1
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- 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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2
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Himel MH, Sikder B, Ahmed T, Choudhury SM. Biomimicry in nanotechnology: a comprehensive review. NANOSCALE ADVANCES 2023; 5:596-614. [PMID: 36756510 PMCID: PMC9890514 DOI: 10.1039/d2na00571a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Biomimicry has been utilized in many branches of science and engineering to develop devices for enhanced and better performance. The application of nanotechnology has made life easier in modern times. It has offered a way to manipulate matter and systems at the atomic level. As a result, the miniaturization of numerous devices has been possible. Of late, the integration of biomimicry with nanotechnology has shown promising results in the fields of medicine, robotics, sensors, photonics, etc. Biomimicry in nanotechnology has provided eco-friendly and green solutions to the energy problem and in textiles. This is a new research area that needs to be explored more thoroughly. This review illustrates the progress and innovations made in the field of nanotechnology with the integration of biomimicry.
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Affiliation(s)
- Mehedi Hasan Himel
- Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology Dhaka 1205 Bangladesh
- Department of Computer Science and Engineering, Brac University 66 Mohakhali Dhaka 1212 Bangladesh
| | - Bejoy Sikder
- Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology Dhaka 1205 Bangladesh
| | - Tanvir Ahmed
- Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology Dhaka 1205 Bangladesh
- Department of Computer Science and Engineering, Brac University 66 Mohakhali Dhaka 1212 Bangladesh
| | - Sajid Muhaimin Choudhury
- Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology Dhaka 1205 Bangladesh
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3
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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4
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Significant impact of deprotonated status on the photoisomerization dynamics of bacteriophytochrome chromophore. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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6
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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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7
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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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8
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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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9
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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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10
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Competing excited-state deactivation processes in bacteriophytochromes. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Wang D, Qin Y, Zhang S, Wang L, Yang X, Zhong D. Elucidating the Molecular Mechanism of Ultrafast Pfr-State Photoisomerization in Bathy Bacteriophytochrome PaBphP. J Phys Chem Lett 2019; 10:6197-6201. [PMID: 31577445 PMCID: PMC7268903 DOI: 10.1021/acs.jpclett.9b02446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bacteriophytochromes are photoreceptors that regulate various physiological processes induced by photoisomerization in a linear tetrapyrrole chromophore upon red/far-red light absorption. Here, we investigate the photoinduced Pfr-state isomerization mechanism of a bathy bacteriophytochrome from Pseudomonas aeruginosa combining femtosecond-resolved fluorescence and absorption methods. We observed initial coherent oscillation motions in the first 1 ps with low-frequency modes below 60 cm-1, then a bifurcation of the wavepacket with the distinct excited-state lifetimes in a few picoseconds, and finally chromophore-protein coupled ground-state conformational evolution on nanosecond time scales. Together with systematic mutational studies, we revealed the critical roles of hydrogen bonds in tuning the photoisomerization dynamics. These results provide a clear molecular picture of the Pfr-state photoisomerization, a mechanism likely applicable to the other phytochromes.
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Affiliation(s)
- Dihao Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Yangzhong Qin
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Sheng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical
Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
- Corresponding Author
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12
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Bizimana LA, Farfan CA, Brazard J, Turner DB. E to Z Photoisomerization of Phytochrome Cph1Δ Exceeds the Born-Oppenheimer Adiabatic Limit. J Phys Chem Lett 2019; 10:3550-3556. [PMID: 31181167 DOI: 10.1021/acs.jpclett.9b01137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Born-Oppenheimer adiabatic limit applies broadly in chemistry because most reactions occur on the ground electronic state. Photochemical reactions involve two or more electronic states and need not be subject to this adiabatic limit. The spectroscopic signatures of nonadiabatic processes are subtle, and therefore, experimental investigations have been limited to the few systems dominated by single photochemical outcomes. Systems with branched excited-state pathways have been neglected, despite their potential to reveal insights into photochemical reactivity. Here we present experimental evidence from coherent three-dimensional electronic spectroscopy that the E to Z photoisomerization of phytochrome Cph1 is strongly nonadiabatic, and the simulations reproduce the measured features only when the photoisomerization proceeds nonadiabatically near, but not through, a conical intersection. The results broaden the general understanding of photoisomerization mechanisms and motivate future studies of nonadiabatic processes with multiple outcomes arising from branching on excited-state potential energy surfaces.
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Affiliation(s)
- Laurie A Bizimana
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Camille A Farfan
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Johanna Brazard
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Daniel B Turner
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
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13
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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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14
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Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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15
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Gourinchas G, Etzl S, Winkler A. Bacteriophytochromes - from informative model systems of phytochrome function to powerful tools in cell biology. Curr Opin Struct Biol 2019; 57:72-83. [PMID: 30878713 DOI: 10.1016/j.sbi.2019.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022]
Abstract
Bacteriophytochromes are a subfamily of the diverse light responsive phytochrome photoreceptors. Considering their preferential interaction with biliverdin IXα as endogenous cofactor, they have recently been used for creating optogenetic tools and engineering fluorescent probes. Ideal absorption characteristics for the activation of bacteriophytochrome-based systems in the therapeutic near-infrared window as well the availability of biliverdin in mammalian tissues have resulted in tremendous progress in re-engineering bacteriophytochromes for diverse applications. At the same time, both the structural analysis and the functional characterization of diverse naturally occurring bacteriophytochrome systems have unraveled remarkable differences in signaling mechanisms and have so far only touched the surface of the evolutionary diversity within the family of bacteriophytochromes. This review highlights recent findings and future challenges.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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16
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Modi V, Donnini S, Groenhof G, Morozov D. Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome. J Phys Chem B 2019; 123:2325-2334. [PMID: 30762368 PMCID: PMC6727380 DOI: 10.1021/acs.jpcb.9b01117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The
tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome
from Deinococcus radiodurans (DrBphP)
is usually assumed to be fully protonated, but this assumption has
not been systematically validated by experiments or extensive computations.
Here, we use force field molecular dynamics simulations and quantum
mechanics/molecular mechanics calculations with density functional
theory and XMCQDPT2 methods to investigate the effect of the five
most probable protonation forms of BV on structural stability, binding
pocket interactions, and absorption spectra in the two photochromic
states of DrBphP. While agreement with X-ray structural data and measured
UV/vis spectra suggest that in both states the protonated form of
the chromophore dominates, we also find that a minor population with
a deprotonated D-ring could contribute to the red-shifted tail in
the absorption spectra.
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17
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Gong J, Liu J, Tan X, Li Z, Li Q, Zhang J. Bio-Preparation and Regulation of Pyrrole Structure Nano-Pigment Based on Biomimetic Membrane. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E114. [PMID: 30669357 PMCID: PMC6359519 DOI: 10.3390/nano9010114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 12/18/2022]
Abstract
Microbial pigments, regarded as the most potential biomass pigments, have lately attracted increasing attention in textile dyeing due to their sustainability and cleaner production. The pyrrole structure microbial pigment, called prodigiosin, recently have become a research hotspot for its bright colors and antibacterial function. However, in most case the extraction and preparation are time-consuming and expensive processes since these kinds of microbial pigments are intracellular metabolites. In order to promote the application of microbial pigments in textile dyeing, a novel idea of preparing dye liquid of pyrrole structure pigments based on fermentation broth was put forward via increasing the proportion of extracellular pigments. A model membrane platform was established with a planar lipid bilayer to investigate transmembrane transport of microbial pigments and permeability barrier of cell membrane. The nano-dispersion of pigments was produced as the dye liquor owing to high-throughput transmembrane transfer of intracellular pigments and the increase of extracellular pigments proportion. The results indicated that the size and surface electrical properties of the pigments had contributed much to the mass transfer. It is also showed that transmembrane transmission of the intracellular pigments could be regulated by physical and chemical methods. With the improvement of transmembrane transfer efficiency of microbial pigments and the proportion of extracellular pigments, the complicated biological separation process could be avoided and the application of microbial pigments in textile dyeing can be promoted.
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Affiliation(s)
- Jixian Gong
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Jiayin Liu
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Xueqiang Tan
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Zheng Li
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Qiujin Li
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Jianfei Zhang
- School of Textiles Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
- Key Laboratory of Advanced Textile Composites Ministry of Education, Tianjin Polytechnic University, Tianjin 300387, China.
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18
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Losi A, Bonomi HR, Michael N, Tang K, Zhao KH. Time-Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome-Related Photoreceptors. Photochem Photobiol 2018; 93:733-740. [PMID: 28500712 DOI: 10.1111/php.12728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
Time-resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light-induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin-binding photoreceptors of prokaryotic origin: (1) the chromophore-binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full-length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub-ns scale, reflecting the low photoisomerization quantum yield (<0.2). This "prompt" step is accompanied by a positive ΔV1 = 5-12.5 mL mol-1 . Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3-G for which ΔV1 = +4.5 mL mol-1 is followed by a time-resolved, energy-conserving contraction ΔV2 = -11.4 mL mol-1 , τ2 = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3-G.
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Affiliation(s)
- Aba Losi
- Department of Physics and Earth Science, University of Parma, Parma, Italy
| | - Hernán R Bonomi
- Immunology and Molecular Microbiology Laboratory, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Kun Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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19
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Zhang W, Zhong H, Lu H, Zhang Y, Deng X, Huang K, Duanmu D. Characterization of Ferredoxin-Dependent Biliverdin Reductase PCYA1 Reveals the Dual Function in Retrograde Bilin Biosynthesis and Interaction With Light-Dependent Protochlorophyllide Oxidoreductase LPOR in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2018; 9:676. [PMID: 29875782 PMCID: PMC5974162 DOI: 10.3389/fpls.2018.00676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/03/2018] [Indexed: 05/27/2023]
Abstract
Bilins are linear tetrapyrroles commonly used as chromophores of phycobiliproteins and phytochromes for light-harvesting or light-sensing in photosynthetic organisms. Many eukaryotic algae lack both phycobiliproteins and phytochromes, but retain the bilin biosynthetic enzymes including heme oxygenase (HO/HMOX) and ferredoxin-dependent biliverdin reductase (FDBR). Previous studies on Chlamydomonas reinhardtii heme oxygenase mutant (hmox1) have shown that bilins are not only essential retrograde signals to mitigate oxidative stress during diurnal dark-to-light transitions, they are also required for chlorophyll accumulation and maintenance of a functional photosynthetic apparatus in the light. However, the underlying mechanism of bilin-mediated regulation of chlorophyll biosynthesis is unclear. In this study, Chlamydomonas phycocyanobilin:ferredoxin oxidoreductase PCYA1 FDBR domain was found to specifically interact with the rate-limiting chlorophyll biosynthetic enzyme LPOR (light-dependent protochlorophyllide oxidoreductase). PCYA1 is partially associated with chloroplast envelope membrane, consistent with the observed export of bilin from chloroplast to cytosol by cytosolic expression of a bilin-binding reporter protein in Chlamydomonas. Both the pcya1-1 mutant with the carboxyl-terminal extension of PCYA1 eliminated and efficient knockdown of PCYA1 expression by artificial microRNA exhibited no significant impact on algal phototrophic growth and photosynthetic proteins accumulation, indicating that the conserved FDBR domain is sufficient and minimally required for bilin biosynthesis and functioning. Taken together, these studies provide novel insights into the regulatory role of PCYA1 in chlorophyll biosynthesis via interaction with key Chl biosynthetic enzyme.
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Affiliation(s)
- Weiqing Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huan Zhong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Lu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxiang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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20
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Falklöf O, Durbeej B. Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited-State Proton Transfer in Bacteriophytochromes. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201800014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Olle Falklöf
- Division of Theoretical Chemistry, IFM; Linköping University; SE-581 83 Linköping Sweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, IFM; Linköping University; SE-581 83 Linköping Sweden
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21
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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