Retinal isomerization and water-pore formation in channelrhodopsin-2.
Retinal isomerization and water-pore formation in channelrhodopsin-2.
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DOI：
10.1073/pnas.1700091115
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发表时间：
2018-04-03
影响因子：
11.1
通讯作者：
Hummer G
中科院分区：
文献类型：
--
作者：
Ardevol A;Hummer G
视紫红质-2（ChR 2）是一种光激活的膜离子通道，广泛应用于生物技术应用和光遗传学。尽管如此，其结构、光循环和作用机制的关键要素仍然没有得到解决。我们应用计算建模和超过14 µs的分子动力学模拟来探索光活化通道开放的分子机制。水作为一个中心角色出现，它润滑了闸门残留物的运动，并打开了一个透水的预开孔。通过解决ChR 2的早期功能动力学，我们的工作还为光遗传学应用的新变体的设计提供了基础。视紫红质-2（ChR 2）是一种广泛应用于光遗传学的光敏离子通道。光活化触发共价结合的视黄醛的反式至顺式异构化。随后的构象变化打开了阳离子选择性通道。我们探索的结构动力学在早期光循环导致通道开放的经典（MM）和量子力学（QM）的分子模拟。通过QM/MM模拟，我们为视网膜发色团生成了一个蛋白质适应的力场，并对吸收光谱进行了验证。在暗适应ChR 2二聚体的4 µs MM模拟中，水进入封闭通道的前庭。视网膜全反式13顺式异构化，模拟metadhesics，引发了一个重大的重组的电荷簇形成的通道门。在微秒的时间尺度上，水穿透闸门，在螺旋H1、H2、H3和H7之间形成跨膜预开孔。这种水流入离子不可渗透的预开孔与时间分辨红外光谱和电生理学实验是一致的。在视网膜13-顺式状态下，D253作为席夫碱的质子受体出现。通过QM/MM模拟，我们得到了一个早期的M/P2390样中间体。未质子化的席夫碱向胞质侧的快速旋转有效地防止了其从细胞外侧的再质子化。从MM和QM模拟，我们获得了详细的洞察ChR 2的光活化和早期事件在孔形成的机制。通过重新排列形成大门的电荷和氢键网络，水成为光驱动的ChR 2通道开放的关键参与者。
Channelrhodopsin-2 (ChR2) is a light-activated membrane ion channel that is widely used in biotechnological applications and optogenetics. Nonetheless, key elements of its structure, photocycle, and mechanism of action remain unresolved. We applied computational modeling and over 14 µs of molecular dynamics simulation to explore the molecular mechanism of photoactivated channel opening. Water emerges as a central player that lubricates the motions of gate residues and opens a water permeable preopen pore. By resolving the early functional dynamics of ChR2, our work also provides a foundation for the design of new variants for optogenetics applications. Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. In a 4-µs MM simulation of a dark-adapted ChR2 dimer, water entered the vestibules of the closed channel. Retinal all-trans to 13-cis isomerization, simulated with metadynamics, triggered a major restructuring of the charge cluster forming the channel gate. On a microsecond time scale, water penetrated the gate to form a membrane-spanning preopen pore between helices H1, H2, H3, and H7. This influx of water into an ion-impermeable preopen pore is consistent with time-resolved infrared spectroscopy and electrophysiology experiments. In the retinal 13-cis state, D253 emerged as the proton acceptor of the Schiff base. Upon proton transfer from the Schiff base to D253, modeled by QM/MM simulations, we obtained an early-M/P2390–like intermediate. Rapid rotation of the unprotonated Schiff base toward the cytosolic side effectively prevents its reprotonation from the extracellular side. From MM and QM simulations, we gained detailed insight into the mechanism of ChR2 photoactivation and early events in pore formation. By rearranging the network of charges and hydrogen bonds forming the gate, water emerges as a key player in light-driven ChR2 channel opening.
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影响因子：
15
作者：
Bravaya, Ksenia;Bochenkova, Anastasia;Nemulkhin, Alexander
通讯作者：
Nemulkhin, Alexander
影响因子：
5.5
作者：
Doemer, Manuel;Maurer, Patrick;Rothlisberger, Ursula
通讯作者：
Rothlisberger, Ursula
DOI：
10.1126/science.1252367
发表时间：
2014-04-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Berndt A;Lee SY;Ramakrishnan C;Deisseroth K
通讯作者：
Deisseroth K
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML
DOI：
10.1073/pnas.202427399
发表时间：
2002-10-01
影响因子：
11.1
作者：
Laio, A;Parrinello, M
通讯作者：
Parrinello, M