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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

The role of side-chain chemistry on ARG274 conformational flexibility.A) The conformation of ARG274 and its hydrogen bonding partners for VDR-1,25D3 at 1.0 ns and 30.0 ns are shown in magenta and light blue respectively. B) The conformation of ARG274 and its hydrogen bonding partners for VDR-MK at 1.0 ns and 23.0 ns are shown in light green and yellow respectively. Water molecules are not shown for clarity.
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Fig4: The role of side-chain chemistry on ARG274 conformational flexibility.A) The conformation of ARG274 and its hydrogen bonding partners for VDR-1,25D3 at 1.0 ns and 30.0 ns are shown in magenta and light blue respectively. B) The conformation of ARG274 and its hydrogen bonding partners for VDR-MK at 1.0 ns and 23.0 ns are shown in light green and yellow respectively. Water molecules are not shown for clarity.

Mentions: In both of the models, the side-chain hydroxyl group of 1,25D3 hydrogen bonds to H305 and H397; the 3β-hydroxy of 1,25D3 is on average 3.5 Å away from the side chain hydroxyl group of S278 and Y143; and the 1α-hydroxy is on average 3.1 Å away from S237. In model a, R274 hydrogen bonds to the 1α-hydroxy of 1,25D3 and three crystal water molecules and over the duration of the MD run did not move from the kinked conformation. In model b, two water molecules were observed between the guanidine head group of R274 and the 1α-hydroxy of 1,25D3 to begin the simulation. One (ns) into the simulation, the carbon chain of R274 moved into a staggered, extended geometry (see Additional file 5: Figure S3) and the 3β-hydroxy of 1,25D3 was proximal to the backbone carbonyl oxygen of R274 (Figure 4A). Between 10 and 20 ns, the two water molecules became displaced from the R274 residue, but the side-chain remained staggered and in close hydrogen bonding distance to H139 and T142 (Figure 4A). These two residues are not actually part of the ligand binding domain, but rather they belong to the hinge domain of the VDR molecule. Thirty (ns) into the MD run the R274 R-group lost contact with H139, and rotated into the ‘kinked’ geometry where the guanidine head group formed the hydrogen bond with the 1-OH group of 1,25D3 observed in the x-ray structures (Figure 4A). During the VDR-MK MD run, it was observed that the extended geometry of R274 became ‘kinked’ 8 ns into the simulation; however, the guanidine head group did not get within H-bonding distance to the 1α-OH group of MK (Figure 4B and Additional file 6: Figure S4). Instead the R274 polar side-chain remained in a hydrogen bond network with H139, K240 and/or T142 (Figure 4B).Figure 4


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)

The role of side-chain chemistry on ARG274 conformational flexibility.A) The conformation of ARG274 and its hydrogen bonding partners for VDR-1,25D3 at 1.0 ns and 30.0 ns are shown in magenta and light blue respectively. B) The conformation of ARG274 and its hydrogen bonding partners for VDR-MK at 1.0 ns and 23.0 ns are shown in light green and yellow respectively. Water molecules are not shown for clarity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215818&req=5

Fig4: The role of side-chain chemistry on ARG274 conformational flexibility.A) The conformation of ARG274 and its hydrogen bonding partners for VDR-1,25D3 at 1.0 ns and 30.0 ns are shown in magenta and light blue respectively. B) The conformation of ARG274 and its hydrogen bonding partners for VDR-MK at 1.0 ns and 23.0 ns are shown in light green and yellow respectively. Water molecules are not shown for clarity.
Mentions: In both of the models, the side-chain hydroxyl group of 1,25D3 hydrogen bonds to H305 and H397; the 3β-hydroxy of 1,25D3 is on average 3.5 Å away from the side chain hydroxyl group of S278 and Y143; and the 1α-hydroxy is on average 3.1 Å away from S237. In model a, R274 hydrogen bonds to the 1α-hydroxy of 1,25D3 and three crystal water molecules and over the duration of the MD run did not move from the kinked conformation. In model b, two water molecules were observed between the guanidine head group of R274 and the 1α-hydroxy of 1,25D3 to begin the simulation. One (ns) into the simulation, the carbon chain of R274 moved into a staggered, extended geometry (see Additional file 5: Figure S3) and the 3β-hydroxy of 1,25D3 was proximal to the backbone carbonyl oxygen of R274 (Figure 4A). Between 10 and 20 ns, the two water molecules became displaced from the R274 residue, but the side-chain remained staggered and in close hydrogen bonding distance to H139 and T142 (Figure 4A). These two residues are not actually part of the ligand binding domain, but rather they belong to the hinge domain of the VDR molecule. Thirty (ns) into the MD run the R274 R-group lost contact with H139, and rotated into the ‘kinked’ geometry where the guanidine head group formed the hydrogen bond with the 1-OH group of 1,25D3 observed in the x-ray structures (Figure 4A). During the VDR-MK MD run, it was observed that the extended geometry of R274 became ‘kinked’ 8 ns into the simulation; however, the guanidine head group did not get within H-bonding distance to the 1α-OH group of MK (Figure 4B and Additional file 6: Figure S4). Instead the R274 polar side-chain remained in a hydrogen bond network with H139, K240 and/or T142 (Figure 4B).Figure 4

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