1
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Dey P, Santra S, Ghosh D. Effect of the protein environment on the excited state phenomena in a bacteriophytochrome. Phys Chem Chem Phys 2024; 26:20875-20882. [PMID: 39044617 DOI: 10.1039/d4cp02112f] [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: 07/25/2024]
Abstract
The excited state processes of a bacteriophytochrome are studied using high-level multireference methods. The various non-radiative channels of deactivation are identified for the chromophore. The effects of the protein environment and substituents are elucidated for these excited state processes. It is observed that while the excited states are completely delocalized in the Franck-Condon (FC) region, they acquire significant charge transfer character near the conical intersections. Earlier studies have emphasized the delocalized nature of the excited states in the FC region, which leads to absorption spectra with minimal Stokes shift [Rumyantsev et al., Sci. Rep., 2015, 5, 18348]. The effect of the protein environment on the vertical excitation energies was minimal, while that on the conical intersection (CI) energetics was significant. This may lead one to believe that it is charge transfer driven. However, energy decomposition analysis shows that it is the effect of the dispersion of nearby residues and the steric effect on the rings and substituents that lead to the large effect of proteins on the energetics of the CIs.
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Affiliation(s)
- Pradipta Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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2
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Santra S, Manna RN, Chakrabarty S, Ghosh D. Conformational Effects on the Absorption Spectra of Phytochromes. J Phys Chem B 2024; 128:3614-3620. [PMID: 38581077 DOI: 10.1021/acs.jpcb.4c00859] [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: 04/07/2024]
Abstract
Bacteriophytochrome is a photoreceptor protein that contains the biliverdin (BV) chromophore as its active component. The spectra of BV upon mutation remain remarkably unchanged, as far as spectral positions are concerned. This points toward the minimal effect of electrostatic effects on the electronic structure of the chromophore. However, the relative intensities of the Q and Soret bands of the chromophore change dramatically upon mutation. In this work, we delve into the molecular origin of this unusual intensity modulation. Using extensive classical MD and QM/MM calculations, we show that due to mutation, the conformational population of the chromophore changes significantly. The noncovalent interactions, especially the stacking interactions, lead to extra stabilization of the cyclic form in the D207H mutated species as opposed to the open form in the wild-type BV. Thus, unlike the commonly observed direct electrostatic effect on the spectral shift, in the case of BV the difference observed is in varying intensities, and this in turn is driven by a conformational shift due to enhanced stacking interaction.
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Affiliation(s)
- Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rabindra Nath Manna
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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3
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Mishima K, Shoji M, Umena Y, Boero M, Shigeta Y. Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores. Biophys Physicobiol 2021; 18:196-214. [PMID: 34552842 PMCID: PMC8421246 DOI: 10.2142/biophysico.bppb-v18.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/20/2021] [Indexed: 12/01/2022] Open
Abstract
In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors (intermolecular structural factors), intermolecular center-to-center distances (intermolecular structural factors), spectral overlaps of absorption and emission spectra (photophysical factors), and refractive index (material factor) to the excitation energy transfer (EET) rate constant. To benchmark their validity, we focused on the EET occurring in C-phycocyanin (C-PC) chromophores. To this aim, we resorted to quantum chemistry calculations to get optimized molecular structures of the C-PC chromophores within the density functional theory (DFT) framework. The absorption and emission spectra, as well as transition dipole moments, were computed by using the time-dependent DFT (TDDFT). Our method was applied to several types of C-PCs showing that the EET rates are determined by an interplay of their specific physical, chemical, and geometrical features. These results show that our formulas can become a useful tool for a reliable estimation of the relative contributions of the factors regulating the EET transfer rate.
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Affiliation(s)
- Kenji Mishima
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.,JST-PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Yasufumi Umena
- Department of Physiology, Division of Biophysics, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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4
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Liu X, Zhang T, Fang Q, Fang W, González L, Cui G. Hydrogen‐Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiang‐Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
- College of Chemistry and Material Science Sichuan Normal University Chengdu 610068 China
| | - Teng‐Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Wei‐Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Leticia González
- Institute of Theoretical Chemistry Faculty of Chemistry University of Vienna Währinger Straße 17 1090 Vienna Austria
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
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5
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Liu XY, Zhang TS, Fang Q, Fang WH, González L, Cui G. Hydrogen-Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes. Angew Chem Int Ed Engl 2021; 60:18688-18693. [PMID: 34097335 PMCID: PMC8456922 DOI: 10.1002/anie.202104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Indexed: 11/14/2022]
Abstract
Phytochrome proteins are light receptors that play a pivotal role in regulating the life cycles of plants and microorganisms. Intriguingly, while cyanobacterial phytochrome Cph1 and cyanobacteriochrome AnPixJ use the same phycocyanobilin (PCB) chromophore to absorb light, their excited‐state behavior is very different. We employ multiscale calculations to rationalize the different early photoisomerization mechanisms of PCB in Cph1 and AnPixJ. We found that their electronic S1, T1, and S0 potential minima exhibit distinct geometric and electronic structures due to different hydrogen bond networks with the protein environment. These specific interactions influence the S1 electronic structures along the photoisomerization paths, ultimately leading to internal conversion in Cph1 but intersystem crossing in AnPixJ. This explains why the excited‐state relaxation in AnPixJ is much slower (ca. 100 ns) than in Cph1 (ca. 30 ps). Further, we predict that efficient internal conversion in AnPixJ can be achieved upon protonating the carboxylic group that interacts with PCB.
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Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China.,College of Chemistry and Material Science, Sichuan Normal University, Chengdu, 610068, China
| | - Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
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6
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Macaluso V, Salvadori G, Cupellini L, Mennucci B. The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation. Chem Sci 2021; 12:5555-5565. [PMID: 34168792 PMCID: PMC8179611 DOI: 10.1039/d1sc00186h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 12/28/2022] Open
Abstract
Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway.
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Affiliation(s)
- Veronica Macaluso
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
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7
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Grigorenko BL, Polyakov IV, Nemukhin AV. Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4. J Chem Phys 2021; 154:065101. [PMID: 33588533 DOI: 10.1063/5.0026475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An enhanced interest in the phytochrome-based fluorescent proteins is explained by their ability to absorb and emit light in the far-red and infra-red regions particularly suitable for bioimaging. The fluorescent protein IFP1.4 was engineered from the chromophore-binding domain of a bacteriophytochrome in attempts to increase the fluorescence quantum yield. We report the results of simulations of structures in the ground S0 and excited S1 electronic states of IFP1.4 using the methods of quantum chemistry and quantum mechanics/molecular mechanics. We construct different protonation states of the biliverdin (BV) chromophore in the red-absorbing form of the protein by moving protons from the BV pyrrole rings to a suitable acceptor within the system and show that these structures are close in energy but differ by absorption bands. For the first time, we report structures of the minimum energy conical intersection points S1/S0 on the energy surfaces of BV in the protein environment and describe their connection to the local minima in the excited S1 state. These simulations allow us to characterize the deactivation routes in IFP1.4.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation
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8
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Mishima K, Shoji M, Umena Y, Boero M, Shigeta Y. Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis Process. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Kenji Mishima
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yasufumi Umena
- Department of Physiology, Division of Biophysics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Mauro Boero
- University of Strasbourg, Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS, UMR 7504, 23 rue du Loess, F-67034 France
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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9
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Jähnigen S, Sebastiani D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules 2020; 25:E5505. [PMID: 33255423 PMCID: PMC7727823 DOI: 10.3390/molecules25235505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.
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Affiliation(s)
| | - Daniel Sebastiani
- Institut für Chemie, Naturwissenschaftliche Fakultät II, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany;
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10
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Villegas-Escobar N, Matute RA. The Keto-Enol Tautomerism of Biliverdin in Bacteriophytochrome: Could it Explain the Bathochromic Shift in the Pfr Form? †. Photochem Photobiol 2020; 97:99-109. [PMID: 33053203 DOI: 10.1111/php.13341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/08/2020] [Indexed: 01/21/2023]
Abstract
Phytochromes are ubiquitous photoreceptors found in plants, eukaryotic algae, bacteria and fungi. Particularly, when bacteriophytochrome is irradiated with light, a Z-to-E (photo)isomerization takes place in the biliverdin chromophore as part of the Pr-to-Pfr conversion. This photoisomerization is concomitant with a bathochromic shift in the Q-band. Based on experimental evidence, we studied a possible keto-enol tautomerization of BV, as an alternative reaction channel after its photoisomerization. In this contribution, the noncatalyzed and water-assisted reaction pathways for the lactam-lactim interconversion through consecutive keto-enol tautomerization of a model BV species were studied deeply. It was found that in the absence of water molecules, the proton transfer reaction is unable to take place at normal conditions, due to large activation energies, and the endothermic formation of lactim derivatives prevents its occurrence. However, when a water molecule assists the process by catalyzing the proton transfer reaction, the activation free energy lowers considerably. The drastic lowering in the activation energy for the keto-enol tautomerism is due to the stabilization of the water moiety through hydrogen bonds along the reaction coordinate. The absorption spectra were computed for all tautomers. It was found that the UV-visible absorption bands are in reasonable agreement with the experimental data. Our results suggest that although the keto-enol equilibrium is likely favoring the lactam tautomer, the equilibrium could eventually be shifted in favor of the lactim, as it has been reported to occur in the dark reversion mechanism of bathy phytochromes.
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Affiliation(s)
- Nery Villegas-Escobar
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo OHiggins, Santiago, Chile
| | - Ricardo A Matute
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo OHiggins, Santiago, Chile.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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11
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Macaluso V, Cupellini L, Salvadori G, Lipparini F, Mennucci B. Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome. Phys Chem Chem Phys 2020; 22:8585-8594. [DOI: 10.1039/d0cp00372g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics and a multiscale polarizable QM/MM strategy allow reproducing absorption, circular dichroism, and resonance Raman spectra of a bacteriophytochrome.
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Affiliation(s)
- Veronica Macaluso
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Filippo Lipparini
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
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12
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QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules 2019; 24:molecules24091720. [PMID: 31058803 PMCID: PMC6540152 DOI: 10.3390/molecules24091720] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes.
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13
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Wiebeler C, Rao AG, Gärtner W, Schapiro I. Die effektive Konjugationslänge ist für die spektrale Verschiebung im rot/grün schaltenden Cyanobakteriochrom Slr1393g3 verantwortlich. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Aditya G. Rao
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Wolfgang Gärtner
- Institut für Analytische Chemie; Fakultät für Chemie und Mineralogie; Universität Leipzig; 04103 Leipzig Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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14
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Wiebeler C, Rao AG, Gärtner W, Schapiro I. The Effective Conjugation Length Is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3. Angew Chem Int Ed Engl 2019; 58:1934-1938. [PMID: 30508317 DOI: 10.1002/anie.201810266] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 01/19/2023]
Abstract
The origin of the spectral shift from a red- to a green-absorbing form in a cyanobacteriochrome, Slr1393g3, was identified by combined quantum mechanics/molecular mechanics simulations. This protein, related to classical phytochromes, carries the open-chain tetrapyrrole chromophore phycocyanobilin. Our calculations reveal that the effective conjugation length in the chromophore becomes shorter upon conversion from the red to the green form. This is related to the planarity of the entire chromophore. A large distortion was found for the terminal pyrrole rings A and D; however, the D ring contributes more strongly to the photoproduct tuning, despite a larger change in the twist of the A ring. Our findings implicate that the D ring twist can be exploited to regulate the absorption of the photoproduct. Hence, mutations that affect the D ring twist can lead to rational tuning of the photoproduct absorption, allowing the tailoring of cyanobacteriochromes for biotechnological applications such as optogenetics and bioimaging.
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Affiliation(s)
- Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, 04103, Leipzig, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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15
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Polyakov IV, Grigorenko BL, Mironov VA, Nemukhin AV. Modeling structure and excitation of biliverdin-binding domains in infrared fluorescent proteins. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Scarbath-Evers LK, Jähnigen S, Elgabarty H, Song C, Narikawa R, Matysik J, Sebastiani D. Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy. Phys Chem Chem Phys 2018; 19:13882-13894. [PMID: 28513754 DOI: 10.1039/c7cp01218g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental 13C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.
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Affiliation(s)
- Laura Katharina Scarbath-Evers
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.
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17
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Feliks M, Lafaye C, Shu X, Royant A, Field M. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry 2016; 55:4263-74. [DOI: 10.1021/acs.biochem.6b00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikolaj Feliks
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Céline Lafaye
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Xiaokun Shu
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California, San Francisco, California 94158, United States
| | - Antoine Royant
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Martin Field
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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18
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Singer P, Wörner S, Lamparter T, Diller R. Spectroscopic Investigation on the Primary Photoreaction of Bathy Phytochrome Agp2-Pr ofAgrobacterium fabrum: Isomerization in a pH-dependent H-bond Network. Chemphyschem 2016; 17:1288-97. [DOI: 10.1002/cphc.201600199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick Singer
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
| | - Sybille Wörner
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Tilman Lamparter
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Rolf Diller
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
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19
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Yang Y, Linke M, von Haimberger T, Matute R, González L, Schmieder P, Heyne K. Active and silent chromophore isoforms for phytochrome Pr photoisomerization: An alternative evolutionary strategy to optimize photoreaction quantum yields. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2014; 1:014701. [PMID: 26798771 PMCID: PMC4711594 DOI: 10.1063/1.4865233] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/11/2014] [Indexed: 05/12/2023]
Abstract
Photoisomerization of a protein bound chromophore is the basis of light sensing of many photoreceptors. We tracked Z-to-E photoisomerization of Cph1 phytochrome chromophore PCB in the Pr form in real-time. Two different phycocyanobilin (PCB) ground state geometries with different ring D orientations have been identified. The pre-twisted and hydrogen bonded PCB(a) geometry exhibits a time constant of 30 ps and a quantum yield of photoproduct formation of 29%, about six times slower and ten times higher than that for the non-hydrogen bonded PCB(b) geometry. This new mechanism of pre-twisting the chromophore by protein-cofactor interaction optimizes yields of slow photoreactions and provides a scaffold for photoreceptor engineering.
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Affiliation(s)
| | - Martin Linke
- Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | | | - Ricardo Matute
- Department of Chemistry and Biochemistry, UCLA , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
| | - Leticia González
- Universität Wien, Institut für Theoretische Chemie , Währinger Str. 17, A-1090 Wien
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Rössle Str. 10, 13125 Berlin, Germany
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20
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Watermann T, Elgabarty H, Sebastiani D. Phycocyanobilin in solution – a solvent triggered molecular switch. Phys Chem Chem Phys 2014; 16:6146-52. [DOI: 10.1039/c3cp54307b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chromophore phycocyanobilin changes its spectroscopic behaviour upon solvent change. Our calculations trace this effect back to conformational switching, induced by changes in the hydrogen bonding pattern.
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Affiliation(s)
- Tobias Watermann
- Institute of Chemistry
- Martin Luther University Halle-Wittenberg
- 06120 Halle (Saale), Germany
| | - Hossam Elgabarty
- Institute of Physical Chemistry
- Johannes Gutenberg University Mainz
- 55128 Mainz, Germany
| | - Daniel Sebastiani
- Institute of Chemistry
- Martin Luther University Halle-Wittenberg
- 06120 Halle (Saale), Germany
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21
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Zhuang X, Wang J, Lan Z. Tracking of the Molecular Motion in the Primary Event of Photoinduced Reactions of a Phytochromobilin Model. J Phys Chem B 2013; 117:15976-86. [DOI: 10.1021/jp408799b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xuhui Zhuang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Jun Wang
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
| | - Zhenggang Lan
- Key
Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- The
Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, P. R. China
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22
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Falklöf O, Durbeej B. Modeling of phytochrome absorption spectra. J Comput Chem 2013; 34:1363-74. [DOI: 10.1002/jcc.23265] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Olle Falklöf
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
| | - Bo Durbeej
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
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23
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Varlan A, Hillebrand M. Exploring the capabilities of TDDFT calculations to explain the induced chirality upon a binding process: A simple case, 3-carboxycoumarin. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.11.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Ionescu S, Matei I, Tablet C, Hillebrand M. Theoretical ECD calculations – a useful tool for estimating the conformational change of a ligand in the binding pocket of proteins. Phys Chem Chem Phys 2013; 15:11604-14. [DOI: 10.1039/c3cp50466b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Spillane KM, Dasgupta J, Mathies RA. Conformational homogeneity and excited-state isomerization dynamics of the bilin chromophore in phytochrome Cph1 from resonance Raman intensities. Biophys J 2012; 102:709-17. [PMID: 22325295 DOI: 10.1016/j.bpj.2011.11.4019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/23/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
The ground-state structure and excited-state isomerization dynamics of the P(r) and P(fr) forms of phytochrome Cph1 are investigated using resonance Raman intensity analysis. Electronic absorption and stimulated resonance Raman spectra of P(r) and P(fr) are presented; vibronic analysis of the Raman intensities and absorption spectra reveals that both conformers exist as a single, homogeneous population of molecules in the ground state. The homogeneous and inhomogeneous contributions to the overall electronic broadening are determined, and it is found that the broadening is largely homogeneous in nature, pointing to fast excited-state decay. Franck-Condon displacements derived from the Raman intensity analysis reveal the initial atomic motions in the excited state, including the highly displaced, nontotally symmetric torsional and C(15)-H HOOP modes that appear because of symmetry-reducing distortions about the C(14)-C(15) and C(15)=C(16) bonds. P(fr) is especially well primed for ultrafast isomerization and torsional Franck-Condon analysis predicts a <200 fs P(fr) → P(r) isomerization. This time is significantly faster than the observed 700 fs reaction time, indicating that the P(fr) S(1) surface has a D-ring rotational barrier caused by steric interactions with the protein.
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Affiliation(s)
- Katelyn M Spillane
- Department of Chemistry, University of California, Berkeley, California, USA
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26
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Yang Y, Linke M, von Haimberger T, Hahn J, Matute R, González L, Schmieder P, Heyne K. Real-Time Tracking of Phytochrome’s Orientational Changes During Pr Photoisomerization. J Am Chem Soc 2012; 134:1408-11. [DOI: 10.1021/ja209413d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yang Yang
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
- Center for Supramolecular Interactions, Takustr. 3, 14195 Berlin, Germany
| | - Martin Linke
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
| | | | - Janina Hahn
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle
Str. 10, 13125 Berlin, Germany
| | - Ricardo Matute
- Institut für Physikalische
Chemie, Friedrich-Schiller Universität Jena, Helmholtzweg 4, 07743 Jena, Germany
- Departamento de Quimica, Universidad de Chile, Facultad de Ciencias, Casilla
653, Santiago, Chile
| | - Leticia González
- Institut für Physikalische
Chemie, Friedrich-Schiller Universität Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle
Str. 10, 13125 Berlin, Germany
| | - Karsten Heyne
- Department
of Physics, Freie Universität Berlin, Arnimallee 14, 14195
Berlin, Germany
- Center for Supramolecular Interactions, Takustr. 3, 14195 Berlin, Germany
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27
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Dietzek B, Fey S, Matute RA, González L, Schmitt M, Popp J, Yartsev A, Hermann G. Wavelength-dependent photoproduct formation of phycocyanobilin in solution – Indications for competing reaction pathways. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Strambi A, Durbeej B. Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study. Photochem Photobiol Sci 2011; 10:569-79. [DOI: 10.1039/c0pp00307g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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29
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Neugebauer J. Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies. Chemphyschem 2009; 10:3148-73. [DOI: 10.1002/cphc.200900538] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Spillane KM, Dasgupta J, Lagarias JC, Mathies RA. Homogeneity of phytochrome Cph1 vibronic absorption revealed by resonance Raman intensity analysis. J Am Chem Soc 2009; 131:13946-8. [PMID: 19739629 PMCID: PMC2880177 DOI: 10.1021/ja905822m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phytochromes are an important class of red/far-red responsive photoreceptors that act as light-activated biological switches, ultimately driving growth and development in plants, bacteria, and fungi. The composition of the red-absorbing ground-state has been widely debated due to the presence of a shoulder feature on the blue edge of electronic absorption spectra, which many have attributed to the presence of multiple ground-state conformers. Here we use resonance Raman intensity analysis to calculate the vibronic absorption profile of cyanobacterial phytochrome Cph1 and show that this shoulder feature is due simply to vibronic transitions from a single species, thus reflecting a homogeneous ground-state population.
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Affiliation(s)
- Katelyn M. Spillane
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Jyotishman Dasgupta
- Department of Chemistry, University of California, Berkeley, California 94720
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Richard A. Mathies
- Department of Chemistry, University of California, Berkeley, California 94720
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31
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Sorokina O, Kapus A, Terecskei K, Dixon LE, Kozma-Bognar L, Nagy F, Millar AJ. A switchable light-input, light-output system modelled and constructed in yeast. J Biol Eng 2009; 3:15. [PMID: 19761615 PMCID: PMC2758823 DOI: 10.1186/1754-1611-3-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/17/2009] [Indexed: 11/18/2022] Open
Abstract
Background Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media. Results The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation. Conclusion Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic.
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Affiliation(s)
- Oxana Sorokina
- Institute of Molecular Plant Sciences, The University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JH, UK
| | - Anita Kapus
- Institute of Plant Biology, Biological Research Center, Temesvari krt. 62, H-6726, Szeged, Hungary
| | - Kata Terecskei
- Institute of Plant Biology, Biological Research Center, Temesvari krt. 62, H-6726, Szeged, Hungary
| | - Laura E Dixon
- Institute of Molecular Plant Sciences, The University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JH, UK.,Centre for Systems Biology at Edinburgh, C.H. Waddington Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JD, UK
| | - Laszlo Kozma-Bognar
- Institute of Plant Biology, Biological Research Center, Temesvari krt. 62, H-6726, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Molecular Plant Sciences, The University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JH, UK.,Institute of Plant Biology, Biological Research Center, Temesvari krt. 62, H-6726, Szeged, Hungary
| | - Andrew J Millar
- Institute of Molecular Plant Sciences, The University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JH, UK.,Centre for Systems Biology at Edinburgh, C.H. Waddington Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JD, UK
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