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Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.

Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N - PLoS Comput. Biol. (2014)

Bottom Line: Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism.We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal.We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel.

ABSTRACT
Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought to be independent of the membrane potential, and their gating regulated by cytosolic cyclic nucleotide-binding domains. Mutations in these channels result in severe, degenerative retinal diseases, which remain untreatable. The lack of structural information on CNG channels has prevented mechanistic understanding of disease-causing mutations, precluded structure-based drug design, and hampered in silico investigation of the gating mechanism. To address this, we built a 3D model of the cone tetrameric CNG channel, based on homology to two distinct templates with known structures: the transmembrane (TM) domain of a bacterial channel, and the cyclic nucleotide-binding domain of the mouse HCN2 channel. Since the TM-domain template had low sequence-similarity to the TM domains of the CNG channels, and to reconcile conflicts between the two templates, we developed a novel, hybrid approach, combining homology modeling with evolutionary coupling constraints. Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism. We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal. We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.

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The three principal motions.The cross-correlations between the residues in each motion type are shown on the left panels (A, C, E); the channel is colored according to the correlation of the VSD of chain A with the other residues. The corresponding motions are presented on the right panels (B, D, F). Snapshots are colored according to the direction of motion, ranging from green to red. (A, C, E) In each panel, chain A represents an arbitrary CNGA3 chain (the channel comprises four identical chains). The magnitude of positive and negative correlations between the fluctuations of the residues is color-coded according to the blue-to-red scale at the bottom of the picture. Positive correlation indicates motion of two residues in the same direction, while negative correlation indicates motion in opposite directions. In panel A, the arrows indicate the location of the pivot points of the rotational motion at the termini of the S6 helices, i.e., the border between the dynamics units (See Discussion). The CNBDs in panel D and the TM domain in panel F are omitted for clarity.
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pcbi-1003976-g004: The three principal motions.The cross-correlations between the residues in each motion type are shown on the left panels (A, C, E); the channel is colored according to the correlation of the VSD of chain A with the other residues. The corresponding motions are presented on the right panels (B, D, F). Snapshots are colored according to the direction of motion, ranging from green to red. (A, C, E) In each panel, chain A represents an arbitrary CNGA3 chain (the channel comprises four identical chains). The magnitude of positive and negative correlations between the fluctuations of the residues is color-coded according to the blue-to-red scale at the bottom of the picture. Positive correlation indicates motion of two residues in the same direction, while negative correlation indicates motion in opposite directions. In panel A, the arrows indicate the location of the pivot points of the rotational motion at the termini of the S6 helices, i.e., the border between the dynamics units (See Discussion). The CNBDs in panel D and the TM domain in panel F are omitted for clarity.

Mentions: A complete description of the results is provided in Text S1. Briefly, the channel dynamics are dominated by three types of motion. In motion I the channel is divided into two dynamic units: the TM domain and the cytosolic domain (Fig. 4A). The two domains rotate around the membrane normal in opposite directions (Fig. 4B). In motion II the VSDs are swinging, while the pore domain, as well as the C-linkers and the CNBDs, are essentially stationary (Fig. 4D and Figure S7B). The fluctuations of the VSDs are positively correlated with those of the C-linker and the CNBD of the same subunit, and with those of the pore region of the adjacent subunit (Fig. 4C). In motion III the pairs of diagonal CNBDs alternately move towards and away from each other (Fig. 4F). The fluctuations of the VSDs are positively correlated with those of the CNBD, C-linker and pore region of the adjacent subunits (Fig. 4E).


Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.

Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N - PLoS Comput. Biol. (2014)

The three principal motions.The cross-correlations between the residues in each motion type are shown on the left panels (A, C, E); the channel is colored according to the correlation of the VSD of chain A with the other residues. The corresponding motions are presented on the right panels (B, D, F). Snapshots are colored according to the direction of motion, ranging from green to red. (A, C, E) In each panel, chain A represents an arbitrary CNGA3 chain (the channel comprises four identical chains). The magnitude of positive and negative correlations between the fluctuations of the residues is color-coded according to the blue-to-red scale at the bottom of the picture. Positive correlation indicates motion of two residues in the same direction, while negative correlation indicates motion in opposite directions. In panel A, the arrows indicate the location of the pivot points of the rotational motion at the termini of the S6 helices, i.e., the border between the dynamics units (See Discussion). The CNBDs in panel D and the TM domain in panel F are omitted for clarity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256070&req=5

pcbi-1003976-g004: The three principal motions.The cross-correlations between the residues in each motion type are shown on the left panels (A, C, E); the channel is colored according to the correlation of the VSD of chain A with the other residues. The corresponding motions are presented on the right panels (B, D, F). Snapshots are colored according to the direction of motion, ranging from green to red. (A, C, E) In each panel, chain A represents an arbitrary CNGA3 chain (the channel comprises four identical chains). The magnitude of positive and negative correlations between the fluctuations of the residues is color-coded according to the blue-to-red scale at the bottom of the picture. Positive correlation indicates motion of two residues in the same direction, while negative correlation indicates motion in opposite directions. In panel A, the arrows indicate the location of the pivot points of the rotational motion at the termini of the S6 helices, i.e., the border between the dynamics units (See Discussion). The CNBDs in panel D and the TM domain in panel F are omitted for clarity.
Mentions: A complete description of the results is provided in Text S1. Briefly, the channel dynamics are dominated by three types of motion. In motion I the channel is divided into two dynamic units: the TM domain and the cytosolic domain (Fig. 4A). The two domains rotate around the membrane normal in opposite directions (Fig. 4B). In motion II the VSDs are swinging, while the pore domain, as well as the C-linkers and the CNBDs, are essentially stationary (Fig. 4D and Figure S7B). The fluctuations of the VSDs are positively correlated with those of the C-linker and the CNBD of the same subunit, and with those of the pore region of the adjacent subunit (Fig. 4C). In motion III the pairs of diagonal CNBDs alternately move towards and away from each other (Fig. 4F). The fluctuations of the VSDs are positively correlated with those of the CNBD, C-linker and pore region of the adjacent subunits (Fig. 4E).

Bottom Line: Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism.We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal.We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel.

ABSTRACT
Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought to be independent of the membrane potential, and their gating regulated by cytosolic cyclic nucleotide-binding domains. Mutations in these channels result in severe, degenerative retinal diseases, which remain untreatable. The lack of structural information on CNG channels has prevented mechanistic understanding of disease-causing mutations, precluded structure-based drug design, and hampered in silico investigation of the gating mechanism. To address this, we built a 3D model of the cone tetrameric CNG channel, based on homology to two distinct templates with known structures: the transmembrane (TM) domain of a bacterial channel, and the cyclic nucleotide-binding domain of the mouse HCN2 channel. Since the TM-domain template had low sequence-similarity to the TM domains of the CNG channels, and to reconcile conflicts between the two templates, we developed a novel, hybrid approach, combining homology modeling with evolutionary coupling constraints. Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism. We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal. We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.

Show MeSH
Related in: MedlinePlus