBP side-chain residues are labeled if the entropy difference was > 0.3 kcal/mol in the comparsion. Only the lower portion of the VDR is shown for simplicity (compare to Figure 1).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Fig5: Changes in the backbone and side-chain molecular dynamics (MD) of apoVDR complexes. In the figure panels helix 12 is colored yellow; increased (green ribbon) or reduced (magenta ribbon) backbone flexibility; and increased (red tube structure) or reduced (blue tube structure) side-chain flexibility are highlighted and labeled. A) Changes in the MD when helix 12 is closed and the 1,25D3 ligand removed (apoVDR) when compared to VDR-1,25D3. B) Changes in the flexibility of the homology modeled helix 12 opened apoVDR moleclule backbone and side-chain residues when compared to the helix 12 closed apoVDR molecule. C) Changes in the flexibility of the backbone and side-chain atoms of the closed helix 12 apoVDR_FF conformation when compared to the helix 12 closed, apoVDR conformer. D) Changes in the backbone and side-chain flexibility of the helix 12 opened, apoVDR_FF conformation when compared to helix 12 opened apoVDR conformer. As in Figure 2, only changes in the backbone flexibility of residues with an entropy difference > 0.14 kcal/mol are labeled in the figure. Flexibility changes of LBP side-chain residues are labeled if the entropy difference was > 0.3 kcal/mol in the comparsion. Only the lower portion of the VDR is shown for simplicity (compare to Figure 1).
Mentions: Removal of 1,25D3 from VDRwt resulted in no major overall change in the ligand binding pocket (LBP) backbone entropy. Perhaps most importantly, helix 12 did not show a significant change in backbone motion in the absence of ligand when compared to VDR-1,25D3 (Figure 5A). Overall, not many changes in the VDR side-chain flexibility was observed; however, H305 did become more flexible and L230 more rigid during the run (Figure 5A).Figure 5

Bottom Line: This differs from the x-ray, kinked geometry, where the side-chain forms an H-bond with the 1α-OH group.Furthermore, 1,25D3, but not MK was observed to stabilize the x-ray geometry of R274 during the > 30 ns MD runs.The MD methodology applied herein provides an in silico foundation to be expanded upon to better understand the intrinsic flexibility of the VDR and better understand key side-chain and backbone movements involved in the bimolecular interaction between the VDR and its' ligands.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of California, Riverside, California.

ABSTRACT

Purpose: The thermodynamically favored complex between the nuclear vitamin D receptor (VDR) and 1α,25(OH)2-vitamin D3 (1,25D3) triggers a shift in equilibrium to favor VDR binding to DNA, heterodimerization with the nuclear retinoid x receptor (RXR) and subsequent regulation of gene transcription. The key amino acids and structural requirements governing VDR binding to nuclear coactivators (NCoA) are well defined. Yet very little is understood about the internal changes in amino acid flexibility underpinning the control of ligand affinity, helix 12 conformation and function. Herein, we use molecular dynamics (MD) to study how the backbone and side-chain flexibility of the VDR differs when a) complexed to 1α,25(OH)2-vitamin D3 (1,25D3, agonist) and (23S),25-dehydro-1α(OH)-vitamin D3-26,23-lactone (MK, antagonist); b) residues that form hydrogen bonds with the C25-OH (H305 and H397) of 1,25D3 are mutated to phenylalanine; c) helix 12 conformation is changed and ligand is removed; and d) x-ray water near the C1- and C3-OH groups of 1,25D3 are present or replaced with explicit solvent.

Methods: We performed molecular dynamic simulations on the apo- and holo-VDRs and used T-Analyst to monitor the changes in the backbone and side-chain flexibility of residues that form regions of the VDR ligand binding pocket (LBP), NCoA surface and control helix 12 conformation.

Results: The VDR-1,25D3 and VDR-MK MD simulations demonstrate that 1,25D3 and MK induce highly similar changes in backbone and side-chain flexibility in residues that form the LBP. MK however did increase the backbone and side-chain flexibility of L404 and R274 respectively. MK also induced expansion of the VDR charge clamp (i.e. NCoA surface) and weakened the intramolecular interaction between H305---V418 (helix 12) and TYR401 (helix 11). In VDR_FF, MK induced a generally more rigid LBP and stronger interaction between F397 and F422 than 1,25D3, and reduced the flexibility of the R274 side-chain. Lastly the VDR MD simulations indicate that R274 can sample multiple conformations in the presence of ligand. When the R274 is extended, the β-OH group of 1,25D3 lies proximal to the backbone carbonyl oxygen of R274 and the side-chain forms H-bonds with hinge domain residues. This differs from the x-ray, kinked geometry, where the side-chain forms an H-bond with the 1α-OH group. Furthermore, 1,25D3, but not MK was observed to stabilize the x-ray geometry of R274 during the > 30 ns MD runs.

Conclusions: The MD methodology applied herein provides an in silico foundation to be expanded upon to better understand the intrinsic flexibility of the VDR and better understand key side-chain and backbone movements involved in the bimolecular interaction between the VDR and its' ligands.

No MeSH data available.


Related in: MedlinePlus