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Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar AN, Askari A, Brown LS, Spudich JL, Ernst OP. Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K + and Na + selectivities. Nat Commun 2023; 14:4365. [PMID: 37474513 PMCID: PMC10359266 DOI: 10.1038/s41467-023-40041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K+ versus Na+ selectivity is determined at two distinct sites on the putative ion conduction pathway: in a patch of critical residues in the intracellular segment (Leu69/Phe69, Ile73/Ser73 and Asp116) and within a cluster of aromatic residues in the extracellular segment (primarily, Trp102 and Tyr222). The two filters are on the opposite sides of the photoactive site involved in channel gating.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Hai Li
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Elena G Govorunova
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Oleg A Sineshchekov
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Yumei Wang
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Lei Zheng
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Éva Bertalan
- Physikzentrum, RWTH-Aachen University, Aachen, Germany
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Măgurele, Romania
- Institute of Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
| | - Azam Askari
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - John L Spudich
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Adam S, Wiebeler C, Schapiro I. Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2. J Chem Theory Comput 2021; 17:6302-6313. [PMID: 34255519 DOI: 10.1021/acs.jctc.1c00160] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Channelrhodopsins are photosensitive proteins that trigger flagella motion in single-cell algae and have been successfully utilized in optogenetic applications. In optogenetics, light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using quantum mechanical/molecular mechanical molecular dynamics and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified time-dependent density functional theory. In contrast to previous reports, we found that different hydrogen-bonding networks-involving the retinal protonated Schiff base, the putative counterions E162 and D292, and water molecules-had only a small impact on the absorption spectrum. However, in the case of deprotonated E162, increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factors were found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 and 82%, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.
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Affiliation(s)
- Suliman Adam
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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3
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Shtyrov AA, Nikolaev DM, Mironov VN, Vasin AV, Panov MS, Tveryanovich YS, Ryazantsev MN. Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima. Int J Mol Sci 2021; 22:ijms22063029. [PMID: 33809708 PMCID: PMC8002287 DOI: 10.3390/ijms22063029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/22/2023] Open
Abstract
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.
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Affiliation(s)
- Andrey A. Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
| | - Dmitrii M. Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
| | - Vladimir N. Mironov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Andrey V. Vasin
- Institute of Biomedical Systems and Botechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Street, 195251 St. Petersburg, Russia;
| | - Maxim S. Panov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Yuri S. Tveryanovich
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Mikhail N. Ryazantsev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
- Correspondence:
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4
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Tsujimura M, Ishikita H. Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins. J Phys Chem B 2020; 124:11819-11826. [PMID: 33236904 DOI: 10.1021/acs.jpcb.0c08910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using a quantum mechanical/molecular mechanical approach, the absorption wavelength of the retinal Schiff base was calculated based on 13 microbial rhodopsin crystal structures. The results showed that the protein electrostatic environment decreases the absorption wavelength significantly in the cation-conducting rhodopsin but only slightly in the sensory rhodopsin. Among the microbial rhodopsins with different functions, the differences in the absorption wavelengths are caused by differences in the arrangement of the charged residues at the retinal Schiff base binding moiety, namely, one or two counterions at the three common positions. Among the microbial rhodopsins with similar functions, the differences in the polar residues at the retinal Schiff base binding site are responsible for the differences in the absorption wavelengths. Counterions contribute to an absorption wavelength shift of 50-120 nm, whereas polar groups contribute to a shift of up to ∼10 nm. It seems likely that protein function is directly associated with the absorption wavelength in microbial rhodopsins.
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Affiliation(s)
- Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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Bold BM, Sokolov M, Maity S, Wanko M, Dohmen PM, Kranz JJ, Kleinekathöfer U, Höfener S, Elstner M. Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes. Phys Chem Chem Phys 2020; 22:10500-10518. [PMID: 31950960 DOI: 10.1039/c9cp05753f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.
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Affiliation(s)
- Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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6
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Lee C, Sekharan S, Mertz B. Theoretical Insights into the Mechanism of Wavelength Regulation in Blue-Absorbing Proteorhodopsin. J Phys Chem B 2019; 123:10631-10641. [PMID: 31757123 DOI: 10.1021/acs.jpcb.9b08189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Choongkeun Lee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sivakumar Sekharan
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- XtalPi Inc, 245 Main Street, 12th Floor, Cambridge, Massachusetts 01242, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
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7
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Guareschi R, Valsson O, Curutchet C, Mennucci B, Filippi C. Electrostatic versus Resonance Interactions in Photoreceptor Proteins: The Case of Rhodopsin. J Phys Chem Lett 2016; 7:4547-4553. [PMID: 27786481 DOI: 10.1021/acs.jpclett.6b02043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light sensing in photoreceptor proteins is subtly modulated by the multiple interactions between the chromophoric unit and its binding pocket. Many theoretical and experimental studies have tried to uncover the fundamental origin of these interactions but reached contradictory conclusions as to whether electrostatics, polarization, or intrinsically quantum effects prevail. Here, we select rhodopsin as a prototypical photoreceptor system to reveal the molecular mechanism underlying these interactions and regulating the spectral tuning. Combining a multireference perturbation method and density functional theory with a classical but atomistic and polarizable embedding scheme, we show that accounting for electrostatics only leads to a qualitatively wrong picture, while a responsive environment can successfully capture both the classical and quantum dominant effects. Several residues are found to tune the excitation by both differentially stabilizing ground and excited states and through nonclassical "inductive resonance" interactions. The results obtained with such a quantum-in-classical model are validated against both experimental data and fully quantum calculations.
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Affiliation(s)
- Riccardo Guareschi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Omar Valsson
- Department of Chemistry and Applied Bioscience, ETH Zurich and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera italiana , Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII, s/n 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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8
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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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9
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Guo Y, Beyle FE, Bold BM, Watanabe HC, Koslowski A, Thiel W, Hegemann P, Marazzi M, Elstner M. Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant. Chem Sci 2016; 7:3879-3891. [PMID: 30155032 PMCID: PMC6013792 DOI: 10.1039/c6sc00468g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
We show by extensive ground state and absorption spectra simulations that the channelrhodopsin-2 active site samples three different hydrogen-bonding patterns.
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.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Franziska E Beyle
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Beatrix M Bold
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Hiroshi C Watanabe
- Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Peter Hegemann
- Institute of Biology , Experimental Biophysics , Humboldt-Universität , Invalidenstraße 42 , D-10115 Berlin , Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
| | - Marcus Elstner
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry , KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany . ;
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10
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García-Iriepa C, Gueye M, Léonard J, Martínez-López D, Campos PJ, Frutos LM, Sampedro D, Marazzi M. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement. Phys Chem Chem Phys 2016; 18:6742-53. [DOI: 10.1039/c5cp07599h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A combined experimental and computational study of a peptide-linked retinal-like molecular switch shows the effects on photoreactivity and the α-helix structure.
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Affiliation(s)
- Cristina García-Iriepa
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Moussa Gueye
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - David Martínez-López
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Pedro J. Campos
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | | | - Diego Sampedro
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- KIT
- 76131 Karlsruhe
- Germany
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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; 54:4953-7. [PMID: 25537168 DOI: 10.1002/anie.201410180] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/20/2014] [Indexed: 11/10/2022]
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels that are widely used in optogenetics. They allow precise control of neuronal activity with light, but a detailed understanding of how the channel is gated and the ions are conducted is still lacking. The recent determination of the X-ray structural model in the closed state marks an important milestone. Herein the open state structure is presented and the early formation of the ion conducting pore is elucidated in atomic detail using time-resolved FTIR spectroscopy. Photo-isomerization of the retinal-chromophore causes a downward movement of the highly conserved E90, which opens the pore. Molecular dynamic (MD) simulations show that water molecules invade through this opened pore, Helix 2 tilts and the channel fully opens within ms. Since E90 is a highly conserved residue, the proposed E90-Helix2-tilt (EHT) model might describe a general activation mechanism and provides a new avenue for further mechanistic studies and engineering.
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Affiliation(s)
- Jens Kuhne
- Lehrstuhl für Biophysik, Ruhr Universität Bochum, Universitätsstrasse 150, 44780 Bochum (Germany)
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12
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Kuhne J, Eisenhauer K, Ritter E, Hegemann P, Gerwert K, Bartl F. Die frühe Entstehung der ionenleitenden Pore in Channelrhodopsin-2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Li H, Govorunova EG, Sineshchekov OA, Spudich JL. Role of a helix B lysine residue in the photoactive site in channelrhodopsins. Biophys J 2014; 106:1607-17. [PMID: 24739160 DOI: 10.1016/j.bpj.2014.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/20/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022] Open
Abstract
In most studied microbial rhodopsins two conserved carboxylic acid residues (the homologs of Asp-85 and Asp-212 in bacteriorhodopsin) and an arginine residue (the homolog of Arg-82) form a complex counterion to the protonated retinylidene Schiff base, and neutralization of the negatively charged carboxylates causes red shifts of the absorption maximum. In contrast, the corresponding neutralizing mutations in some relatively low-efficiency channelrhodopsins (ChRs) result in blue shifts. These ChRs do not contain a lysine residue in the second helix, conserved in higher efficiency ChRs (Lys-132 in the crystallized ChR chimera). By action spectroscopy of photoinduced channel currents in HEK293 cells and absorption spectroscopy of detergent-purified pigments, we found that in tested ChRs the Lys-132 homolog controls the direction of spectral shifts in the mutants of the photoactive site carboxylic acid residues. Analysis of double mutants shows that red spectral shifts occur when this Lys is present, whether naturally or by mutagenesis, and blue shifts occur when it is replaced with a neutral residue. A neutralizing mutation of the Lys-132 homolog alone caused a red spectral shift in high-efficiency ChRs, whereas its introduction into low-efficiency ChR1 from Chlamydomonas augustae (CaChR1) caused a blue shift. Taking into account that the effective charge of the carboxylic acid residues is a key factor in microbial rhodopsin spectral tuning, these findings suggest that the Lys-132 homolog modulates their pKa values. On the other hand, mutation of the Arg-82 homolog that fulfills this role in bacteriorhodopsin caused minimal spectral changes in the tested ChRs. Titration revealed that the pKa of the Asp-85 homolog in CaChR1 lies in the alkaline region unlike in most studied microbial rhodopsins, but is substantially decreased by introduction of a Lys-132 homolog or neutralizing mutation of the Asp-212 homolog. In the three ChRs tested the Lys-132 homolog also alters channel current kinetics.
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Affiliation(s)
- Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas.
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UV–vis absorption spectrum of a novel Ru(II) complex intercalated in DNA: [Ru(2,2′-bipy)(dppz)(2,2′-ArPy)]+. J Mol Model 2014; 20:2082. [DOI: 10.1007/s00894-014-2082-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 10/09/2013] [Indexed: 12/26/2022]
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15
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Thellamurege NM, Hirao H. Effect of protein environment within cytochrome P450cam evaluated using a polarizable-embedding QM/MM method. J Phys Chem B 2014; 118:2084-92. [PMID: 24484442 DOI: 10.1021/jp412538n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloenzymes accommodate cofactors and substrates in their active sites, thereby exerting powerful catalytic effects. Understanding the key elements of the mechanism via which such binding is accomplished using a number of atoms in a protein is a fundamental challenge. To address this issue computationally, here we used mechanical-embedding (ME), electronic-embedding (EE), and polarizable-embedding (PE) hybrid quantum mechanics and molecular mechanics (QM/MM) methods and performed an energy decomposition analysis (EDA) of the nonbonding protein environmental effect in the "compound I" intermediate state of cytochrome P450cam. The B3LYP and AMBER99/QP302 methods were used to deal with the QM and MM subsystems, respectively, and the nonbonding interaction energy between these subsystems was decomposed into electrostatic, van der Waals, and polarization contributions. The PE-QM/MM calculation was performed using polarizable force fields that were capable of describing induced dipoles within the MM subsystem, which arose in response to the electric field generated by QM electron density, QM nuclei, and MM point charges. The present QM/MM EDA revealed that the electrostatic term constituted the largest stabilizing interaction between the QM and MM subsystems. When proper adjustment was made for the point charges of the MM atoms located at the QM-MM boundary, EE-QM/MM and PE-QM/MM calculations yielded similar QM electron density distributions, indicating that the MM polarization effect does not have a significant influence on the extent of QM polarization in this particular enzyme system.
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Affiliation(s)
- Nandun M Thellamurege
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore 637371
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16
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Wolter T, Welke K, Phatak P, Bondar AN, Elstner M. Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation. Phys Chem Chem Phys 2013; 15:12582-90. [DOI: 10.1039/c3cp44280b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Kamiya M, Kato HE, Ishitani R, Nureki O, Hayashi S. Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.11.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Welke K, Watanabe HC, Wolter T, Gaus M, Elstner M. QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2. Phys Chem Chem Phys 2013; 15:6651-9. [DOI: 10.1039/c3cp44181d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Gámez JA, Weingart O, Koslowski A, Thiel W. Periodic decay in the photoisomerisation of p-aminoazobenzene. Phys Chem Chem Phys 2013; 15:11814-21. [DOI: 10.1039/c3cp51316e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Sneskov K, Olsen JMH, Schwabe T, Hättig C, Christiansen O, Kongsted J. Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants. Phys Chem Chem Phys 2013; 15:7567-76. [DOI: 10.1039/c3cp44350g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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21
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Sekharan S, Wei JN, Batista VS. The Active Site of Melanopsin: The Biological Clock Photoreceptor. J Am Chem Soc 2012; 134:19536-9. [DOI: 10.1021/ja308763b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sivakumar Sekharan
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
| | - Jennifer N. Wei
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
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22
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Gámez JA, Weingart O, Koslowski A, Thiel W. Cooperating Dinitrogen and Phenyl Rotations in trans-Azobenzene Photoisomerization. J Chem Theory Comput 2012; 8:2352-8. [DOI: 10.1021/ct300303s] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José A. Gámez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Oliver Weingart
- Institut für Theoretische
Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225
Düsseldorf, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
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23
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Valsson O, Filippi C. Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage. J Phys Chem Lett 2012; 3:908-912. [PMID: 26286419 DOI: 10.1021/jz300183g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We employ state-of-the-art first-principle approaches to investigate whether temperature effects are responsible for the unusually broad and flat spectrum of protonated Schiff base retinal observed in photodissociation spectroscopy, as has recently been proposed. We first carefully calibrate how to construct a realistic geometrical model of retinal and show that the exchange-correlation M06-2X functional yields an accurate description while the commonly used complete active space self-consistent field method (CASSCF) is not adequate. Using modern multiconfigurational perturbative methods (NEVPT2) to compute the excitations, we then demonstrate that conformations with different orientations of the β-ionone ring are characterized by similar excitations. Moreover, other degrees of freedom identified as active in room-temperature molecular dynamics simulations do not yield the shift required to explain the anomalous spectral shape. Our findings indicate that photodissociation experiments are not representative of the optical spectrum of retinal in the gas phase and call for further experimental characterization of the dissociation spectra.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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