Active Site Structure and Absorption Spectrum of Channelrhodopsin-2 Wild-type and C128T Mutant

Overview

Journal Chem Sci

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2018 Aug 30

PMID 30155032

Citations 16

Authors

Yanan Guo

Franziska E Beyle

Beatrix M Bold

Hiroshi C Watanabe

Axel Koslowski

Walter Thiel

Peter Hegemann

Marco Marazzi

Marcus Elstner

Affiliations

Soon will be listed here.

Abstract

In spite of considerable interest, the active site of channelrhodopsin still lacks a detailed atomistic description, the understanding of which could strongly enhance the development of novel optogenetics tools. We present a computational study combining different state-of-the-art techniques, including hybrid quantum mechanics/molecular mechanics schemes and high-level quantum chemical methods, to properly describe the hydrogen-bonding pattern between the retinal chromophore and its counterions in channelrhodopsin-2 Wild-Type and C128T mutant. Especially, we show by extensive ground state dynamics that the active site, containing a glutamic acid (E123) and a water molecule, is highly dynamic, sampling three different hydrogen-bonding patterns. This results in a broad absorption spectrum that is representative of the different structural motifs found. A comparison with bacteriorhodopsin, characterized by a pentagonal hydrogen-bonded active site structure, elucidates their different absorption properties.

Citing Articles

Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.

Kubar T, Elstner M, Cui Q Annu Rev Biophys. 2023; 52:525-551.

PMID: 36791746 PMC: 10810093. DOI: 10.1146/annurev-biophys-111622-091140.

Modeling the -cycle in the light activated opening of the channelrhodopsin-2 ion channel.

Xin Q, Cheng J, Wang H, Zhang W, Lu H, Zhou J RSC Adv. 2022; 12(11):6515-6524.

PMID: 35424642 PMC: 8981705. DOI: 10.1039/d1ra08521b.

The effect on ion channel of different protonation states of E90 in channelrhodopsin-2: a molecular dynamics simulation.

Cheng J, Zhang W, Zhou S, Ran X, Shang Y, Lo G RSC Adv. 2022; 11(24):14542-14551.

PMID: 35424009 PMC: 8697799. DOI: 10.1039/d1ra01879e.

Gate-keeper of ion transport-a highly conserved helix-3 tryptophan in a channelrhodopsin chimera, C1C2/ChRWR.

Nagasaka Y, Hososhima S, Kubo N, Nagata T, Kandori H, Inoue K Biophys Physicobiol. 2020; 17:59-70.

PMID: 33173715 PMC: 7593130. DOI: 10.2142/biophysico.BSJ-2020007.

NeoR, a near-infrared absorbing rhodopsin.

Broser M, Spreen A, Konold P, Schiewer E, Adam S, Borin V Nat Commun. 2020; 11(1):5682.

PMID: 33173168 PMC: 7655827. DOI: 10.1038/s41467-020-19375-8.

References

Nack M, Radu I, Bamann C, Bamberg E, Heberle J . The retinal structure of channelrhodopsin-2 assessed by resonance Raman spectroscopy. FEBS Lett. 2009; 583(22):3676-80. DOI: 10.1016/j.febslet.2009.10.052. View

Schertler G, LOZIER R, Michel H, Oesterhelt D . Chromophore motion during the bacteriorhodopsin photocycle: polarized absorption spectroscopy of bacteriorhodopsin and its M-state in bacteriorhodopsin crystals. EMBO J. 1991; 10(9):2353-61. PMC: 452930. DOI: 10.1002/j.1460-2075.1991.tb07774.x. View

Gaus M, Cui Q, Elstner M . DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput. 2012; 7(4):931-948. PMC: 3509502. DOI: 10.1021/ct100684s. View

Sneskov K, Olsen J, Schwabe T, Hattig C, Christiansen O, Kongsted J . Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants. Phys Chem Chem Phys. 2013; 15(20):7567-76. DOI: 10.1039/c3cp44350g. View

Kuhne J, Eisenhauer K, Ritter E, Hegemann P, Gerwert K, Bartl F . Early formation of the ion-conducting pore in channelrhodopsin-2. Angew Chem Int Ed Engl. 2014; 54(16):4953-7. DOI: 10.1002/anie.201410180. View

Fischer W, Sonar S, Marti T, Khorana H, Rothschild K . Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction. Biochemistry. 1994; 33(43):12757-62. DOI: 10.1021/bi00209a005. View

Ernst O, Murcia P, Daldrop P, Tsunoda S, Kateriya S, Hegemann P . Photoactivation of channelrhodopsin. J Biol Chem. 2007; 283(3):1637-1643. DOI: 10.1074/jbc.M708039200. View

Stehfest K, Ritter E, Berndt A, Bartl F, Hegemann P . The branched photocycle of the slow-cycling channelrhodopsin-2 mutant C128T. J Mol Biol. 2010; 398(5):690-702. DOI: 10.1016/j.jmb.2010.03.031. View

Wolter T, Welke K, Phatak P, Bondar A, Elstner M . Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation. Phys Chem Chem Phys. 2013; 15(30):12582-90. DOI: 10.1039/c3cp44280b. View

10.

Kubar T, Welke K, Groenhof G . New QM/MM implementation of the DFTB3 method in the gromacs package. J Comput Chem. 2015; 36(26):1978-89. DOI: 10.1002/jcc.24029. View

11.

Gunaydin L, Yizhar O, Berndt A, Sohal V, Deisseroth K, Hegemann P . Ultrafast optogenetic control. Nat Neurosci. 2010; 13(3):387-92. DOI: 10.1038/nn.2495. View

12.

Koslowski A, Beck M, Thiel W . Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach. J Comput Chem. 2003; 24(6):714-26. DOI: 10.1002/jcc.10210. View

13.

Verhoefen M, Bamann C, Blocher R, Forster U, Bamberg E, Wachtveitl J . The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps. Chemphyschem. 2010; 11(14):3113-22. DOI: 10.1002/cphc.201000181. View

14.

Ritter E, Stehfest K, Berndt A, Hegemann P, Bartl F . Monitoring light-induced structural changes of Channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy. J Biol Chem. 2008; 283(50):35033-41. PMC: 3259888. DOI: 10.1074/jbc.M806353200. View

15.

Hess B, Kutzner C, van der Spoel D, Lindahl E . GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput. 2015; 4(3):435-47. DOI: 10.1021/ct700301q. View

16.

Hoffmann M, Wanko M, Strodel P, Konig P, Frauenheim T, Schulten K . Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc. 2006; 128(33):10808-18. DOI: 10.1021/ja062082i. View

17.

Becker-Baldus J, Bamann C, Saxena K, Gustmann H, Brown L, Brown R . Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci U S A. 2015; 112(32):9896-901. PMC: 4538646. DOI: 10.1073/pnas.1507713112. View

18.

Watanabe H, Welke K, Schneider F, Tsunoda S, Zhang F, Deisseroth K . Structural model of channelrhodopsin. J Biol Chem. 2012; 287(10):7456-66. PMC: 3293557. DOI: 10.1074/jbc.M111.320309. View

19.

Lorenz-Fonfria V, Schultz B, Resler T, Schlesinger R, Bamann C, Bamberg E . Pre-gating conformational changes in the ChETA variant of channelrhodopsin-2 monitored by nanosecond IR spectroscopy. J Am Chem Soc. 2015; 137(5):1850-61. DOI: 10.1021/ja5108595. View

20.

Berndt A, Yizhar O, Gunaydin L, Hegemann P, Deisseroth K . Bi-stable neural state switches. Nat Neurosci. 2008; 12(2):229-34. DOI: 10.1038/nn.2247. View