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Structure and Energetics of Allosteric Regulation of HCN2 Ion Channels by Cyclic Nucleotides.

DeBerg HA, Brzovic PS, Flynn GE, Zagotta WN, Stoll S - J. Biol. Chem. (2015)

Bottom Line: Binding of cyclic nucleotides increases the rate and extent of channel activation and shifts it to less hyperpolarized voltages.We probed the allosteric mechanism of different cyclic nucleotides on the CNBD and on channel gating.We explain these results with a model where different allosteric mechanisms in the CNBD all converge to have the same effect on the C-linker and render all three cyclic nucleotides similarly potent activators of the channel.

View Article: PubMed Central - PubMed

Affiliation: From the Departments of Chemistry, Physiology and Biophysics, and.

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DEER distance distributions involving residue 624.A, structure of HCN2-CL + CNBD (Protein Data Bank code 3ETQ), in gray, with predicted spin label rotamers, in color, at residues 537, 563, and 624. Spin label rotamers were predicted using MMM software (25). B, DEER distance distributions of HCN2-CL + CNBD 537/624. C, DEER distance distributions of HCN2-CL + CNBD 563/624. Distance distributions for apo HCN2-CL + CNBD are in black, of HCN2-CL + CNBD bound to 1 mm cAMP in red, bound to 1 mm cGMP in green, and bound to 1 mm cCMP in cyan.
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Figure 5: DEER distance distributions involving residue 624.A, structure of HCN2-CL + CNBD (Protein Data Bank code 3ETQ), in gray, with predicted spin label rotamers, in color, at residues 537, 563, and 624. Spin label rotamers were predicted using MMM software (25). B, DEER distance distributions of HCN2-CL + CNBD 537/624. C, DEER distance distributions of HCN2-CL + CNBD 563/624. Distance distributions for apo HCN2-CL + CNBD are in black, of HCN2-CL + CNBD bound to 1 mm cAMP in red, bound to 1 mm cGMP in green, and bound to 1 mm cCMP in cyan.

Mentions: The rotamer predictions shown in Figs. 5 and 6 were obtained using MMM software (25). DEER distance distributions were obtained using DeerAnalysis2013 (26). A homogeneous three-dimensional background was used for background correction. Time traces were converted to distance distributions using Tikhonov regularization, a model-free least-squares approach. The regularization parameter was visually optimized separately for each data set according to the L-curve criterion. Regularization parameter values of 10 or 100 were used for all datasets. To estimate errors in the obtained distance distributions, the noise in the time domain traces was linearly transformed to the distance domain. The shaded error bands shown in the distance distributions correspond to 2 S.D. (±2σ) of the time domain noise.


Structure and Energetics of Allosteric Regulation of HCN2 Ion Channels by Cyclic Nucleotides.

DeBerg HA, Brzovic PS, Flynn GE, Zagotta WN, Stoll S - J. Biol. Chem. (2015)

DEER distance distributions involving residue 624.A, structure of HCN2-CL + CNBD (Protein Data Bank code 3ETQ), in gray, with predicted spin label rotamers, in color, at residues 537, 563, and 624. Spin label rotamers were predicted using MMM software (25). B, DEER distance distributions of HCN2-CL + CNBD 537/624. C, DEER distance distributions of HCN2-CL + CNBD 563/624. Distance distributions for apo HCN2-CL + CNBD are in black, of HCN2-CL + CNBD bound to 1 mm cAMP in red, bound to 1 mm cGMP in green, and bound to 1 mm cCMP in cyan.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4697172&req=5

Figure 5: DEER distance distributions involving residue 624.A, structure of HCN2-CL + CNBD (Protein Data Bank code 3ETQ), in gray, with predicted spin label rotamers, in color, at residues 537, 563, and 624. Spin label rotamers were predicted using MMM software (25). B, DEER distance distributions of HCN2-CL + CNBD 537/624. C, DEER distance distributions of HCN2-CL + CNBD 563/624. Distance distributions for apo HCN2-CL + CNBD are in black, of HCN2-CL + CNBD bound to 1 mm cAMP in red, bound to 1 mm cGMP in green, and bound to 1 mm cCMP in cyan.
Mentions: The rotamer predictions shown in Figs. 5 and 6 were obtained using MMM software (25). DEER distance distributions were obtained using DeerAnalysis2013 (26). A homogeneous three-dimensional background was used for background correction. Time traces were converted to distance distributions using Tikhonov regularization, a model-free least-squares approach. The regularization parameter was visually optimized separately for each data set according to the L-curve criterion. Regularization parameter values of 10 or 100 were used for all datasets. To estimate errors in the obtained distance distributions, the noise in the time domain traces was linearly transformed to the distance domain. The shaded error bands shown in the distance distributions correspond to 2 S.D. (±2σ) of the time domain noise.

Bottom Line: Binding of cyclic nucleotides increases the rate and extent of channel activation and shifts it to less hyperpolarized voltages.We probed the allosteric mechanism of different cyclic nucleotides on the CNBD and on channel gating.We explain these results with a model where different allosteric mechanisms in the CNBD all converge to have the same effect on the C-linker and render all three cyclic nucleotides similarly potent activators of the channel.

View Article: PubMed Central - PubMed

Affiliation: From the Departments of Chemistry, Physiology and Biophysics, and.

Show MeSH