Biophysics of rhodopsins and optogenetics

Biophysical Reviews - Tập 12 Số 2 - Trang 355-361 - 2020
Hideki Kandori1
1Nagoya Institute of Technology, Nagoya, Japan

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Avelar GM, Schumacher RI, Zaini PA, Leonard G, Richards TA, Gomes SL (2014) A rhodopsin-guanylyl cyclase gene fusion functions in visual perception in a fungus. Curr Biol 24:1234–1240

Berndt A, Lee SY, Ramakrishnan C, Deisseroth K (2014) Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science 344:420–424

Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8:1263–1268

Chow BY, Han X, Dobry AS, Qian X, Chuong AS, Li M, Henninger MA, Belfort GM, Lin Y, Monahan PE, Boyden ES (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463:98–102

Deisseroth K (2011) Optogenetics. Nat Methods 8:26–29

Deisseroth K, Hegemann P (2017) The form and function of channelrhodopsin. Science. 15:357

Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H (2014) Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 114:126–163

Gerwert K, Freier E, Wolf S (2014) The role of protein-bound water molecules in microbial rhodopsins. Biochim Biophys Acta 1837:606–613

Govorunova EG, Sineshchekov OA, Janz R, Liu X, Spudich JL (2015) NEUROSCIENCE. Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics. Science 349:647–650

Govorunova EG, Sineshchekov OA, Li H, Spudich JL (2017) Microbial rhodopsins: diversity, mechanisms, and optogenetic applications. Annu Rev Biochem 86:845–872

Gozem S, Luk HL, Schapiro I, Olivucci M (2017) Theory and simulation of the ultrafast double-bond isomerization of biological chromophores. Chem Rev 117:13502–13565

Henderson R, Unwin PN (1975) Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257:28–32

Inoue K, Ono H, Abe-Yoshizumi R, Yoshizawa S, Ito H, Kogure K, Kandori H (2013) A light-driven sodium ion pump in marine bacteria. Nat Commun 4:1678

Inoue K, Ito S, Kato Y, Nomura Y, Shibata M, Uchihashi T, Tsunoda SP, Kandori H (2016) A natural light-driven inward proton pump. Nat Commun 7:13415

Ishizuka T, Kakuda M, Araki R, Yawo H (2006) Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neurosci Res 54:85–94

Kakegawa W, Katoh A, Narumi S, Miura E, Motohashi J, Takahashi A, Kohda K, Fukazawa Y, Yuzaki M, Matsuda S (2018) Optogenetic control of synaptic AMPA receptor endocytosis reveals roles of LTD in motor learning. Neuron 99:985–998

Kamikubo H, Kataoka M, Váró G, Oka T, Tokunaga F, Needleman R, Lanyi JK (1996) Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction. Proc Natl Acad Sci U S A 93:1386–1390

Kandori H (2000) Role of internal water molecules in bacteriorhodopsin. Biochim Biophys Acta 1460:177–191

Kandori H (2015) Ion-pumping microbial rhodopsins. Front Mol Biosci 2:52

Kandori H, Inoue K, Tsunoda SP (2018) Light-driven sodium-pumping rhodopsin: a new concept of active transport. Chem Rev 118:10646–10658

Kato HE, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S, Hegemann P, Maturana AD, Ishitani R, Deisseroth K, Nureki O (2012) Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482:369–374

Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, Nureki O (2015) Structural basis for Na+ transport mechanism by a light-driven Na+ pump. Nature. 521:48–53

Kato HE, Kim YS, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK, Deisseroth K (2018) Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature. 561:349–354

Kawanabe A, Furutani Y, Jung KH, Kandori H (2009) Engineering an inward proton transport from a bacterial sensor rhodopsin. J Am Chem Soc 131:16439–16444

Kim YS, Kato HE, Yamashita K, Ito S, Inoue K, Ramakrishnan C, Fenno LE, Evans KE, Paggi JM, Dror RO, Kandori H, Kobilka BK, Deisseroth K (2018) Crystal structure of the natural anion-conducting channelrhodopsin GtACR1. Nature 561:343–348

Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Boyden ES (2014) Independent optical excitation of distinct neural populations. Nat Methods 11:338–346

Kleinlogel S, Feldbauer K, Dempski RE, Fotis H, Wood PG, Bamann C, Bamberg E (2011) Ultra light-sensitive and fast neuronal activation with the Ca2+-permiable channelrhodopsin CatCh. Nat Neurosci 14:513–518

Konno M, Kato Y, Kato HE, Inoue K, Nureki O, Kandori H (2016) Mutant of a light-driven sodium ion pump can transport cesium ions. J Phys Chem Lett 7:51–55

Lin JY, Knutsen PM, Muller A, Kleinfeld D, Tsien RY (2013) ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation. Nat Neurosci 16:1499–1508

Lórenz-Fonfría VA, Heberle J (2014) Channelrhodopsin unchained: structure and mechanism of a light-gated cation channel. Biochim Biophys Acta 1837:626–642

Nagel G, Ollig D, Fuhrmann M, Kateriya S, Musti AM, Bamberg E, Hegemann P (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296:2395–2398

Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, Ollig D, Hegemann P, Bamberg E (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci U S A 100:13940–13945

Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, Iwata S (2016) A three-dimensional movie of structural changes in bacteriorhodopsin. Science 354:1552–1557

Nass Kovacs G, Colletier JP, Grünbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I (2019) Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nat Commun 10:317

Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, Standfuss J (2018) Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 361, eaat0094

Oesterhelt D, Stoeckenius W (1971) Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233:149–152

Schneider F, Grimm C, Hegemann P (2015) Biophysics of channelrhodopsin. Annu Rev Biophys 44:167–186

Shibata M, Yamashita H, Uchihashi T, Kandori H, Ando T (2010) High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. Nat Nanotechnol 5:208–212

Sineshchekov OA, Jung KH, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 99:8689–8694

Suzuki T, Yamasaki K, Fujita S, Oda K, Iseki M, Yoshida K, Watanabe M, Daiyasu H, Toh H, Asamizu E, Tabata S, Miura K, Fukuzawa H, Nakamura S, Takahashi T (2003) Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization. Biochem Biophys Res Commun 301:711–717

Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V (2017) Structural insights into ion conduction by channelrhodopsin 2. Science. 358:6366

Wietek J, Wiegert JS, Adeeishvili N, Schneider F, Watanabe H, Tsunoda SP, Vogt A, Elstner M, Oertner TG, Hegemann P (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science 344:409–412

Yoshida K, Tsunoda SP, Brown LS, Kandori H (2017) A unique choanoflagellate enzyme rhodopsin exhibits light-dependent cyclic nucleotide phosphodiesterase activity. J Biol Chem 292:7531–7541

Zhang F, Wang LP, Brauner M, Liewald JF, Kay K, Watzke N, Wood PG, Bamberg E, Nagel G, Gottschalk A, Deisseroth K (2007) Multimodal fast optical interrogation of neural circuitry. Nature 446:633–639

Zhang F, Prigge M, Beyrière F, Tsunoda SP, Mattis J, Yizhar O, Hegemann P, Deisseroth K (2008) Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri. Nat Neurosci 11:631–633