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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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Motion I of CNGA3 appears to describe channel gating.For clarity, only helices S5 and S6 (or corresponding KirBac helices) of two juxtaposed subunits are shown in each panel. (A, B) The similarity between the predicted conformations in panel B and the crystal structures in panel A is apparent, verifying the relation between these conformations and channel gating. (A) Side view of the KirBac3.1 crystal structures in open (pale green, PDB entry 3ZRS [43]) and closed (pale red, PDB entry 2WLJ [44]) states. The α-carbons of the two gate-residues, namely G120 and Y132, are shown as a space-filling model. (B–D) The edge conformations of KirBac3.1 (B), CNGA3 (C) and CNGA3 lacking the VSDs (D), as predicted by the elastic network models in the slowest mode of motion. The two edge conformations are shown in red and green. (C) The CNGA3 conformations resemble the conformations predicted for the KirBac channel (panel B), but the pore region is rigid. (D) The CNGA3 without VSD conformations are identical to the KirBac conformations (panel B).
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pcbi-1003976-g005: Motion I of CNGA3 appears to describe channel gating.For clarity, only helices S5 and S6 (or corresponding KirBac helices) of two juxtaposed subunits are shown in each panel. (A, B) The similarity between the predicted conformations in panel B and the crystal structures in panel A is apparent, verifying the relation between these conformations and channel gating. (A) Side view of the KirBac3.1 crystal structures in open (pale green, PDB entry 3ZRS [43]) and closed (pale red, PDB entry 2WLJ [44]) states. The α-carbons of the two gate-residues, namely G120 and Y132, are shown as a space-filling model. (B–D) The edge conformations of KirBac3.1 (B), CNGA3 (C) and CNGA3 lacking the VSDs (D), as predicted by the elastic network models in the slowest mode of motion. The two edge conformations are shown in red and green. (C) The CNGA3 conformations resemble the conformations predicted for the KirBac channel (panel B), but the pore region is rigid. (D) The CNGA3 without VSD conformations are identical to the KirBac conformations (panel B).

Mentions: Motion I of the CNGA3 channel is a rotational, iris-like opening (Figs. 4A and 4B). This motion is unique in that it is associated with the only (non-degenerate) slow mode that manifests cooperativity among all subunits and allows symmetry-preserving conformational transition. Here we compare this motion with the gating motion in KirBac channels, prokaryotic homologs of mammalian inwardly rectifying potassium channels. KirBac channels share the architecture of the pore domain with other members of the voltage-gated-like ion channel superfamily, but they lack the VSD. Similarly to CNG channels, KirBac channels feature a cytoplasmic regulatory domain [42]. Recent crystal structures of the KirBac3.1 channel in the open and closed states (Fig. 5A) revealed its gating mechanism: upon activation, the TM and cytoplasmic domains of KirBac3.1 rotate in opposite directions around the membrane normal [43], [44]. For comparison, we performed elastic network analysis of the KirBac3.1 channel in its closed state.


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)

Motion I of CNGA3 appears to describe channel gating.For clarity, only helices S5 and S6 (or corresponding KirBac helices) of two juxtaposed subunits are shown in each panel. (A, B) The similarity between the predicted conformations in panel B and the crystal structures in panel A is apparent, verifying the relation between these conformations and channel gating. (A) Side view of the KirBac3.1 crystal structures in open (pale green, PDB entry 3ZRS [43]) and closed (pale red, PDB entry 2WLJ [44]) states. The α-carbons of the two gate-residues, namely G120 and Y132, are shown as a space-filling model. (B–D) The edge conformations of KirBac3.1 (B), CNGA3 (C) and CNGA3 lacking the VSDs (D), as predicted by the elastic network models in the slowest mode of motion. The two edge conformations are shown in red and green. (C) The CNGA3 conformations resemble the conformations predicted for the KirBac channel (panel B), but the pore region is rigid. (D) The CNGA3 without VSD conformations are identical to the KirBac conformations (panel B).
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Related In: Results  -  Collection

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

pcbi-1003976-g005: Motion I of CNGA3 appears to describe channel gating.For clarity, only helices S5 and S6 (or corresponding KirBac helices) of two juxtaposed subunits are shown in each panel. (A, B) The similarity between the predicted conformations in panel B and the crystal structures in panel A is apparent, verifying the relation between these conformations and channel gating. (A) Side view of the KirBac3.1 crystal structures in open (pale green, PDB entry 3ZRS [43]) and closed (pale red, PDB entry 2WLJ [44]) states. The α-carbons of the two gate-residues, namely G120 and Y132, are shown as a space-filling model. (B–D) The edge conformations of KirBac3.1 (B), CNGA3 (C) and CNGA3 lacking the VSDs (D), as predicted by the elastic network models in the slowest mode of motion. The two edge conformations are shown in red and green. (C) The CNGA3 conformations resemble the conformations predicted for the KirBac channel (panel B), but the pore region is rigid. (D) The CNGA3 without VSD conformations are identical to the KirBac conformations (panel B).
Mentions: Motion I of the CNGA3 channel is a rotational, iris-like opening (Figs. 4A and 4B). This motion is unique in that it is associated with the only (non-degenerate) slow mode that manifests cooperativity among all subunits and allows symmetry-preserving conformational transition. Here we compare this motion with the gating motion in KirBac channels, prokaryotic homologs of mammalian inwardly rectifying potassium channels. KirBac channels share the architecture of the pore domain with other members of the voltage-gated-like ion channel superfamily, but they lack the VSD. Similarly to CNG channels, KirBac channels feature a cytoplasmic regulatory domain [42]. Recent crystal structures of the KirBac3.1 channel in the open and closed states (Fig. 5A) revealed its gating mechanism: upon activation, the TM and cytoplasmic domains of KirBac3.1 rotate in opposite directions around the membrane normal [43], [44]. For comparison, we performed elastic network analysis of the KirBac3.1 channel in its closed state.

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