Limits...
Interactions of L-3,5,4'-Triiodothyronine, Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes.

Westergard T, Salari R, Martin JV, Brannigan G - PLoS ONE (2015)

Bottom Line: T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces.Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites.In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey, United States of America.

ABSTRACT
Structural mechanisms of modulation of γ-aminobutyric acid (GABA) type A receptors by neurosteroids and hormones remain unclear. The thyroid hormone L-3,5,3'-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Here we use functional experiments on α2β1γ2 GABAA receptors expressed in Xenopus oocytes to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces. Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites. In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.

No MeSH data available.


Related in: MedlinePlus

Molecular Dynamics Simulations of GABAA receptors with T3 bound.A) GABAA receptor-membrane complex, shown in cartoon with surface overlay, from a view parallel to the membrane. Lipids in the membrane are in licorice with POPC molecules colored by atom name and cholesterol molecules in pink. T3 molecules colored by atom name are shown at the interfaces between the α (silver) and β (green) subunits. B) Initial (gray) and final (orange) poses of T3 from 200 ns MD simulation. C) Representative frame showing interactions between T3 at one of the β-α interfaces, corresponding to the first column of S1–S3 Tables. Numbers shown in parentheses in residue labels represent the contribution of hydrogen bonds with the residue to the total number of hydrogen bonds observed in the second (equilibrated) half of the MD simulation (listed for all interfaces in S3 Table). T3 frequently formed simultaneous hydrogen bonds to αM1 I228 and βM2 S265, as shown here. D) Total energy of T3 molecules across trajectory, relative to that of the β-α interface shown in first column and in Panel C, and in left to right order of increasing average energy/decreasing favorability. Energy trajectories were smoothed with a 20 ns window, with the initial and final 20 ns removed due to distortion from the windowing process. Solid region of the trajectory curve indicates the equilibrated regions used in calculating the average listed in S2 Table, and represented here by the horizontal solid line. Decomposition of the total energies can be found in S2 Table and S4 Fig
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4589331&req=5

pone.0139072.g006: Molecular Dynamics Simulations of GABAA receptors with T3 bound.A) GABAA receptor-membrane complex, shown in cartoon with surface overlay, from a view parallel to the membrane. Lipids in the membrane are in licorice with POPC molecules colored by atom name and cholesterol molecules in pink. T3 molecules colored by atom name are shown at the interfaces between the α (silver) and β (green) subunits. B) Initial (gray) and final (orange) poses of T3 from 200 ns MD simulation. C) Representative frame showing interactions between T3 at one of the β-α interfaces, corresponding to the first column of S1–S3 Tables. Numbers shown in parentheses in residue labels represent the contribution of hydrogen bonds with the residue to the total number of hydrogen bonds observed in the second (equilibrated) half of the MD simulation (listed for all interfaces in S3 Table). T3 frequently formed simultaneous hydrogen bonds to αM1 I228 and βM2 S265, as shown here. D) Total energy of T3 molecules across trajectory, relative to that of the β-α interface shown in first column and in Panel C, and in left to right order of increasing average energy/decreasing favorability. Energy trajectories were smoothed with a 20 ns window, with the initial and final 20 ns removed due to distortion from the windowing process. Solid region of the trajectory curve indicates the equilibrated regions used in calculating the average listed in S2 Table, and represented here by the horizontal solid line. Decomposition of the total energies can be found in S2 Table and S4 Fig

Mentions: Initial (following minimization) and final poses of T3 (after 200 ns of Molecular Dynamics simulation) are shown in Fig 6A and 6B. Root-mean-squared-displacements (RMSD) between T3 in the initial and final frames ranged from 5.5–8.5 Å (S3 Fig, for comparison, an extended T3 molecule is about 15 Å in length). However, root-mean-squared-fluctuations (RMSF) for the heavy atoms of the T3 molecule over the last 100 ns of simulation ranged between 0.7 and 1.8 Å (S3 Fig), indicating that the T3 molecules become less fluid in the sites (and potentially more tightly bound) as the simulation proceeds.


Interactions of L-3,5,4'-Triiodothyronine, Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes.

Westergard T, Salari R, Martin JV, Brannigan G - PLoS ONE (2015)

Molecular Dynamics Simulations of GABAA receptors with T3 bound.A) GABAA receptor-membrane complex, shown in cartoon with surface overlay, from a view parallel to the membrane. Lipids in the membrane are in licorice with POPC molecules colored by atom name and cholesterol molecules in pink. T3 molecules colored by atom name are shown at the interfaces between the α (silver) and β (green) subunits. B) Initial (gray) and final (orange) poses of T3 from 200 ns MD simulation. C) Representative frame showing interactions between T3 at one of the β-α interfaces, corresponding to the first column of S1–S3 Tables. Numbers shown in parentheses in residue labels represent the contribution of hydrogen bonds with the residue to the total number of hydrogen bonds observed in the second (equilibrated) half of the MD simulation (listed for all interfaces in S3 Table). T3 frequently formed simultaneous hydrogen bonds to αM1 I228 and βM2 S265, as shown here. D) Total energy of T3 molecules across trajectory, relative to that of the β-α interface shown in first column and in Panel C, and in left to right order of increasing average energy/decreasing favorability. Energy trajectories were smoothed with a 20 ns window, with the initial and final 20 ns removed due to distortion from the windowing process. Solid region of the trajectory curve indicates the equilibrated regions used in calculating the average listed in S2 Table, and represented here by the horizontal solid line. Decomposition of the total energies can be found in S2 Table and S4 Fig
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589331&req=5

pone.0139072.g006: Molecular Dynamics Simulations of GABAA receptors with T3 bound.A) GABAA receptor-membrane complex, shown in cartoon with surface overlay, from a view parallel to the membrane. Lipids in the membrane are in licorice with POPC molecules colored by atom name and cholesterol molecules in pink. T3 molecules colored by atom name are shown at the interfaces between the α (silver) and β (green) subunits. B) Initial (gray) and final (orange) poses of T3 from 200 ns MD simulation. C) Representative frame showing interactions between T3 at one of the β-α interfaces, corresponding to the first column of S1–S3 Tables. Numbers shown in parentheses in residue labels represent the contribution of hydrogen bonds with the residue to the total number of hydrogen bonds observed in the second (equilibrated) half of the MD simulation (listed for all interfaces in S3 Table). T3 frequently formed simultaneous hydrogen bonds to αM1 I228 and βM2 S265, as shown here. D) Total energy of T3 molecules across trajectory, relative to that of the β-α interface shown in first column and in Panel C, and in left to right order of increasing average energy/decreasing favorability. Energy trajectories were smoothed with a 20 ns window, with the initial and final 20 ns removed due to distortion from the windowing process. Solid region of the trajectory curve indicates the equilibrated regions used in calculating the average listed in S2 Table, and represented here by the horizontal solid line. Decomposition of the total energies can be found in S2 Table and S4 Fig
Mentions: Initial (following minimization) and final poses of T3 (after 200 ns of Molecular Dynamics simulation) are shown in Fig 6A and 6B. Root-mean-squared-displacements (RMSD) between T3 in the initial and final frames ranged from 5.5–8.5 Å (S3 Fig, for comparison, an extended T3 molecule is about 15 Å in length). However, root-mean-squared-fluctuations (RMSF) for the heavy atoms of the T3 molecule over the last 100 ns of simulation ranged between 0.7 and 1.8 Å (S3 Fig), indicating that the T3 molecules become less fluid in the sites (and potentially more tightly bound) as the simulation proceeds.

Bottom Line: T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces.Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites.In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey, United States of America.

ABSTRACT
Structural mechanisms of modulation of γ-aminobutyric acid (GABA) type A receptors by neurosteroids and hormones remain unclear. The thyroid hormone L-3,5,3'-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Here we use functional experiments on α2β1γ2 GABAA receptors expressed in Xenopus oocytes to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces. Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites. In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.

No MeSH data available.


Related in: MedlinePlus