Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.
Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.
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DOI：
10.1371/journal.pcbi.1003976
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发表时间：
2014-12
影响因子：
4.3
通讯作者：
Ben-Tal N
中科院分区：
文献类型：
--
作者：
Gofman Y;Schärfe C;Marks DS;Haliloglu T;Ben-Tal N
环核苷酸门控 (CNG) 离子通道是非选择性阳离子通道，对于视觉和嗅觉感觉转导至关重要。尽管这些通道包括电压传感器域（VSD），但它们的电导被认为独立于膜电位，并且它们的门控受到胞质环核苷酸结合域的调节。这些通道的突变会导致严重的退行性视网膜疾病，而这种疾病仍然无法治愈。 CNG 通道结构信息的缺乏阻碍了对致病突变的机制理解，阻碍了基于结构的药物设计，并阻碍了门控机制的计算机研究。为了解决这个问题，我们基于与具有已知结构的两个不同模板的同源性，构建了锥体四聚 CNG 通道的 3D 模型：细菌通道的跨膜 (TM) 结构域和小鼠 HCN2 通道的环核苷酸结合结构域。由于 TM 域模板与 CNG 通道的 TM 域的序列相似性较低，为了协调两个模板之间的冲突，我们开发了一种新颖的混合方法，将同源建模与进化耦合约束相结合。接下来，我们使用模型结构的弹性网络分析来研究通道的全局运动并阐明其门控机制。我们发现以下内容：（i）在主要运动模式中，TM 和胞质域围绕正常膜反向旋转。我们将这种运动与门控联系起来，这一命题得到了先前实验数据的支持，并与细菌 KirBac 通道的已知门控机制进行了比较。 (ii) VSD 可以促进门控（补充孔门），解释它们在这种“电压不敏感”通道中的存在。 (iii)我们对 CNGA3 通道的弹性网络模型分析支持变构门控的模块化模型，根据该模型，蛋白质结构域是准独立的：它们可以独立移动，但彼此变构耦合。环核苷酸门控 (CNG) 通道介导阳离子通过细胞质膜的通道。它们参与视杆细胞和视锥细胞感光器以及脑、肾、心脏和其他细胞的感觉转导和细胞发育，并与全色盲和其他罕见遗传病有关。我们使用混合建模方法，结合比较建模和进化保守性和耦合的估计，对人锥 CNG 通道的结构进行建模。该通道包含允许离子通过的膜结构域和结合环核苷酸的调节胞质结构域。每个结构域的结构是在合适的模板的基础上通过同源性建模的。我们的混合方法使我们能够评估模型结构，并确定模板重叠并呈现相互冲突的结构证据的区域的构象。然后我们进行了正常模式分析以揭示通道的全局运动。我们认为主要的运动模式，即膜的反向旋转和正常膜周围的胞质域，与通道门控相关。这种旋转运动对脂质膜产生最小的扰动，这可以解释为什么在其他类型的通道中观察到这种运动。
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. Cyclic nucleotide-gated (CNG) channels mediate the passage of cations through the cytoplasmic membrane. They are involved in sensory transduction and cellular development in the rod and cone photoreceptors, as well as in brain, kidney, heart and other cells, and are linked to achromatopsia and other rare genetic diseases. We used a hybrid modeling approach, combining comparative modeling and estimates of evolutionary conservation and couplings, to model the structure of a human cone CNG channel. The channel comprises a membrane domain that allows ion passage, and a regulatory cytosolic domain that binds cyclic nucleotides. The structure of each domain was modeled by homology on the basis of a suitable template. Our hybrid approach allowed us to evaluate the model structure, as well as to determine the conformations of regions where the templates overlapped and presented conflicting structural evidence. We then conducted normal mode analysis to reveal global motions of the channel. We suggest that the main mode of motion, counter-rotation of the membrane and cytosolic domains around the membrane normal, is associated with channel gating. Such rotational motion induces minimal perturbation to the lipid membrane, which could explain why the motion is observed in other types of channels.
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DOI：
10.1073/pnas.0711533105
发表时间：
2008-02-05
影响因子：
11.1
作者：
Clayton, Gina M.;Altieri, Steve;Morais-Cabral, Joao H.
通讯作者：
Morais-Cabral, Joao H.
影响因子：
5.6
作者：
Altieri, Stephen L.;Clayton, Gina M.;Morais-Cabral, Joao H.
通讯作者：
Morais-Cabral, Joao H.
DOI：
10.1016/s1359-0278(97)00024-2
发表时间：
1997-01-01
期刊：
FOLDING & DESIGN
影响因子：
--
作者：
Bahar, I;Atilgan, AR;Erman, B
通讯作者：
Erman, B
影响因子：
2.4
作者：
Ekeberg, Magnus;Lovkvist, Cecilia;Aurell, Erik
通讯作者：
Aurell, Erik
DOI：
10.1007/978-1-4614-0631-0_98
发表时间：
2012-01-01
期刊：
RETINAL DEGENERATIVE DISEASES
影响因子：
--
作者：
Ding, Xi-Qin;Matveev, Alexander;Matsumoto, Hiroyuki
通讯作者：
Matsumoto, Hiroyuki