1
|
Singer NK, González L, Monari A. Molecular Photoswitches Regulating the Activity of the Human Serotonin Transporter. J Phys Chem Lett 2023; 14:10333-10339. [PMID: 37944933 DOI: 10.1021/acs.jpclett.3c02655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Serotonin is an essential mediator regulating diverse neural processes, and its deregulation is related to the development of debilitating neurological diseases. In particular, the human serotonin transporter (hSERT) is fundamental in completing the synaptic neural cycle by allowing reuptake of serotonin. Its inhibition is particularly attractive, especially as a pharmacological target against depressive syndrome. Here, we analyze, by using long-range molecular dynamic simulations, the behavior of a molecular photoswitch whose cis- and trans-isomers inhibit the hSERT differently. In particular, we evidence the structural and molecular basis behind the higher inhibiting capacity of the cis-isomer, which blocks more efficiently the hSERT conformational cycle, leading to serotonin uptake.
Collapse
Affiliation(s)
- Nadja K Singer
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna Austria
- Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Str. 17, 1090 Vienna Austria
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
| |
Collapse
|
2
|
Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [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] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
Collapse
Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
3
|
Shibata K, Oda K, Nishizawa T, Hazama Y, Ono R, Takaramoto S, Bagherzadeh R, Yawo H, Nureki O, Inoue K, Akiyama H. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. J Am Chem Soc 2023; 145:10779-10789. [PMID: 37129501 DOI: 10.1021/jacs.3c01879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.
Collapse
Affiliation(s)
- Keisei Shibata
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Kazumasa Oda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Yuji Hazama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Ryohei Ono
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Shunki Takaramoto
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hidefumi Akiyama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
4
|
Xin Q, Cheng J, Wang H, Zhang W, Lu H, Zhou J, Lo GV, Dou Y, Yuan S. Modeling the syn-cycle in the light activated opening of the channelrhodopsin-2 ion channel. RSC Adv 2022; 12:6515-6524. [PMID: 35424642 PMCID: PMC8981705 DOI: 10.1039/d1ra08521b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
The ion channel of channelrhodopsin-2 (ChR2) is activated by absorbing light. The light stimulates retinal to isomerize to start the photocycle. There are two pathways for photocycles, which are caused by isomerization of the retinal from all-trans, 15-anti to 13-cis, 15-anti in the dark-adapted state (anti-cycle) and from 13-cis, 15-syn to all-trans, 15-syn in the light-adapted state (syn-cycle). In this work, the structure of the syn-cycle intermediate and mechanism of channel opening were studied by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Due to the lack of crystal structure of intermediates in the syn-cycle of ChR2, the intermediate models were constructed from the homologous intermediates in the anti-cycle. The isomerization of retinal was shown to cause the central gate (CG) hydrogen bond network to rearrange, cutting the link between TM2 and TM7. TM2 is moved by the intrahelical hydrogen bond of E90 and K93, and induced the intracellular gate (ICG) to expand. The ion penetration pathway between TM1, TM2, TM3 and TM7 in the P500* state was observed by MD simulations. However, this channel is not fully opened compared with the homologous P500 state in the anti-cycle. In addition, the protons on Schiff bases were found to be unable to form hydrogen bonds with the counter residues (E123 and D253) in the P500* state, preventing an evolution of the P500* state to a P390-like state in the syn-cycle. Modelling the syn-cycle is a series of operations on the ChR2 crystal structure (PDB ID: 6EID). By replacement and isomerization, we obtained P500* and P480 intermediates. A feasible explanation that no P390* was observed in experiment was inferred.![]()
Collapse
Affiliation(s)
- Qi Xin
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Jie Cheng
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Hongwei Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, Australia
| | - Wenying Zhang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Hong Lu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Junpeng Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| | - Glenn V. Lo
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, LA 70310, USA
| | - Yusheng Dou
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, LA 70310, USA
| | - Shuai Yuan
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 40065, China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Liang R, Yu JK, Meisner J, Liu F, Martinez TJ. Electrostatic Control of Photoisomerization in Channelrhodopsin 2. J Am Chem Soc 2021; 143:5425-5437. [PMID: 33794085 DOI: 10.1021/jacs.1c00058] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.
Collapse
Affiliation(s)
- Ruibin Liang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jimmy K Yu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States.,Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Jan Meisner
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Fang Liu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martinez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
7
|
Cheng J, Zhang W, Zhou S, Ran X, Shang Y, Lo GV, Dou Y, Yuan S. The effect on ion channel of different protonation states of E90 in channelrhodopsin-2: a molecular dynamics simulation. RSC Adv 2021; 11:14542-14551. [PMID: 35424009 PMCID: PMC8697799 DOI: 10.1039/d1ra01879e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/13/2021] [Indexed: 11/21/2022] Open
Abstract
Channelrhodopsin-2 (ChR2) is a cationic channel protein that has been extensively studied in optogenetics. The ion channel is opened via a series of proton transfers and H-bond changes during the photocycle but the detailed mechanism is still unknown. Molecular dynamics (MD) simulations with enhanced sampling were performed on the dark-adapted state (i.e., D470) and two photocycle intermediates (P1500 and P2390) to study the proton transfer path of the Schiff base and the subsequent conformational changes. The results suggest there are two possible proton transfer pathways from the Schiff base to proton acceptors (i.e., E123 or D253), depending on the protonation of E90. If E90 is protonated in the P1500 state, the proton on the Schiff base will transfer to E123. The polyene chain of 13-cis retinal tilts and opens the channel that detours the blocking central gate (CG) and forms a narrow channel through the transmembrane helices (TM) 2, 3, 6 and 7. In contrast, if E90 deprotonates after retinal isomerization, the primary proton acceptor is D253, and an almost-open channel through TM1, 2, 3 and 7 is generated. The channel diameter is very close to the experimental value. The potential mean force (PMF) suggests that the free energy is extremely low for ions passing through this channel. With E90 protonated, the proton acceptor of RSBH+ is E123 with a narrow channel along TM3; while with E90 deprotonated, proton transfer from RSBH+ to D253 generates an approximately open channel along TM2.![]()
Collapse
Affiliation(s)
- Jie Cheng
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Wenying Zhang
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Shuangyan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Xu Ran
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Yiwen Shang
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| | - Glenn V. Lo
- Department of Chemistry and Physical Sciences
- Nicholls State University
- Thibodaux
- USA
| | - Yusheng Dou
- Department of Chemistry and Physical Sciences
- Nicholls State University
- Thibodaux
- USA
| | - Shuai Yuan
- Chongqing Key Laboratory of Big Data for Bio Intelligence
- Chongqing University of Posts and Telecommunications
- Chongqing 40065
- China
| |
Collapse
|
8
|
Nagasaka Y, Hososhima S, Kubo N, Nagata T, Kandori H, Inoue K, Yawo H. Gate-keeper of ion transport-a highly conserved helix-3 tryptophan in a channelrhodopsin chimera, C1C2/ChRWR. Biophys Physicobiol 2020; 17:59-70. [PMID: 33173715 PMCID: PMC7593130 DOI: 10.2142/biophysico.bsj-2020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/01/2022] Open
Abstract
Microbial rhodopsin is a large family of membrane proteins having seven transmembrane helices (TM1-7) with an all-trans retinal (ATR) chromophore that is covalently bound to Lys in the TM7. The Trp residue in the middle of TM3, which is homologous to W86 of bacteriorhodopsin (BR), is highly conserved among microbial rhodopsins with various light-driven functions. However, the significance of this Trp for the ion transport function of microbial rhodopsins has long remained unknown. Here, we replaced the W163 (BR W86 counterpart) of a channelrhodopsin (ChR), C1C2/ChRWR, which is a chimera between ChR1 and 2, with a smaller aromatic residue, Phe to verify its role in the ion transport. Under whole-cell patch clamp recordings from the ND7/23 cells that were transfected with the DNA plasmid coding human codon optimized C1C2/ChRWR (hWR) or its W163F mutant (hWR-W163F), the photocurrents were evoked by a pulsatile light at 475 nm. The ion-transporting activity of hWR was strongly altered by the W163F mutation in 3 points: (1) the H+ leak at positive membrane potential (Vm) and its light-adaptation, (2) the attenuation of cation channel activity and (3) the manifestation of outward H+ pump activity. All of these results strongly suggest that W163 has a role in stabilizing the structure involved in the gating-on and -off of the cation channel, the role of “gate keeper”. We can attribute the attenuation of cation channel activity to the incomplete gating-on and the H+ leak to the incomplete gating-off.
Collapse
Affiliation(s)
- Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Naoko Kubo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Department of Physiology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO) , Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
9
|
Broser M, Spreen A, Konold PE, Schiewer E, Adam S, Borin V, Schapiro I, Seifert R, Kennis JTM, Bernal Sierra YA, Hegemann P. NeoR, a near-infrared absorbing rhodopsin. Nat Commun 2020; 11:5682. [PMID: 33173168 PMCID: PMC7655827 DOI: 10.1038/s41467-020-19375-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
The Rhizoclosmatium globosum genome encodes three rhodopsin-guanylyl cyclases (RGCs), which are predicted to facilitate visual orientation of the fungal zoospores. Here, we show that RGC1 and RGC2 function as light-activated cyclases only upon heterodimerization with RGC3 (NeoR). RGC1/2 utilize conventional green or blue-light-sensitive rhodopsins (λmax = 550 and 480 nm, respectively), with short-lived signaling states, responsible for light-activation of the enzyme. The bistable NeoR is photoswitchable between a near-infrared-sensitive (NIR, λmax = 690 nm) highly fluorescent state (QF = 0.2) and a UV-sensitive non-fluorescent state, thereby modulating the activity by NIR pre-illumination. No other rhodopsin has been reported so far to be functional as a heterooligomer, or as having such a long wavelength absorption or high fluorescence yield. Site-specific mutagenesis and hybrid quantum mechanics/molecular mechanics simulations support the idea that the unusual photochemical properties result from the rigidity of the retinal chromophore and a unique counterion triad composed of two glutamic and one aspartic acids. These findings substantially expand our understanding of the natural potential and limitations of spectral tuning in rhodopsin photoreceptors.
Collapse
Affiliation(s)
- Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Anika Spreen
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Patrick E Konold
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Veniamin Borin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Reinhard Seifert
- Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | | | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| |
Collapse
|
10
|
Kaufmann JCD, Krause BS, Adam S, Ritter E, Schapiro I, Hegemann P, Bartl FJ. Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR. Biophys J 2020; 119:705-716. [PMID: 32697975 DOI: 10.1016/j.bpj.2020.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022] Open
Abstract
The function of photoreceptors relies on efficient transfer of absorbed light energy from the chromophore to the protein to drive conformational changes that ultimately generate an output signal. In retinal-binding proteins, mainly two mechanisms exist to store the photon energy after photoisomerization: 1) conformational distortion of the prosthetic group retinal, and 2) charge separation between the protonated retinal Schiff base (RSBH+) and its counterion complex. Accordingly, energy transfer to the protein is achieved by chromophore relaxation and/or reduction of the charge separation in the RSBH+-counterion complex. Combining FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the widely used, red-activatable Volvox carteri channelrhodopsin-1 derivate ReaChR that energy storage and transfer into the protein depends on the protonation state of glutamic acid E163 (Ci1), one of the counterions of the RSBH+. Ci1 retains a pKa of 7.6 so that both its protonated and deprotonated forms equilibrate at physiological conditions. Protonation of Ci1 leads to a rigid hydrogen-bonding network in the active-site region. This stabilizes the distorted conformation of the retinal after photoactivation and decelerates energy transfer into the protein by impairing the release of the strain energy. In contrast, with deprotonated Ci1 or removal of the Ci1 glutamate side chain, the hydrogen-bonded system is less rigid, and energy transfer by chromophore relaxation is accelerated. Based on the hydrogen out-of-plane (HOOP) band decay kinetics, we determined the activation energy for these processes in dependence of the Ci1 protonation state.
Collapse
Affiliation(s)
- Joel C D Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité Berlin, Berlin, Germany
| | - Benjamin S Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eglof Ritter
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Franz J Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
11
|
Marazzi M, Francés-Monerris A, Mourer M, Pasc A, Monari A. Trans-to-cis photoisomerization of cyclocurcumin in different environments rationalized by computational photochemistry. Phys Chem Chem Phys 2020; 22:4749-4757. [PMID: 32057038 DOI: 10.1039/c9cp06565b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclocurcumin is a turmeric component that has attracted much less attention compared to the well-known curcumin. In spite of the less deep characterization of its properties, cyclocurcumin has shown promising anticancer effects when used in combination with curcumin. Especially, due to its peculiar molecular structure, cyclocurcumin can be regarded as an almost ideal photoswitch, whose capabilities can also be exploited for relevant biological applications. Here, by means of state-of-the-art computational methods for electronic excited-state calculations (TD-DFT, MS-CASPT2, and XMS-CASPT2), we analyze in detail the absorption and photoisomerization pathways leading from the more stable trans isomer to the cis one. The different molecular surroundings, taken into account by means of the electrostatic solvent effect and compared with available experimental data, have been found to be critical in describing the fate of irradiated cyclocurcumin: when in non-polar environments, an excited state barrier prevents photoisomerization and favours fluorescence, whereas in polar solvents, an almost barrierless path results in a striking decrease of fluorescence, opening the way toward a crossing region with the ground state and thus funneling the photoproduction of the cis isomer.
Collapse
Affiliation(s)
- Marco Marazzi
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33, 600, E-28805, Alcalá de Henares, Madrid, Spain. and Chemical Research Institute "Andrés M. del Rio" (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33, 600, E-28805, Alcalá de Henares, Madrid, Spain
| | - Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR-7019, F-5400 Nancy, France. and Departement de Quimica Fisica, Universitat de Valencia, 46100 Burjassot, Spain
| | - Maxime Mourer
- Université de Lorraine and CNRS, L2CM UMR 7053, F-54000 Nancy, France
| | - Andreea Pasc
- Université de Lorraine and CNRS, L2CM UMR 7053, F-54000 Nancy, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR-7019, F-5400 Nancy, France.
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Atomistic Insight into the Role of Threonine 127 in the Functional Mechanism of Channelrhodopsin-2. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9224905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Channelrhodopsins (ChRs) belong to the unique class of light-gated ion channels. The structure of channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) has been resolved, but the mechanistic link between light-induced isomerization of the chromophore retinal and channel gating remains elusive. Replacements of residues C128 and D156 (DC gate) resulted in drastic effects in channel closure. T127 is localized close to the retinal Schiff base and links the DC gate to the Schiff base. The homologous residue in bacteriorhodopsin (T89) has been shown to be crucial for the visible absorption maximum and dark–light adaptation, suggesting an interaction with the retinylidene chromophore, but the replacement had little effect on photocycle kinetics and proton pumping activity. Here, we show that the T127A and T127S variants of CrChR2 leave the visible absorption maximum unaffected. We inferred from hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and resonance Raman spectroscopy that the hydroxylic side chain of T127 is hydrogen-bonded to E123 and the latter is hydrogen-bonded to the retinal Schiff base. The C=N–H vibration of the Schiff base in the T127A variant was 1674 cm−1, the highest among all rhodopsins reported to date. We also found heterogeneity in the Schiff base ground state vibrational properties due to different rotamer conformations of E123. The photoreaction of T127A is characterized by a long-lived P2380 state during which the Schiff base is deprotonated. The conservative replacement of T127S hardly affected the photocycle kinetics. Thus, we inferred that the hydroxyl group at position 127 is part of the proton transfer pathway from D156 to the Schiff base during rise of the P3530 intermediate. This finding provides molecular reasons for the evolutionary conservation of the chemically homologous residues threonine, serine, and cysteine at this position in all channelrhodopsins known so far.
Collapse
|
14
|
Paulikat M, Mata RA, Gelabert R. A high-throughput computational approach to UV-Vis spectra in protein mutants. Phys Chem Chem Phys 2019; 21:20678-20692. [PMID: 31508628 DOI: 10.1039/c9cp03908b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.
Collapse
Affiliation(s)
- Mirko Paulikat
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Goettingen, Tammannstraße 6, D-37077 Göttingen, Germany.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| |
Collapse
|
15
|
Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
Collapse
Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
| |
Collapse
|
16
|
Moron V, Marazzi M, Wanko M. Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore? J Chem Theory Comput 2019; 15:4228-4240. [PMID: 31146524 DOI: 10.1021/acs.jctc.9b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.
Collapse
Affiliation(s)
- Victor Moron
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry, KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares, Madrid , Spain
- "Andrés M. del Rı́o" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
| | - Marius Wanko
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| |
Collapse
|
17
|
Liang R, Liu F, Martínez TJ. Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2. J Phys Chem Lett 2019; 10:2862-2868. [PMID: 31083920 DOI: 10.1021/acs.jpclett.9b00701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn-Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the "aborted bicycle-pedal" mechanism. In addition, RPSB photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which could trigger subsequent channel opening and ion conduction.
Collapse
Affiliation(s)
- Ruibin Liang
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Fang Liu
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| |
Collapse
|
18
|
Wolff FE, Höfener S, Elstner M, Wesołowski TA. Origin of the Solvatochromism in Organic Fluorophores with Flexible Side Chains: A Case Study of Flugi-2. J Phys Chem A 2019; 123:4581-4587. [DOI: 10.1021/acs.jpca.9b02474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Tomasz A. Wesołowski
- Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| |
Collapse
|
19
|
Marazzi M, Gattuso H, Fumanal M, Daniel C, Monari A. Charge-Transfer versus Charge-Separated Triplet Excited States of [Re I (dmp)(CO) 3 (His124)(Trp122)] + in Water and in Modified Pseudomonas aeruginosa Azurin Protein. Chemistry 2019; 25:2519-2526. [PMID: 30379366 DOI: 10.1002/chem.201803685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/17/2018] [Indexed: 12/20/2022]
Abstract
A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.
Collapse
Affiliation(s)
- Marco Marazzi
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Madre de Dios, 53, 26006, Logroño, Spain
| | - Hugo Gattuso
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
| | - Maria Fumanal
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
| |
Collapse
|
20
|
Dokukina I, Nenov A, Garavelli M, Marian CM, Weingart O. QM/MM Photodynamics of Retinal in the Channelrhodopsin Chimera C1C2 with OM3/MRCI. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Irina Dokukina
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Christel M. Marian
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| |
Collapse
|
21
|
Adam S, Bondar AN. Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin. PLoS One 2018; 13:e0201298. [PMID: 30086158 PMCID: PMC6080761 DOI: 10.1371/journal.pone.0201298] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Channelrhodopsins are light-sensitive ion channels whose reaction cycles involve conformation-coupled transfer of protons. Understanding how channelrhodopsins work is important for applications in optogenetics, where light activation of these proteins triggers changes in the transmembrane potential across excitable membranes. A fundamental open question is how the protein environment ensures that unproductive proton transfer from the retinal Schiff base to the nearby carboxylate counterion is avoided in the resting state of the channel. To address this question, we performed combined quantum mechanical/molecular mechanical proton transfer calculations with explicit treatment of the surrounding lipid membrane. The free energy profiles computed for proton transfer to the counterion, either via a direct jump or mediated by a water molecule, demonstrate that, when retinal is all-trans, water and protein electrostatic interactions largely favour the protonated retinal Schiff base state. We identified a conserved lysine group as an essential structural element for the proton transfer energetics in channelrhodopsins.
Collapse
Affiliation(s)
- Suliman Adam
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| |
Collapse
|
22
|
Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
Collapse
Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| |
Collapse
|
23
|
Abstract
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.
Collapse
Affiliation(s)
- Albert Ardevol
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany;
- Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| |
Collapse
|
24
|
Deisseroth K, Hegemann P. The form and function of channelrhodopsin. Science 2018; 357:357/6356/eaan5544. [PMID: 28912215 PMCID: PMC5723383 DOI: 10.1126/science.aan5544] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022]
Abstract
Channelrhodopsins are light-gated ion channels that, via regulation of flagellar function, enable single-celled motile algae to seek ambient light conditions suitable for photosynthesis and survival. These plant behavioral responses were initially investigated more than 150 years ago. Recently, major principles of function for light-gated ion channels have been elucidated by creating channelrhodopsins with kinetics that are accelerated or slowed over orders of magnitude, by discovering and designing channelrhodopsins with altered spectral properties, by solving the high-resolution channelrhodopsin crystal structure, and by structural model-guided redesign of channelrhodopsins for altered ion selectivity. Each of these discoveries not only revealed basic principles governing the operation of light-gated ion channels, but also enabled the creation of new proteins for illuminating, via optogenetics, the fundamentals of brain function.
Collapse
Affiliation(s)
- Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Peter Hegemann
- Institute for Biology, Humboldt Universität zu Berlin, D-10115 Berlin, Germany. .,Experimental Biophysics, Humboldt Universität zu Berlin, D-10115 Berlin, Germany
| |
Collapse
|
25
|
Guo Y, Wolff FE, Schapiro I, Elstner M, Marazzi M. Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2. Phys Chem Chem Phys 2018; 20:27501-27509. [DOI: 10.1039/c8cp05210g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.
Collapse
Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Franziska E. Wolff
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research
- Institute of Chemistry
- Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Marcus Elstner
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| |
Collapse
|
26
|
Wietek J, Rodriguez-Rozada S, Tutas J, Tenedini F, Grimm C, Oertner TG, Soba P, Hegemann P, Wiegert JS. Anion-conducting channelrhodopsins with tuned spectra and modified kinetics engineered for optogenetic manipulation of behavior. Sci Rep 2017; 7:14957. [PMID: 29097684 PMCID: PMC5668261 DOI: 10.1038/s41598-017-14330-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic engineering of natural light-gated ion channels has proven a powerful way to generate optogenetic tools for a wide variety of applications. In recent years, blue-light activated engineered anion-conducting channelrhodopsins (eACRs) have been developed, improved, and were successfully applied in vivo. We asked whether the approaches used to create eACRs can be transferred to other well-characterized cation-conducting channelrhodopsins (CCRs) to obtain eACRs with a broad spectrum of biophysical properties. We generated 22 variants using two conversion strategies applied to 11 CCRs and screened them for membrane expression, photocurrents and anion selectivity. We obtained two novel eACRs, Phobos and Aurora, with blue- and red-shifted action spectra and photocurrents similar to existing eACRs. Furthermore, step-function mutations greatly enhanced the cellular operational light sensitivity due to a slowed-down photocycle. These bi-stable eACRs can be reversibly toggled between open and closed states with brief light pulses of different wavelengths. All new eACRs reliably inhibited action potential firing in pyramidal CA1 neurons. In Drosophila larvae, eACRs conveyed robust and specific light-dependent inhibition of locomotion and nociception.
Collapse
Affiliation(s)
- Jonas Wietek
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Janine Tutas
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Federico Tenedini
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Christiane Grimm
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Thomas G Oertner
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Peter Soba
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - J Simon Wiegert
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany.
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Falkenried 94, 20251, Hamburg, Germany.
| |
Collapse
|
27
|
Vierock J, Grimm C, Nitzan N, Hegemann P. Molecular determinants of proton selectivity and gating in the red-light activated channelrhodopsin Chrimson. Sci Rep 2017; 7:9928. [PMID: 28855540 PMCID: PMC5577340 DOI: 10.1038/s41598-017-09600-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022] Open
Abstract
Channelrhodopsins are light-gated ion channels of green algae used for the precise temporal and spatial control of transmembrane ion fluxes. The channelrhodopsin Chrimson from Chlamydomonas noctigama allows unprecedented deep tissue penetration due to peak absorption at 590 nm. We demonstrate by electrophysiological recordings and imaging techniques that Chrimson is highly proton selective causing intracellular acidification in HEK cells that is responsible for slow photocurrent decline during prolonged illumination. We localized molecular determinants of both high proton selectivity and red light activation to the extracellular pore. Whereas exchange of Glu143 only drops proton conductance and generates an operational Na-channel with 590 nm activation, exchange of Glu139 in addition increased the open state lifetime and shifted the absorption hypsochromic by 70 nm. In conjunction with Glu300 in the center and Glu124 and Glu125 at the intracellular end of the pore, Glu139 contributes to a delocalized activation gate and stabilizes by long-range interaction counterion configuration involving protonation of Glu165 that we identified as a key determinant of the large opsin shift in Chrimson.
Collapse
Affiliation(s)
- Johannes Vierock
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Christiane Grimm
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Noam Nitzan
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Neuroscience Research Center, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| |
Collapse
|
28
|
Kaufmann JCD, Krause BS, Grimm C, Ritter E, Hegemann P, Bartl FJ. Proton transfer reactions in the red light-activatable channelrhodopsin variant ReaChR and their relevance for its function. J Biol Chem 2017; 292:14205-14216. [PMID: 28659342 PMCID: PMC5572910 DOI: 10.1074/jbc.m117.779629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/27/2017] [Indexed: 11/06/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels widely used for activating selected cells in large cellular networks. ChR variants with a red-shifted absorption maximum, such as the modified Volvox carteri ChR1 red-activatable channelrhodopsin ("ReaChR," λmax = 527 nm), are of particular interest because longer wavelengths allow optical excitation of cells in deeper layers of organic tissue. In all ChRs investigated so far, proton transfer reactions and hydrogen bond changes are crucial for the formation of the ion-conducting pore and the selectivity for protons versus cations, such as Na+, K+, and Ca2+ (1). By using a combination of electrophysiological measurements and UV-visible and FTIR spectroscopy, we characterized the proton transfer events in the photocycle of ReaChR and describe their relevance for its function. 1) The central gate residue Glu130 (Glu90 in Chlamydomonas reinhardtii (Cr) ChR2) (i) undergoes a hydrogen bond change in D → K transition and (ii) deprotonates in K → M transition. Its negative charge in the open state is decisive for proton selectivity. 2) The counter-ion Asp293 (Asp253 in CrChR2) receives the retinal Schiff base proton during M-state formation. Starting from M, a photocycle branching occurs involving (i) a direct M → D transition and (ii) formation of late photointermediates N and O. 3) The DC pair residue Asp196 (Asp156 in CrChR2) deprotonates in N → O transition. Interestingly, the D196N mutation increases 15-syn-retinal at the expense of 15-anti, which is the predominant isomer in the wild type, and abolishes the peak current in electrophysiological measurements. This suggests that the peak current is formed by 15-anti species, whereas 15-syn species contribute only to the stationary current.
Collapse
Affiliation(s)
- Joel C D Kaufmann
- From the Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,.
| | | | | | | | | | - Franz J Bartl
- From the Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,; Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany.
| |
Collapse
|
29
|
Abstract
Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
Collapse
|
30
|
Gruden M, Andjeklović L, Jissy AK, Stepanović S, Zlatar M, Cui Q, Elstner M. Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. J Comput Chem 2017; 38:2171-2185. [PMID: 28736893 DOI: 10.1002/jcc.24866] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 01/08/2023]
Abstract
Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Maja Gruden
- Center for Computational Chemistry and Bioinformatics, Faculty of Chemistry, University of Belgrade, Studentski Trg 12-16, Belgrade, 11001, Serbia
| | - Ljubica Andjeklović
- Department of Chemistry, IChTM, University of Belgrade, Studentski Trg 12-16, 11001, Belgrade, Serbia
| | - Akkarapattiakal Kuriappan Jissy
- Institute of Physical Chemistry & Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Kaiserstr. 12, Karlsruhe, 76131, Germany
| | - Stepan Stepanović
- Department of Chemistry, IChTM, University of Belgrade, Studentski Trg 12-16, 11001, Belgrade, Serbia
| | - Matija Zlatar
- Department of Chemistry, IChTM, University of Belgrade, Studentski Trg 12-16, 11001, Belgrade, Serbia
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin
| | - Marcus Elstner
- Institute of Physical Chemistry & Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Kaiserstr. 12, Karlsruhe, 76131, Germany
| |
Collapse
|
31
|
Gattuso H, García-Iriepa C, Sampedro D, Monari A, Marazzi M. Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations. J Chem Theory Comput 2017; 13:3290-3296. [DOI: 10.1021/acs.jctc.7b00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hugo Gattuso
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Cristina García-Iriepa
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
- Unidad
Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| |
Collapse
|
32
|
Melaccio F, del Carmen Marín M, Valentini A, Montisci F, Rinaldi S, Cherubini M, Yang X, Kato Y, Stenrup M, Orozco-Gonzalez Y, Ferré N, Luk HL, Kandori H, Olivucci M. Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology. J Chem Theory Comput 2016; 12:6020-6034. [DOI: 10.1021/acs.jctc.6b00367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Alessio Valentini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Fabio Montisci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Silvia Rinaldi
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Marco Cherubini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Xuchun Yang
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoshitaka Kato
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Michael Stenrup
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Yoelvis Orozco-Gonzalez
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Hoi Ling Luk
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Hideki Kandori
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
| |
Collapse
|
33
|
Nagaya K, Motomura K, Kukk E, Takahashi Y, Yamazaki K, Ohmura S, Fukuzawa H, Wada S, Mondal S, Tachibana T, Ito Y, Koga R, Sakai T, Matsunami K, Nakamura K, Kanno M, Rudenko A, Nicolas C, Liu XJ, Miron C, Zhang Y, Jiang Y, Chen J, Anand M, Kim DE, Tono K, Yabashi M, Yao M, Kono H, Ueda K. Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses. Faraday Discuss 2016; 194:537-562. [DOI: 10.1039/c6fd00085a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH3I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C4H3IN2O2, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH3I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.
Collapse
|