10 Applications of Molecular Dynamics Simulations …
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constrained the bonds with hydrogens and applied long-range interactions for the
non-bonded interactions. Two-thousand-step steepest descent minimization followed
by 8000-step conjugated gradient minimization was carried out for each entire system
prior to the final production run. Each system was subjected to 200 ps of equilibration
to reach the stable states. The equilibrated system was subsequently subjected to a
10 ns production run at 300 K temperature, 1 atm pressure, and 2 fs of time steps.
The resultant trajectory files were used to calculate the RMSD values, demonstrating that the α4β2 complexes reached stable states. The last snapshot from each
trajectory file was selected to elucidate the interactions between the 11 ligands and
the critical residues in the active site of α4β2 (Table 10.2).
10.6.2 Identification of the Ligand Binding Mode
in α-Fetoprotein
By aid of a transport protein, endocrine disrupting chemicals (EDCs) enter the cell
and cause adverse effects by disrupting endocrine receptors including androgen and
estrogen receptors. α-fetoprotein (AFP) blocks AR and ER mediated responses by
binding with androgens and estrogens to prevent entry into the target cells. Thus,
to understand the endocrine disruptive potential of a chemical, it is important to
elucidate binding to AFP. In 2012, Hong et al. measured the AFP binding affinity
of 125 structurally diverse chemicals and discovered that 53 chemicals are AFP
binders and 72 are non-binders. To assess risk of endocrine disrupting chemicals,
the binding mode of rat AFP–ligand was studied. Initially, homology modeling was
used to constructed a 3D structure of rat AF which was further optimized by an MD
simulation. The resultant trajectory file from the MD simulation informed selection
of one representative AFP protein 3D structure. This chosen structure was used
as a receptor to dock the 13 classes of chemicals in its active site. Finally, the 13
complexes selected from the molecular docking were refined using MD simulations
to understand the binding patterns of these chemicals in the active site of rat AFP
protein [69].
Molecular docking is one of the well-known techniques to predict ligand pose in
the active site of a protein. The major drawback of the rigid molecular docking is its
failure to give flexibility to the protein. AFP is a flexible protein which undergoes
an active site ligand binding-induced conformational change [70]. Hence, the MD
simulation method gave flexibility to the AFP–ligand complex and optimized complexes obtained from molecular docking. The 13 rat AFP–ligand complexes from
molecular docking were subjected to MD simulations to provide insight into the
conformational changes of rat AFP due to the 13 structurally diverse ligands binding
in the active site.
Prior to molecular docking, the 13 diverse ligands were optimized using Gaussian
09 with the basis set of 6-31G. The electrostatic potential of the ligands was calculated
with the mechanical method (B3LYP). For MD simulations, GAFF was applied
199
constrained the bonds with hydrogens and applied long-range interactions for the
non-bonded interactions. Two-thousand-step steepest descent minimization followed
by 8000-step conjugated gradient minimization was carried out for each entire system
prior to the final production run. Each system was subjected to 200 ps of equilibration
to reach the stable states. The equilibrated system was subsequently subjected to a
10 ns production run at 300 K temperature, 1 atm pressure, and 2 fs of time steps.
The resultant trajectory files were used to calculate the RMSD values, demonstrating that the α4β2 complexes reached stable states. The last snapshot from each
trajectory file was selected to elucidate the interactions between the 11 ligands and
the critical residues in the active site of α4β2 (Table 10.2).
10.6.2 Identification of the Ligand Binding Mode
in α-Fetoprotein
By aid of a transport protein, endocrine disrupting chemicals (EDCs) enter the cell
and cause adverse effects by disrupting endocrine receptors including androgen and
estrogen receptors. α-fetoprotein (AFP) blocks AR and ER mediated responses by
binding with androgens and estrogens to prevent entry into the target cells. Thus,
to understand the endocrine disruptive potential of a chemical, it is important to
elucidate binding to AFP. In 2012, Hong et al. measured the AFP binding affinity
of 125 structurally diverse chemicals and discovered that 53 chemicals are AFP
binders and 72 are non-binders. To assess risk of endocrine disrupting chemicals,
the binding mode of rat AFP–ligand was studied. Initially, homology modeling was
used to constructed a 3D structure of rat AF which was further optimized by an MD
simulation. The resultant trajectory file from the MD simulation informed selection
of one representative AFP protein 3D structure. This chosen structure was used
as a receptor to dock the 13 classes of chemicals in its active site. Finally, the 13
complexes selected from the molecular docking were refined using MD simulations
to understand the binding patterns of these chemicals in the active site of rat AFP
protein [69].
Molecular docking is one of the well-known techniques to predict ligand pose in
the active site of a protein. The major drawback of the rigid molecular docking is its
failure to give flexibility to the protein. AFP is a flexible protein which undergoes
an active site ligand binding-induced conformational change [70]. Hence, the MD
simulation method gave flexibility to the AFP–ligand complex and optimized complexes obtained from molecular docking. The 13 rat AFP–ligand complexes from
molecular docking were subjected to MD simulations to provide insight into the
conformational changes of rat AFP due to the 13 structurally diverse ligands binding
in the active site.
Prior to molecular docking, the 13 diverse ligands were optimized using Gaussian
09 with the basis set of 6-31G. The electrostatic potential of the ligands was calculated
with the mechanical method (B3LYP). For MD simulations, GAFF was applied