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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

Molecular dynamics (MD) simulations of holo VDR complexes. A) The average charge clamp distance between K246 and E420 is shown for the holoVDR models (also see supplemental Fig. 3C). B) The distance in relation to time, between H397 and Y401 (bottom panel), Y401 and V418 (middle panel) and H305 and Y401 (top panel) during the 23ns MD run is plotted for VDR-1,25D3 (magenta), VDR_FF-1,25D3 (purple), VDR-MK (light green) and VDR_FF-MK (yellow). The backbone and ligand binding pocket (LBP) side-chain dynamics of C) VDR-MK compared to VDR-1,25D3 (Table 1), D) VDR_FF-MK compared to VDR-MK and E) VDR_FF-1,25D3 compared to VDR-1,25D3. Regions of the VDR where the backbone flexibility is increased or decreased are indicated by coloring the ribbon light green and blue respectively. Changes in backbone flexibility are only mentioned for the residues with the entropy difference > 0.14 kcal/mol. In these panels more flexible or rigid side-chains are rendered in tube structure, colored magenta and red respectively. The flexibility changes for side-chains within the LBP are only mentioned when the entropy difference was above 0.3 kcal/mol. In these panels H12 is colored yellow and only the lower portion of the VDR is shown for clarity (compare to Figure 1).
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Fig2: Molecular dynamics (MD) simulations of holo VDR complexes. A) The average charge clamp distance between K246 and E420 is shown for the holoVDR models (also see supplemental Fig. 3C). B) The distance in relation to time, between H397 and Y401 (bottom panel), Y401 and V418 (middle panel) and H305 and Y401 (top panel) during the 23ns MD run is plotted for VDR-1,25D3 (magenta), VDR_FF-1,25D3 (purple), VDR-MK (light green) and VDR_FF-MK (yellow). The backbone and ligand binding pocket (LBP) side-chain dynamics of C) VDR-MK compared to VDR-1,25D3 (Table 1), D) VDR_FF-MK compared to VDR-MK and E) VDR_FF-1,25D3 compared to VDR-1,25D3. Regions of the VDR where the backbone flexibility is increased or decreased are indicated by coloring the ribbon light green and blue respectively. Changes in backbone flexibility are only mentioned for the residues with the entropy difference > 0.14 kcal/mol. In these panels more flexible or rigid side-chains are rendered in tube structure, colored magenta and red respectively. The flexibility changes for side-chains within the LBP are only mentioned when the entropy difference was above 0.3 kcal/mol. In these panels H12 is colored yellow and only the lower portion of the VDR is shown for clarity (compare to Figure 1).

Mentions: VDR-1,25D3 molecular dynamics (MD) simulations demonstrated that the average charge clamp distance between the side chain nitrogen of K246 and the delta carbon of E420 remained constant over a 32ns run (Figure 2A and Additional file 3: Table S2a). Similar average charge clamp distances were observed in the VDR_H305F-1,25D3 and VDR_H397F-1,25D3 models. Consistent with the functional results, the VDR_FF-MK charge clamp distance was observed to be more similar to the hVDRwt-1,25D3 than the VDRwt-MK model. In the latter model, the charge clamp equilibrated to be over 1.5 Å greater than VDRwt-1,25D3 (Figure 2A). The one model that did not correlate with functional data was the VDR_FF-1,25D3 model, where the charge clamp distance was on average 2.5 Å greater than VDR-1,25D3 (Figures 1 and 2A).Figure 2


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)

Molecular dynamics (MD) simulations of holo VDR complexes. A) The average charge clamp distance between K246 and E420 is shown for the holoVDR models (also see supplemental Fig. 3C). B) The distance in relation to time, between H397 and Y401 (bottom panel), Y401 and V418 (middle panel) and H305 and Y401 (top panel) during the 23ns MD run is plotted for VDR-1,25D3 (magenta), VDR_FF-1,25D3 (purple), VDR-MK (light green) and VDR_FF-MK (yellow). The backbone and ligand binding pocket (LBP) side-chain dynamics of C) VDR-MK compared to VDR-1,25D3 (Table 1), D) VDR_FF-MK compared to VDR-MK and E) VDR_FF-1,25D3 compared to VDR-1,25D3. Regions of the VDR where the backbone flexibility is increased or decreased are indicated by coloring the ribbon light green and blue respectively. Changes in backbone flexibility are only mentioned for the residues with the entropy difference > 0.14 kcal/mol. In these panels more flexible or rigid side-chains are rendered in tube structure, colored magenta and red respectively. The flexibility changes for side-chains within the LBP are only mentioned when the entropy difference was above 0.3 kcal/mol. In these panels H12 is colored yellow and only the lower portion of the VDR is shown for clarity (compare to Figure 1).
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Related In: Results  -  Collection

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Fig2: Molecular dynamics (MD) simulations of holo VDR complexes. A) The average charge clamp distance between K246 and E420 is shown for the holoVDR models (also see supplemental Fig. 3C). B) The distance in relation to time, between H397 and Y401 (bottom panel), Y401 and V418 (middle panel) and H305 and Y401 (top panel) during the 23ns MD run is plotted for VDR-1,25D3 (magenta), VDR_FF-1,25D3 (purple), VDR-MK (light green) and VDR_FF-MK (yellow). The backbone and ligand binding pocket (LBP) side-chain dynamics of C) VDR-MK compared to VDR-1,25D3 (Table 1), D) VDR_FF-MK compared to VDR-MK and E) VDR_FF-1,25D3 compared to VDR-1,25D3. Regions of the VDR where the backbone flexibility is increased or decreased are indicated by coloring the ribbon light green and blue respectively. Changes in backbone flexibility are only mentioned for the residues with the entropy difference > 0.14 kcal/mol. In these panels more flexible or rigid side-chains are rendered in tube structure, colored magenta and red respectively. The flexibility changes for side-chains within the LBP are only mentioned when the entropy difference was above 0.3 kcal/mol. In these panels H12 is colored yellow and only the lower portion of the VDR is shown for clarity (compare to Figure 1).
Mentions: VDR-1,25D3 molecular dynamics (MD) simulations demonstrated that the average charge clamp distance between the side chain nitrogen of K246 and the delta carbon of E420 remained constant over a 32ns run (Figure 2A and Additional file 3: Table S2a). Similar average charge clamp distances were observed in the VDR_H305F-1,25D3 and VDR_H397F-1,25D3 models. Consistent with the functional results, the VDR_FF-MK charge clamp distance was observed to be more similar to the hVDRwt-1,25D3 than the VDRwt-MK model. In the latter model, the charge clamp equilibrated to be over 1.5 Å greater than VDRwt-1,25D3 (Figure 2A). The one model that did not correlate with functional data was the VDR_FF-1,25D3 model, where the charge clamp distance was on average 2.5 Å greater than VDR-1,25D3 (Figures 1 and 2A).Figure 2

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