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Zhu R, Li W, Zhen Z, Zou J, Liao G, Wang J, Wang Z, Chen H, Qin S, Weng Y. Quantum phase synchronization via exciton-vibrational energy dissipation sustains long-lived coherence in photosynthetic antennas. Nat Commun 2024; 15:3171. [PMID: 38609379 PMCID: PMC11015008 DOI: 10.1038/s41467-024-47560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The lifetime of electronic coherences found in photosynthetic antennas is known to be too short to match the energy transfer time, rendering the coherent energy transfer mechanism inactive. Exciton-vibrational coherence time in excitonic dimers which consist of two chromophores coupled by excitation transfer interaction, can however be much longer. Uncovering the mechanism for sustained coherences in a noisy biological environment is challenging, requiring the use of simpler model systems as proxies. Here, via two-dimensional electronic spectroscopy experiments, we present compelling evidence for longer exciton-vibrational coherence time in the allophycocyanin trimer, containing excitonic dimers, compared to isolated pigments. This is attributed to the quantum phase synchronization of the resonant vibrational collective modes of the dimer, where the anti-symmetric modes, coupled to excitonic states with fast dephasing, are dissipated. The decoupled symmetric counterparts are subject to slower energy dissipation. The resonant modes have a predicted nearly 50% reduction in the vibrational amplitudes, and almost zero amplitude in the corresponding dynamical Stokes shift spectrum compared to the isolated pigments. Our findings provide insights into the mechanisms for protecting coherences against the noisy environment.
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Affiliation(s)
- Ruidan Zhu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Zhanghe Zhen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China
| | - Jiading Zou
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Guohong Liao
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jiayu Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Zhuan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Hailong Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
- Songshan Lake Materials Laboratory, Dongguan, 523808, Guangdong, P.R. China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
- Songshan Lake Materials Laboratory, Dongguan, 523808, Guangdong, P.R. China.
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2
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Guan J, Lu Y, Sen K, Abdul Nasir J, Desmoutier AW, Hou Q, Zhang X, Logsdail AJ, Dutta G, Beale AM, Strange RW, Yong C, Sherwood P, Senn HM, Catlow CRA, Keal TW, Sokol AA. Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220234. [PMID: 37211033 PMCID: PMC10200352 DOI: 10.1098/rsta.2022.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/23/2023]
Abstract
Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Jingcheng Guan
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Jamal Abdul Nasir
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Qing Hou
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Institute of Photonic Chips, University of Shanghai for Science of Technology, Shanghai 201512, People’s Republic of China
| | - Xingfan Zhang
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew J. Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Physics, Balurghat College, Balurghat 733101, West Bengal, India
| | - Andrew M. Beale
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK
| | - Hans M. Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Thomas W. Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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3
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Hildebrandt P. Vibrational Spectroscopy of Phytochromes. Biomolecules 2023; 13:1007. [PMID: 37371587 DOI: 10.3390/biom13061007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Phytochromes are biological photoswitches that translate light into physiological functions. Spectroscopic techniques are essential tools for molecular research into these photoreceptors. This review is directed at summarizing how resonance Raman and IR spectroscopy contributed to an understanding of the structure, dynamics, and reaction mechanism of phytochromes, outlining the substantial experimental and theoretical challenges and describing the strategies to master them. It is shown that the potential of the various vibrational spectroscopic techniques can be most efficiently exploited using integral approaches via a combination of theoretical methods as well as other experimental techniques.
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Affiliation(s)
- Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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4
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Cui L, Xin Y, Yang K, Li H, Tan F, Zhang Y, Li X, Zhu Z, Yang J, Kao SJ, Ren B, Zhu YG, Musat F, Musat N. Live tracking metabolic networks and physiological responses within microbial assemblages at single-cell level. PNAS NEXUS 2023; 2:pgad006. [PMID: 36896131 PMCID: PMC9991459 DOI: 10.1093/pnasnexus/pgad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023]
Abstract
Microbial interactions impact the functioning of both natural and engineered systems, yet our ability to directly monitor these highly dynamic and spatially resolved interactions in living cells is very limited. Here, we developed a synergistic approach coupling single-cell Raman microspectroscopy with 15N2 and 13CO2 stable isotope probing in a microfluidic culture system (RMCS-SIP) for live tracking of the occurrence, rate, and physiological shift of metabolic interactions in active microbial assemblages. Quantitative and robust Raman biomarkers specific for N2 and CO2 fixation in both model and bloom-forming diazotrophic cyanobacteria were established and cross-validated. By designing a prototype microfluidic chip allowing simultaneous microbial cultivation and single-cell Raman acquisition, we achieved temporal tracking of both intercellular (between heterocyst and vegetative cells of cyanobacteria) and interspecies N and C metabolite exchange (from diazotroph to heterotroph). Moreover, single-cell N and C fixation and bidirectional transfer rate in living cells were quantified via SIP-induced characteristic Raman shifts. Remarkably, RMCS captured physiological responses of metabolically active cells to nutrient stimuli through comprehensive metabolic profiling, providing multimodal information on the evolution of microbial interactions and functions under fluctuating conditions. This noninvasive RMCS-SIP is an advantageous approach for live-cell imaging and represents an important advancement in the single-cell microbiology field. This platform can be extended for real-time tracking of a wide range of microbial interactions with single-cell resolution and advances the understanding and manipulation of microbial interactions for societal benefit.
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Affiliation(s)
- Li Cui
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuhan Xin
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hongzhe Li
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Fengjiao Tan
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yulong Zhang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xingrui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jun Yang
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shuh-Ji Kao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Florin Musat
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca 400084, Romania
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
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5
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Yang Y, Stensitzki T, Lang C, Hughes J, Mroginski MA, Heyne K. Ultrafast protein response in the Pfr state of Cph1 phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:919-930. [PMID: 36653574 DOI: 10.1007/s43630-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of 13C/15N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.
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Affiliation(s)
- Yang Yang
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität Giessen, Senckenbergstr. 3, 35390, Giessen, Germany
| | - Maria Andrea Mroginski
- Institut Für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Karsten Heyne
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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6
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Redshifting and Blueshifting of β82 Chromophores in the Phycocyanin Hexamer of Porphyridium purpureum Phycobilisomes Due to Linker Proteins. Life (Basel) 2022; 12:life12111833. [DOI: 10.3390/life12111833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Phycobilisomes in cyanobacteria and red algae are large protein complexes that absorb light and transfer energy for use in photosynthesis. The light energy absorbed by chromophores binding to phycobiliproteins in the peripheral rods can be funneled to the core through chromophores at very high efficiency. The molecular mechanism of excitation energy transfer within a phycobilisome is an example of a higher and unique function in a living organism. However, the mechanism underlying the high efficiency remains unclear. Thus, this study was carried out as a step to resolve this mechanism theoretically. The three-dimensional structure of phycobilisomes containing the linker proteins of the red alga Porphyridium purpureum was determined by cryoelectron microscopy at 2.82 Å resolution in 2020. Using these data, the absorption wavelength of each β82 chromophore in the phycocyanin hexamer located next to the core was calculated using quantum chemical treatment, considering the electric effect from its surrounding phycocyanin proteins and two linker proteins. In addition to unaffected chromophores, chromophores that were redshifted and blueshifted under the electrical influence of the two linker proteins were found. Namely, the chromophore serving as the energy sink in the rod was determined.
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7
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Ashtari-Jafari S, Jamshidi Z, Visscher L. Efficient simulation of resonance Raman spectra with tight-binding approximations to Density Functional Theory. J Chem Phys 2022; 157:084104. [DOI: 10.1063/5.0107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Resonance Raman spectroscopy has long been established as one of the most sensitive techniques for detection, structure characterization and probing the excited-state dynamics of biochemical systems. However, the analysis of resonance Raman spectra is much facilitated when measurements are accompanied by Density Functional Theory (DFT) calculations which are expensive for large biomolecules. In this work, resonance Raman spectra are therefore computed with the Density Functional Tight-Binding (DFTB) method in the time-dependent excited-state gradient approximation. To test the accuracy of the tight-binding approximations, this method is first applied to typical resonance Raman benchmark molecules like β-carotene and compared to results obtained with pure and range-separated exchange-correlation (xc) functionals. We then demonstrate the efficiency of the approach by considering a computationally challenging heme variation. Overall, we find that the vibrational frequencies and excited-state properties (energies and gradients) which are needed to simulate the spectra are reasonably accurate and suitable for interpretation of experiments. We can therefore recommend DFTB as a fast computational method to interpret resonance Raman spectra.
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Affiliation(s)
- Sahar Ashtari-Jafari
- Chemistry & Chemical Engineering Research Center of Iran (CCERCI), Iran, Islamic Republic of
| | - Zahra Jamshidi
- Chemistry, Sharif University of Technology, Iran, Islamic Republic of
| | - Lucas Visscher
- Division of Theoretical Chemistry, Vrije Universiteit Amsterdam, Netherlands
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8
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López MF, Dahl M, Escobar FV, Bonomi HR, Kraskov A, Michael N, Mroginski MA, Scheerer P, Hildebrandt P. Photoinduced reaction mechanisms in prototypical and bathy phytochromes. Phys Chem Chem Phys 2022; 24:11967-11978. [PMID: 35527718 DOI: 10.1039/d2cp00020b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phytochromes, found in plants, fungi, and bacteria, exploit light as a source of information to control physiological processes via photoswitching between two states of different physiological activity, i.e. a red-absorbing Pr and a far-red-absorbing Pfr state. Depending on the relative stability in the dark, bacterial phytochromes are divided into prototypical and bathy phytochromes, where the stable state is Pr and Pfr, respectively. In this work we studied representatives of these groups (prototypical Agp1 and bathy Agp2 from Agrobacterium fabrum) together with the bathy-like phytochrome XccBphP from Xanthomonas campestris by resonance Raman and IR difference spectroscopy. In all three phytochromes, the photoinduced conversions display the same mechanistic pattern as reflected by the chromophore structures in the various intermediate states. We also observed in each case the secondary structure transition of the tongue, which is presumably crucial for the function of phytochrome. The three phytochromes differ in details of the chromophore conformation in the various intermediates and the energetic barrier of their respective decay reactions. The specific protein environment in the chromophore pocket, which is most likely the origin for these small differences, also controls the proton transfer processes concomitant to the photoconversions. These proton translocations, which are tightly coupled to the structural transition of the tongue, presumably proceed via the same mechanism along the Pr → Pfr conversion whereas the reverse Pfr → Pr photoconversion includes different proton transfer pathways. Finally, classification of phytochromes in prototypical and bathy (or bathy-like) phytochromes is discussed in terms of molecular structure and mechanistic properties.
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Affiliation(s)
- María Fernández López
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Margarethe Dahl
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Francisco Velázquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Hernán Ruy Bonomi
- Leloir Institute Foundation, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Anastasia Kraskov
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
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Okuda Y, Miyoshi R, Kamo T, Fujisawa T, Nagae T, Mishima M, Eki T, Hirose Y, Unno M. Raman Spectroscopy of an Atypical C15-E,syn Bilin Chromophore in Cyanobacteriochrome RcaE. J Phys Chem B 2022; 126:813-821. [DOI: 10.1021/acs.jpcb.1c09652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuji Okuda
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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11
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Kraskov A, von Sass J, Nguyen AD, Hoang TO, Buhrke D, Katz S, Michael N, Kozuch J, Zebger I, Siebert F, Scheerer P, Mroginski MA, Budisa N, Hildebrandt P. Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2. Biochemistry 2021; 60:2967-2977. [PMID: 34570488 DOI: 10.1021/acs.biochem.1c00426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochromes switch between a physiologically inactive and active state via a light-induced reaction cascade, which is initiated by isomerization of the tetrapyrrole chromophore and leads to the functionally relevant secondary structure transition of a protein segment (tongue). Although details of the underlying cause-effect relationships are not known, electrostatic fields are likely to play a crucial role in coupling chromophores and protein structural changes. Here, we studied local electric field changes during the photoconversion of the dark state Pfr to the photoactivated state Pr of the bathy phytochrome Agp2. Substituting Tyr165 and Phe192 in the chromophore pocket by para-cyanophenylalanine (pCNF), we monitored the respective nitrile stretching modes in the various states of photoconversion (vibrational Stark effect). Resonance Raman and IR spectroscopic analyses revealed that both pCNF-substituted variants undergo the same photoinduced structural changes as wild-type Agp2. Based on a structural model for the Pfr state of F192pCNF, a molecular mechanical-quantum mechanical approach was employed to calculate the electric field at the nitrile group and the respective stretching frequency, in excellent agreement with the experiment. These calculations serve as a reference for determining the electric field changes in the photoinduced states of F192pCNF. Unlike F192pCNF, the nitrile group in Y165pCNF is strongly hydrogen bonded such that the theoretical approach is not applicable. However, in both variants, the largest changes of the nitrile stretching modes occur in the last step of the photoconversion, supporting the view that the proton-coupled restructuring of the tongue is accompanied by a change of the electric field.
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Affiliation(s)
- Anastasia Kraskov
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes von Sass
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anh Duc Nguyen
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Tu Oanh Hoang
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Sagie Katz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Freie Universität Berlin, Fachbereich für Physik, Arnimallee 14, D-14195 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Friedrich Siebert
- Albert-Ludwigs-Universität Freiburg, Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Hermann-Herderstr. 9, D-79104 Freiburg, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, R3T 2N2 Winnipeg, Manitoba, Canada
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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12
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Esch BVD, Peters LDM, Sauerland L, Ochsenfeld C. Quantitative Comparison of Experimental and Computed IR-Spectra Extracted from Ab Initio Molecular Dynamics. J Chem Theory Comput 2021; 17:985-995. [PMID: 33512155 DOI: 10.1021/acs.jctc.0c01279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimentally measured infrared spectra are often compared to their computed equivalents. However, the accordance is typically characterized by visual inspection, which is prone to subjective judgment. The primary challenge for a similarity-based analysis is that the artifacts introduced by each approach are very different and, therefore, may require preprocessing steps to determine and correct impeding irregularities. To allow for automated objective assessment, we propose a practical and comprehensive workflow involving scaling factors, a novel baseline correction scheme, and peak smoothing. The resulting spectra can then easily be compared quantitatively using similarity measures, for which we found the Pearson correlation coefficient to be the most suitable. The proposed procedure is then applied to compare the agreement of the experimental infrared spectra from the NIST Chemistry Web book with the calculated spectra using standard harmonic frequency analysis and spectra extracted from ab initio molecular dynamics simulations at different levels of theory. We conclude that the direct, quantitative comparison of calculated and measured IR spectra might become a novel, sophisticated approach to benchmark quantum-chemical methods. In the present benchmark, simulated spectra based on ab initio molecular dynamics show in general better agreement with the experiment than static calculations.
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Affiliation(s)
- Beatriz von der Esch
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Laurens D M Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Lena Sauerland
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
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13
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Hontani Y, Baloban M, Escobar FV, Jansen SA, Shcherbakova DM, Weißenborn J, Kloz M, Mroginski MA, Verkhusha VV, Kennis JTM. Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Commun Chem 2021; 4:3. [PMID: 34746444 PMCID: PMC8570541 DOI: 10.1038/s42004-020-00437-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/09/2020] [Indexed: 01/27/2023] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C-S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
- Present Address: School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Mikhail Baloban
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623 Germany
| | - Swetta A. Jansen
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
| | - Daria M. Shcherbakova
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Jörn Weißenborn
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
- ELI-Beamlines, Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623 Germany
| | - Vladislav V. Verkhusha
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290 Finland
| | - John T. M. Kennis
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
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14
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Kikuchi H. Functional roles of the hexamer structure of C-phycocyanin revealed by calculation of absorption wavelength. FEBS Open Bio 2021; 11:164-172. [PMID: 33190413 PMCID: PMC7780113 DOI: 10.1002/2211-5463.13038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/27/2020] [Accepted: 11/11/2020] [Indexed: 11/11/2022] Open
Abstract
Cyanophyta-phycocyanin (C-PC) is the main constituent of the rod of phycobilisome (PBS), which is a highly ordered and large peripheral light-harvesting protein complex present on the cytoplasmic side of the thylakoid membrane in cyanobacteria and red algae. The C-PC monomer comprises two chains, α- and β-subunits, and aggregates to form ring-shaped trimers (αβ)3 with rotational symmetry. The ring-shaped trimer (αβ)3 is a structural block unit (SBU) that forms the rod of PBS. Two (αβ)3 SBUs are arranged in a face-to-face manner to form an (αβ)6 -hexamer. In this study, the electronic states of three phycocyanobilins, α84, β84, and β155 in C-phycocyanin, constituting the rod of the PBS, were calculated for both the trimer and hexamer models by considering the effect of the electrostatic field of protein moieties and water molecules. For the hexamer, the absorption wavelengths of α84, β84, and β155 were similar to those obtained experimentally; however, for the trimer, only the absorption wavelength of β155 shifted toward a shorter-wavelength. The nature of the hexamer structure as a hierarchical structure is revealed by considering the calculated absorption wavelength and energy transfer.
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Affiliation(s)
- Hiroto Kikuchi
- Department of PhysicsNippon Medical SchoolMusashinoJapan
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15
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Raman Spectroscopy as Noninvasive Method of Diagnosis of Pediatric Onset Inflammatory Bowel Disease. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We propose here a spectroscopic method to diagnose and differentiate inflammatory bowel diseases (IBD), such as ulcerative colitis (UC) and Crohn’s disease (CD) with pediatric onset, in a complete noninvasive way without performing any duodenal biopsy. In particular, the Raman technique was applied to proteic extract from fecal samples in order to achieve information about molecular vibrations that can potentially furnish spectral signatures of cellular modifications occurring as a consequence of specific pathologic conditions. The attention was focused on the investigation of the amide I region, quantitatively accounting the spectral changes in the secondary structures by applying deconvolution and curve-fitting. Inflammation is found to give rise to a significant increasing of the nonreducible (trivalent)/reducible (divalent) cross-linking ratio R of the protein network. This parameter revealed an excellent marker in order to distinguish IBD subjects from non-IBD ones, and, among IBD patients, to differentiate between UC and CD. The proposed methodology was validated by statistical analysis using the receiver operating characteristic (ROC) curve.
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16
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17
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Tong X, Prasanna G, Zhang N, Jing P. Spectroscopic and molecular docking studies on the interaction of phycocyanobilin with peptide moieties of C-phycocyanin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 236:118316. [PMID: 32344374 DOI: 10.1016/j.saa.2020.118316] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/20/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The binding of C-phycocyanin (CPC), a light harvesting pigment with phycocyanobilin (PCB), a chromophore is instrumental for the coloration and bioactivity. In this study, structure-mediated color changes of CPC from Spirulina platensis during various enzymatic hydrolysis was investigated based on UV-visible, circular dichroism, infra-red, fluorescence, mass spectrometry, and molecular docking. CPC was hydrolyzed using 7.09 U/mg protein of each enzyme at their optimal hydrolytic conditions for 3 h as follows: papain (pH 6.6, 60 °C), dispase (pH 6.6, 50 °C), and trypsin (pH 7.8, 37 °C). The degree of hydrolysis was in the order of papain (28.4%) > dispase (20.8%) > trypsin (7.3%). The sequence of color degradation rate and total color difference (ΔE) are dispase (82.9% and 40.37), papain (72.4% and 24.70), and trypsin (58.7% and 25.43). The hydrolyzed peptides were of diverse sequence length ranging from 8 to 9 residues (papain), 7-12 residues (dispase), and 9-63 residues (trypsin). Molecular docking studies showed that key amino acid residues in the peptides interacting with chromophore. Amino acid residues such as Arg86, Asp87, Tyr97, Asp152, Phe164, Ala167, and Val171 are crucial in hydrogen bonding interaction. These results indicate that the color properties of CPC might associate with chromopeptide sequences and their non-covalent interactions.
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Affiliation(s)
- Xueyu Tong
- Shanghai Food Safety and Engineering Technology Research Center, Bor S. Luh Food Safety Research Center, Key Lab of Urban Agriculture (South), School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Govindarajan Prasanna
- Shanghai Food Safety and Engineering Technology Research Center, Bor S. Luh Food Safety Research Center, Key Lab of Urban Agriculture (South), School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nan Zhang
- Shanghai Food Safety and Engineering Technology Research Center, Bor S. Luh Food Safety Research Center, Key Lab of Urban Agriculture (South), School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pu Jing
- Shanghai Food Safety and Engineering Technology Research Center, Bor S. Luh Food Safety Research Center, Key Lab of Urban Agriculture (South), School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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18
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Wahadoszamen M, Krüger TPJ, Ara AM, van Grondelle R, Gwizdala M. Charge transfer states in phycobilisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148187. [PMID: 32173383 DOI: 10.1016/j.bbabio.2020.148187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/17/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Phycobilisomes (PBs) absorb light and supply downstream photosynthetic processes with excitation energy in many cyanobacteria and algae. In response to a sudden increase in light intensity, excess excitation energy is photoprotectively dissipated in PBs by means of the orange carotenoid protein (OCP)-related mechanism or via a light-activated intrinsic decay channel. Recently, we have identified that both mechanisms are associated with far-red emission states. Here, we investigate the far-red states involved with the light-induced intrinsic mechanism by exploring the energy landscape and electro-optical properties of the pigments in PBs. While Stark spectroscopy showed that the far-red states in PBs exhibit a strong charge-transfer (CT) character at cryogenic temperatures, single molecule spectroscopy revealed that CT states should also be present at room temperature. Owing to the strong environmental sensitivity of CT states, the knowledge gained from this study may contribute to the design of a new generation of fluorescence markers.
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Affiliation(s)
- Md Wahadoszamen
- Department of Physics, University of Dhaka, Dhaka 1000, Bangladesh
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa
| | - Anjue Mane Ara
- Department of Physics, Jagannath University, Dhaka 1100, Bangladesh
| | - Rienk van Grondelle
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Pretoria 0023, South Africa; Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, the Netherlands.
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19
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Buhrke D, Battocchio G, Wilkening S, Blain-Hartung M, Baumann T, Schmitt FJ, Friedrich T, Mroginski MA, Hildebrandt P. Red, Orange, Green: Light- and Temperature-Dependent Color Tuning in a Cyanobacteriochrome. Biochemistry 2019; 59:509-519. [PMID: 31840994 DOI: 10.1021/acs.biochem.9b00931] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptor proteins that photoconvert between two parent states and thereby regulate various biological processes. An intriguing property is their variable ultraviolet-visible (UV-vis) absorption that covers the entire spectral range from the far-red to the near-UV region and thus makes CBCRs promising candidates for optogenetic applications. Here, we have studied Slr1393, a CBCR that photoswitches between red- and green-absorbing states (Pr and Pg, respectively). Using UV-vis absorption, fluorescence, and resonance Raman (RR) spectroscopy, a further orange-absorbing state O600 that is in thermal equilibrium with Pr was identified. The different absorption properties of the three states were attributed to the different lengths of the conjugated π-electron system of the phycocyanobilin chromophore. In agreement with available crystal structures and supported by quantum mechanics/molecular mechanics (QM/MM) calculations, the most extended conjugation holds for Pr whereas it is substantially reduced in Pg. Here, the two outer pyrrole rings D and A are twisted out of the plane defined by inner pyrrole rings B and C. For the O600 state, the comparison of the experimental RR spectra with QM/MM-calculated spectra indicates a partially distorted ZZZssa geometry in which ring A is twisted while ring D and the adjacent methine bridge display essentially the same geometry as Pr. The quantitative analysis of temperature-dependent spectra yields an enthalpy barrier of ∼30 kJ/mol for the transition from Pr to O600. This reaction is associated with the movement of a conserved tryptophan residue from the chromophore binding pocket to a solvent-exposed position.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Giovanni Battocchio
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Svea Wilkening
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Matthew Blain-Hartung
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Tobias Baumann
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Thomas Friedrich
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Maria-Andrea Mroginski
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
| | - Peter Hildebrandt
- Technische Universität Berlin , Faculty II-Mathematics and Natural Sciences, Institute of Chemistry , Sekr. PC14, Straße des 17. Juni 135 , D-10623 Berlin , Germany
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20
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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21
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Mohamed-Raseek N, Duan HD, Hildebrandt P, Mroginski MA, Miller AF. Spectroscopic, thermodynamic and computational evidence of the locations of the FADs in the nitrogen fixation-associated electron transfer flavoprotein. Chem Sci 2019; 10:7762-7772. [PMID: 31588324 PMCID: PMC6764259 DOI: 10.1039/c9sc00942f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/24/2019] [Indexed: 01/15/2023] Open
Abstract
Flavin-based electron bifurcation allows enzymes to redistribute energy among electrons by coupling endergonic and exergonic electron transfer reactions. Diverse bifurcating enzymes employ a two-flavin electron transfer flavoprotein (ETF) that accepts hydride from NADH at a flavin (the so-called bifurcating FAD, Bf-FAD). The Bf-FAD passes one electron exergonically to a second flavin thereby assuming a reactive semiquinone state able to reduce ferredoxin or flavodoxin semiquinone. The flavin that accepts one electron and passes it on via exergonic electron transfer is known as the electron transfer FAD (ET-FAD) and is believed to correspond to the single FAD present in canonical ETFs, in domain II. The Bf-FAD is believed to be the one that is unique to bifurcating ETFs, bound between domains I and III. This very reasonable model has yet to be challenged experimentally. Herein we used site-directed mutagenesis to disrupt FAD binding to the presumed Bf site between domains I and III, in the Bf-ETF from Rhodopseudomonas palustris (RpaETF). The resulting protein contained only 0.80 ± 0.05 FAD, plus 1.21 ± 0.04 bound AMP as in canonical ETFs. The flavin was not subject to reduction by NADH, confirming absence of Bf-FAD. The retained FAD displayed visible circular dichroism (CD) similar to that of the ET-FAD of RpaETF. Likewise, the mutant underwent two sequential one-electron reductions forming and then consuming anionic semiquinone, reproducing the reactivity of the ET-FAD. These data confirm that the retained FAD in domain II corresponds the ET-FAD. Quantum chemical calculations of the absorbance and CD spectra of each of WT RpaETF's two flavins reproduced the observed differences between their CD and absorbance signatures. The calculations for the flavin bound in domain II agreed better with the spectra of the ET-flavin, and those calculated based on the flavin between domains I and III agreed better with spectra of the Bf-flavin. Thus calculations independently confirm the locations of each flavin. We conclude that the site in domain II harbours the ET-FAD whereas the mutated site between domains I and III is the Bf-FAD site, confirming the accepted model by two different tests.
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Affiliation(s)
- Nishya Mohamed-Raseek
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
| | - H Diessel Duan
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
| | - Peter Hildebrandt
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
| | - Maria Andrea Mroginski
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
| | - Anne-Frances Miller
- Dept. Chemistry , University of Kentucky , 505 Rose Street , Lexington , KY 40506-0055 , USA .
- Max Volmer Laboratorum für Biophysikalische Chemie , Technische Universität - Berlin , Sekr. PC 14, 135 Straße des 17. Juni , 10623 Berlin , Germany
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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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Osoegawa S, Miyoshi R, Watanabe K, Hirose Y, Fujisawa T, Ikeuchi M, Unno M. Identification of the Deprotonated Pyrrole Nitrogen of the Bilin-Based Photoreceptor by Raman Spectroscopy with an Advanced Computational Analysis. J Phys Chem B 2019; 123:3242-3247. [PMID: 30913882 DOI: 10.1021/acs.jpcb.9b00965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochrome and cyanobacteriochrome utilize a linear methine-bridged tetrapyrrole (bilin) to control numerous biological processes. They show a reversible photoconversion between two spectrally distinct states. This photocycle is initiated by a C═C double-bond photoisomerization of the bilin followed by its thermal relaxations with transient and/or stationary changes in the protonation state of the pyrrole moiety. However, it has never been identified which of the four pyrrole nitrogen atoms is deprotonated. Here, we report a resonance Raman spectroscopic study on cyanobacteriochrome RcaE, which has been proposed to contain a deprotonated bilin for its green-absorbing 15 Z state. The observed Raman spectra were well reproduced by a simulated structure whose bilin B ring is deprotonated, with the aid of molecular dynamics and quantum mechanics/molecular mechanics calculations. The results revealed that the deprotonation of B and C rings has the distinct effect on the overall bilin structure, which will be relevant to the color tuning and photoconversion mechanisms of the phytochrome superfamily. Furthermore, this study documents the ability of vibrational spectroscopy combined with the advanced spectral analysis to visualize a proton of a cofactor molecule embedded in a protein moiety.
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Affiliation(s)
- Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Kouhei Watanabe
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences , Toyohashi University of Technology , Toyohashi , Aichi 441-8580 , Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology) , The University of Tokyo , Meguro, Tokyo 153-8902 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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24
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Stensitzki T, Yang Y, Wölke AL, Knapp EW, Hughes J, Mroginski MA, Heyne K. Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome. Photochem Photobiol 2018; 93:703-712. [PMID: 28500700 DOI: 10.1111/php.12743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/03/2017] [Indexed: 01/23/2023]
Abstract
Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground-state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump-probe and femtosecond polarization-resolved Vis pump-infrared (IR) probe studies of the Pfr photoreaction in native and 13 C/15 N-labeled Cph1 phytochrome with unlabeled PCB chromophore, demonstrating different S0 substates, Pfr-I and Pfr-II, with distinct IR absorptions, orientations and dynamics of the carbonyl vibration of ring D. We derived time constants of 0.24 ps, 0.7 ps and 6 ps, describing the complete initial photoreaction. We identified an isomerizing pathway with 0.7 ps for Pfr-I, and silent dynamics with 6 ps for Pfr-II. We discuss different origins of the Pfr substates, and favor different facial orientations of ring D. The model provides a quantum yield for Pfr-I of 38%, in line with ~35% ring D rotation in the electronic excited state. We tentatively assign the silent form Pfr-II to a dark-adapted state that can convert to Pfr-I upon light absorption.
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Affiliation(s)
- Till Stensitzki
- Department of Physics, Free University Berlin, Berlin, Germany
| | - Yang Yang
- Department of Physics, Free University Berlin, Berlin, Germany
| | - Anna Lena Wölke
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig Universität, Gießen, Germany
| | | | - Karsten Heyne
- Department of Physics, Free University Berlin, Berlin, Germany
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25
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Corbella M, Toa ZSD, Scholes GD, Luque FJ, Curutchet C. Determination of the protonation preferences of bilin pigments in cryptophyte antenna complexes. Phys Chem Chem Phys 2018; 20:21404-21416. [PMID: 30105318 DOI: 10.1039/c8cp02541j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The light-harvesting mechanisms of cryptophyte antenna complexes have attracted considerable attention due to their ability to exhibit maximal photosynthetic activity under very low-light conditions and to display several colors, as well as the observation of vibronic coherent features in their two-dimensional electronic spectra. However, detailed investigations on the interplay between the protein environment and their light-harvesting properties are hampered by the uncertainty related to the protonation state of the underlying bilin pigments. Here we study the protonation preferences of four types of bilin pigments including 15,16-dihydrobiliverdin (DBV), phycoerythrobilin (PEB), phycocyanobilin (PCB) and mesobiliverdin (MBV), which are found in phycoerythrin PE545 and phycocyanin PC577, PC612, PC630 and PC645 complexes. We apply quantum chemical calculations coupled to continuum solvation calculations to predict the intrinsic acidity of bilins in aqueous solution, and then combine molecular dynamics simulations with empirical pKa estimates to investigate the impact of the local protein environment on the acidity of the pigments. We also report measurements of the absorption spectra of the five complexes in a wide range of pH in order to validate our simulations and investigate possible changes in the light harvesting properties of the complexes in the range of physiological pH found in the lumen (pH ∼ 5-7). The results suggest a pKa > 7 for DBV and MBV pigments in the α polypeptide chains of PE545 and PC630/PC645 complexes, which are not coordinated to a negatively charged amino acid. For the other PEB, DBV and PCB pigments, which interact with a Glu or Asp side chain, higher pKa values (pKa > 8) are estimated. Overall, the results support a preferential population of the fully protonated state for bilins in cryptophyte complexes under physiological conditions regardless of the specific type of pigment and local protein environment.
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Affiliation(s)
- Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTCUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.
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26
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Gutiérrez-Sanz O, Forbrig E, Batista AP, Pereira MM, Salewski J, Mroginski MA, Götz R, De Lacey AL, Kozuch J, Zebger I. Catalytic Activity and Proton Translocation of Reconstituted Respiratory Complex I Monitored by Surface-Enhanced Infrared Absorption Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5703-5711. [PMID: 29553272 DOI: 10.1021/acs.langmuir.7b04057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Respiratory complex I (CpI) is a key player in the way organisms obtain energy, being an energy transducer, which couples nicotinamide adenine dinucleotide (NADH)/quinone oxidoreduction with proton translocation by a mechanism that remains elusive so far. In this work, we monitored the function of CpI in a biomimetic, supported lipid membrane system assembled on a 4-aminothiophenol (4-ATP) self-assembled monolayer by surface-enhanced infrared absorption spectroscopy. 4-ATP serves not only as a linker molecule to a nanostructured gold surface but also as pH sensor, as indicated by concomitant density functional theory calculations. In this way, we were able to monitor NADH/quinone oxidoreduction-induced transmembrane proton translocation via the protonation state of 4-ATP, depending on the net orientation of CpI molecules induced by two complementary approaches. An associated change of the amide I/amide II band intensity ratio indicates conformational modifications upon catalysis which may involve movements of transmembrane helices or other secondary structural elements, as suggested in the literature [ Di Luca , Proc. Natl. Acad. Sci. U.S.A. , 2017 , 114 , E6314 - E6321 ].
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Affiliation(s)
- Oscar Gutiérrez-Sanz
- Instituto de Catalisis y Petroleoquimica , CSIC c/ Marie Curie 2 , 28049 Madrid , Spain
| | - Enrico Forbrig
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica-António Xavier , Universidade Nova de Lisboa , Av. da Republica EAN , 2780-157 Oeiras , Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier , Universidade Nova de Lisboa , Av. da Republica EAN , 2780-157 Oeiras , Portugal
| | - Johannes Salewski
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
| | - Maria A Mroginski
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
| | - Robert Götz
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
| | - Antonio L De Lacey
- Instituto de Catalisis y Petroleoquimica , CSIC c/ Marie Curie 2 , 28049 Madrid , Spain
| | - Jacek Kozuch
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
| | - Ingo Zebger
- Institut für Chemie, PC 14 , Technische Universität Berlin , Strasse des 17. Juni 135 , D-10623 Berlin , Germany
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27
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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28
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Forbrig E, Staffa JK, Salewski J, Mroginski MA, Hildebrandt P, Kozuch J. Monitoring the Orientational Changes of Alamethicin during Incorporation into Bilayer Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2373-2385. [PMID: 29353482 DOI: 10.1021/acs.langmuir.7b04265] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antimicrobial peptides (AMPs) are the first line of defense after contact of an infectious invader, for example, bacterium or virus, with a host and an integral part of the innate immune system of humans. Their broad spectrum of biological functions ranges from cell membrane disruption over facilitation of chemotaxis to interaction with membrane-bound or intracellular receptors, thus providing novel strategies to overcome bacterial resistances. Especially, the clarification of the mechanisms and dynamics of AMP incorporation into bacterial membranes is of high interest, and different mechanistic models are still under discussion. In this work, we studied the incorporation of the peptaibol alamethicin (ALM) into tethered bilayer lipid membranes on electrodes in combination with surface-enhanced infrared absorption (SEIRA) spectroscopy. This approach allows monitoring the spontaneous and potential-induced ion channel formation of ALM in situ. The complex incorporation kinetics revealed a multistep mechanism that points to peptide-peptide interactions prior to penetrating the membrane and adopting the transmembrane configuration. On the basis of the anisotropy of the backbone amide I and II infrared absorptions determined by density functional theory calculations, we employed a mathematical model to evaluate ALM reorientations monitored by SEIRA spectroscopy. Accordingly, ALM was found to adopt inclination angles of ca. 69°-78° and 21° in its interfacially adsorbed and transmembrane incorporated states, respectively. These orientations can be stabilized efficiently by the dipolar interaction with lipid head groups or by the application of a potential gradient. The presented potential-controlled mechanistic study suggests an N-terminal integration of ALM into membranes as monomers or parallel oligomers to form ion channels composed of parallel-oriented helices, whereas antiparallel oligomers are barred from intrusion.
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Affiliation(s)
- Enrico Forbrig
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jana K Staffa
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Salewski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Technische Universität Berlin, Institut für Chemie , Sekr. PC14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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29
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Brehm M, Thomas M. Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations. J Phys Chem Lett 2017; 8:3409-3414. [PMID: 28685571 DOI: 10.1021/acs.jpclett.7b01616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present our novel methodology for computing Raman optical activity (ROA) spectra of liquid systems from ab initio molecular dynamics (AIMD) simulations. The method is built upon the recent developments to obtain magnetic dipole moments from AIMD and to integrate molecular properties by using radical Voronoi tessellation. These techniques are used to calculate optical activity tensors for large and complex periodic bulk phase systems. Only AIMD simulations are required as input, and no time-consuming perturbation theory is involved. The approach relies only on the total electron density in each time step and can readily be combined with a wide range of electronic structure methods. To the best of our knowledge, these are the first computed ROA spectra for a periodic bulk phase system. As an example, the experimental ROA spectrum of liquid (R)-propylene oxide is reproduced very well.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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30
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Takiden A, Velazquez-Escobar F, Dragelj J, Woelke AL, Knapp EW, Piwowarski P, Bart F, Hildebrandt P, Mroginski MA. Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1. Photochem Photobiol 2017; 93:713-723. [DOI: 10.1111/php.12737] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Aref Takiden
- Institut für Chemie; Technische Universität Berlin; Berlin Germany
| | | | - Jovan Dragelj
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Anna Lena Woelke
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Ernst-Walter Knapp
- Institut für Chemie und Biochemie; Freie Universität Berlin; Berlin Germany
| | - Patrick Piwowarski
- Institute of Medical Physics and Biophysics; Charité-Medical University Berlin; Berlin Germany
| | - Franz Bart
- Institute of Medical Physics and Biophysics; Charité-Medical University Berlin; Berlin Germany
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31
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Velazquez Escobar F, Lang C, Takiden A, Schneider C, Balke J, Hughes J, Alexiev U, Hildebrandt P, Mroginski MA. Protonation-Dependent Structural Heterogeneity in the Chromophore Binding Site of Cyanobacterial Phytochrome Cph1. J Phys Chem B 2016; 121:47-57. [DOI: 10.1021/acs.jpcb.6b09600] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francisco Velazquez Escobar
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Christina Lang
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Aref Takiden
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Constantin Schneider
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jens Balke
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jon Hughes
- Plant
Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Ulrike Alexiev
- Institut
für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Peter Hildebrandt
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Institut
für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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32
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Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:103-108. [PMID: 27810193 DOI: 10.1016/j.bbabio.2016.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/18/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a3 have been proposed to act as a proton loading site (PLS) in the proton pumping pathway, yet this proposal could not be verified by experimental data so far. We have set up an experiment where the redox states of the two hemes in CcO can be controlled via external electrical potential. Surface enhanced resonance Raman (SERR) spectroscopy was applied to simultaneously monitor the redox state of the hemes and the protonation state of the heme propionates. Simulated spectra based on QM/MM calculations were used to assign the resonant enhanced CH2 twisting modes of the propionates to the protonation state of the individual heme a and heme a3 propionates respectively. The comparison between calculated and measured H2OD2O difference spectra allowed a sound band assignment. In the fully reduced enzyme at least three of the four heme propionates were found to be protonated whereas in the presence of a reduced heme a and an oxidized heme a3 only protonation of one heme a3 propionates was observed. Our data supports the postulated scenario where the heme a3 propionates are involved in the proton pathway.
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33
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Otero LH, Klinke S, Rinaldi J, Velázquez-Escobar F, Mroginski MA, Fernández López M, Malamud F, Vojnov AA, Hildebrandt P, Goldbaum FA, Bonomi HR. Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism. J Mol Biol 2016; 428:3702-20. [PMID: 27107635 DOI: 10.1016/j.jmb.2016.04.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 11/25/2022]
Abstract
Phytochromes constitute a major superfamily of light-sensing proteins that are reversibly photoconverted between a red-absorbing (Pr) and a far-red-absorbing (Pfr) state. Bacteriophytochromes (BphPs) are found among photosynthetic and non-photosynthetic bacteria, including pathogens. To date, several BphPs have been biophysically characterized. However, it is still not fully understood how structural changes are propagated from the photosensory module to the output module during the signal transduction event. Most phytochromes share a common architecture consisting of an N-terminal photosensor that includes the PAS2-GAF-PHY domain triad and a C-terminal variable output module. Here we present the crystal structure of the full-length BphP from the plant pathogen Xanthomonas campestris pv. campestris (XccBphP) bearing its photosensor and its complete output module, a PAS9 domain. In the crystals, the protein was found to be in the Pr state, whereas diffraction data together with resonance Raman spectroscopic and theoretical results indicate a ZZZssa and a ZZEssa chromophore configuration corresponding to a mixture of Pr and Meta-R state, the precursor of Pfr. The XccBphP quaternary assembly reveals a head-to-head dimer in which the output module contributes to the helical dimer interface. The photosensor, which is shown to be a bathy-like BphP, is influenced in its dark reactions by the output module. Our structural analyses suggest that the photoconversion between the Pr and Pfr states in the full-length XccBphP may involve changes in the relative positioning of the output module. This work contributes to understand the light-induced structural changes propagated from the photosensor to the output modules in phytochrome signaling.
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Affiliation(s)
- Lisandro Horacio Otero
- Fundación Instituto Leloir-IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir-IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir-IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Francisco Velázquez-Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135 (10623), Berlin, Germany
| | - María Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135 (10623), Berlin, Germany
| | - María Fernández López
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135 (10623), Berlin, Germany
| | - Florencia Malamud
- UNSAM Campus Miguelete IIB-Instituto de Investigaciones Biotecnológicas, Av. 25 de Mayo y Francia (B1650KNA), Buenos Aires, Argentina
| | - Adrián Alberto Vojnov
- Instituto de Ciencia y Tecnología Dr. Cesar Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135 (10623), Berlin, Germany
| | - Fernando Alberto Goldbaum
- Fundación Instituto Leloir-IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Hernán Ruy Bonomi
- Fundación Instituto Leloir-IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.
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34
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Siebert E, Rippers Y, Frielingsdorf S, Fritsch J, Schmidt A, Kalms J, Katz S, Lenz O, Scheerer P, Paasche L, Pelmenschikov V, Kuhlmann U, Mroginski MA, Zebger I, Hildebrandt P. Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04119] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elisabeth Siebert
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Stefan Frielingsdorf
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Johannes Fritsch
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Andrea Schmidt
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Jacqueline Kalms
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Sagie Katz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Oliver Lenz
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Charité − Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group
Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - Lars Paasche
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Vladimir Pelmenschikov
- Technische
Universität Berlin, Institut für Chemie, Sekr. C7, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Uwe Kuhlmann
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische
Universität Berlin, Institut für Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
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35
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Hardman SJO, Hauck AFE, Clark IP, Heyes DJ, Scrutton NS. Comprehensive analysis of the green-to-blue photoconversion of full-length Cyanobacteriochrome Tlr0924. Biophys J 2015; 107:2195-203. [PMID: 25418104 PMCID: PMC4223177 DOI: 10.1016/j.bpj.2014.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/11/2014] [Accepted: 09/24/2014] [Indexed: 12/18/2022] Open
Abstract
Cyanobacteriochromes are members of the phytochrome superfamily of photoreceptors and are of central importance in biological light-activated signaling mechanisms. These photoreceptors are known to reversibly convert between two states in a photoinitiated process that involves a basic E/Z isomerization of the bilin chromophore and, in certain cases, the breakage of a thioether linkage to a conserved cysteine residue in the bulk protein structure. The exact details and timescales of the reactions involved in these photoconversions have not been conclusively shown. The cyanobacteriochrome Tlr0924 contains phycocyanobilin and phycoviolobilin chromophores, both of which photoconvert between two species: blue-absorbing and green-absorbing, and blue-absorbing and red-absorbing, respectively. Here, we followed the complete green-to-blue photoconversion process of the phycoviolobilin chromophore in the full-length form of Tlr0924 over timescales ranging from femtoseconds to seconds. Using a combination of time-resolved visible and mid-infrared transient absorption spectroscopy and cryotrapping techniques, we showed that after photoisomerization, which occurs with a lifetime of 3.6 ps, the phycoviolobilin twists or distorts slightly with a lifetime of 5.3 μs. The final step, the formation of the thioether linkage with the protein, occurs with a lifetime of 23.6 ms.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Anna F E Hauck
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Ian P Clark
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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36
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Zhang C, Naziga EB, Guidoni L. Asymmetric environmental effects on the structure and vibrations of cis-[Pt(NH3)2Cl2] in condensed phases. J Phys Chem B 2014; 118:11487-95. [PMID: 25144652 DOI: 10.1021/jp500865v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the structural and vibrational properties of anticancer drug cisplatin (cis-[Pt(NH3)2Cl2]) in gas phase, in solid phase, and in aqueous solution using density functional theory (DFT) calculations, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics, and effective normal modes analysis. In contrast with the gas-phase case, asymmetric hydrogen bonding environments are found in both solid phase and aqueous solution. It is shown that the discrepancy of the molecular geometry between previous gas phase calculations and the X-ray crystal structure can be resolved by considering intermolecular hydrogen bonds in the calculations of solid phase. In addition, our simulations in solid phase and aqueous solution reveal that asymmetric environmental effects lead to several spectral features observed in experiments, such as the blue-shift in the N-H stretching region and the frequency splitting of NH3 symmetric deformation modes. Furthermore, a similar decoupling and localization of several vibrational modes of cisplatin is found in solid phase and aqueous solution, in comparison to those of O-H stretching modes of water molecules in liquid water [ J. Phys. Chem. Lett. 2013 , 4 ( 19 ), 3245 - 3250 ].
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Affiliation(s)
- Chao Zhang
- Physics Department, Sapienza-Universita di Roma , P. le A. Moro 5, 00185, Rome, Italy
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37
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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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38
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Salewski J, Escobar FV, Kaminski S, von Stetten D, Keidel A, Rippers Y, Michael N, Scheerer P, Piwowarski P, Bartl F, Frankenberg-Dinkel N, Ringsdorf S, Gärtner W, Lamparter T, Mroginski MA, Hildebrandt P. Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes. J Biol Chem 2013; 288:16800-16814. [PMID: 23603902 DOI: 10.1074/jbc.m113.457531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.
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Affiliation(s)
- Johannes Salewski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Steve Kaminski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - David von Stetten
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany; Structural Biology Group, European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Anke Keidel
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Yvonne Rippers
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Protein X-ray Crystallography, D-10117 Berlin, Germany
| | - Patrick Piwowarski
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Franz Bartl
- Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Nicole Frankenberg-Dinkel
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Simone Ringsdorf
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Tilman Lamparter
- Institut für Allgemeine Botanik, Karlsruher Institut für Technologie, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
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39
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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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40
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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41
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Thomas M, Brehm M, Fligg R, Vöhringer P, Kirchner B. Computing vibrational spectra from ab initio molecular dynamics. Phys Chem Chem Phys 2013; 15:6608-22. [DOI: 10.1039/c3cp44302g] [Citation(s) in RCA: 319] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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42
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Elgabarty H, Schmieder P, Sebastiani D. Unraveling the existence of dynamic water channels in light-harvesting proteins: alpha-C-phycocyanobilin in vitro. Chem Sci 2013. [DOI: 10.1039/c2sc21145a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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43
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Rippers Y, Horch M, Hildebrandt P, Zebger I, Mroginski MA. Revealing the Absolute Configuration of the CO and CN−Ligands at the Active Site of a [NiFe] Hydrogenase. Chemphyschem 2012; 13:3852-6. [DOI: 10.1002/cphc.201200562] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Indexed: 11/12/2022]
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44
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Turner DB, Dinshaw R, Lee KK, Belsley MS, Wilk KE, Curmi PMG, Scholes GD. Quantitative investigations of quantum coherence for a light-harvesting protein at conditions simulating photosynthesis. Phys Chem Chem Phys 2012; 14:4857-74. [PMID: 22374579 DOI: 10.1039/c2cp23670b] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent measurements using two-dimensional electronic spectroscopy (2D ES) have shown that the initial dynamic response of photosynthetic proteins can involve quantum coherence. We show how electronic coherence can be differentiated from vibrational coherence in 2D ES. On that basis we conclude that both electronic and vibrational coherences are observed in the phycobiliprotein light-harvesting complex PC645 from Chroomonas sp. CCMP270 at ambient temperature. These light-harvesting antenna proteins of the cryptophyte algae are suspended in the lumen, where the pH drops significantly under sustained illumination by sunlight. Here we measured 2D ES of PC645 at increasing levels of acidity to determine if the change in pH affects the quantum coherence; quantitative analysis reveals that the dynamics are insensitive to the pH change.
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Affiliation(s)
- Daniel B Turner
- Department of Chemistry, Institute for Optical Sciences, and Centre for Quantum Information and Quantum Control, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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45
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Elucidating photoinduced structural changes in phytochromes by the combined application of resonance Raman spectroscopy and theoretical methods. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.02.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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46
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Rippers Y, Utesch T, Hildebrandt P, Zebger I, Mroginski MA. Insights into the structure of the active site of the O2-tolerant membrane bound [NiFe] hydrogenase of R. eutropha H16 by molecular modelling. Phys Chem Chem Phys 2011; 13:16146-9. [DOI: 10.1039/c1cp21045a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Mroginski MA, Kaminski S, von Stetten D, Ringsdorf S, Gärtner W, Essen LO, Hildebrandt P. Structure of the chromophore binding pocket in the Pr state of plant phytochrome phyA. J Phys Chem B 2010; 115:1220-31. [PMID: 21192668 DOI: 10.1021/jp108265h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A homology structural model was generated for plant phytochrome phyA utilizing the crystal structure of the sensory module of cyanobacterial phytochrome Cph1 (Cph1Δ2). As chromophores, either the native phytochromobilin cofactor (PΦB) or phycocyanobilin (PCB), the natural cofactor in Cph1, was incorporated. These homology models were further optimized by molecular dynamics (MD) simulations revealing a satisfying overall agreement with the crystal structure of Cph1Δ2. Notable differences in the PΦB adduct of phyA result from a restructuring of the small helical segment α(7) that leads to displacements of a few amino acids away from the cofactor. This repositioning of residues also include aspartate 218 such that, instead of its carbonyl function as in Cph1Δ2, an additional water molecule forms hydrogen bonds with the ring B and C NH groups. To validate the phyA structural model in the chromophore binding pocket, Raman spectra of the cofactor were calculated by means of the quantum mechanics/molecular mechanics (QM/MM) hybrid methodology and compared with the experimental resonance Raman (RR) spectra. The satisfactory overall agreement between calculated and experimental spectra is taken as an indication for the good quality of the structural model. Moreover, the methine bridge stretching modes and the effects of isotopic labeling at selected positions of the chromophore are very well reproduced to allow confirming even details of the methine bridge geometry as predicted by the homology model. Specifically, it is demonstrated that the experimental RR spectra are consistent with a torsional angle of ring D with respect to ring C that is distinctly higher for phyA-PCB (45°) and phyA-PΦB (42°) than for Cph1Δ2 (30°). Raman spectra calculated from different points of the MD trajectory display variations of the mode frequencies and intensities reflecting the structural fluctuations from snapshot to snapshot. The snapshot spectrum of the lowest energy structure and the sum of all snapshot spectra afford an equally good description of the experimental data. Particularly large variations between the snapshots are noted for the N-H in-plane bending mode of the pyrrole rings B and C, which reflect alterations of the hydrogen bond interactions brought about by fluctuations of water molecules in the cofactor cavity. This overestimation of the water molecule mobility is a consequence of the deficiency of the current QM/MM methodology that, due to the lack of appropriate protein force fields, cannot adequately account for the electrostatics in the cofactor pocket.
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48
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Frähmcke JS, Wanko M, Phatak P, Mroginski MA, Elstner M. The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B 2010; 114:11338-52. [PMID: 20698519 DOI: 10.1021/jp104537w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structure and spectroscopy of rhodopsin have been intensely studied in the past decade both experimentally and theoretically; however, important issues still remain unresolved. Of central interest is the protonation state of Glu181, where controversial and contradictory experimental evidence has appeared. While FTIR measurements indicate this residue to be unprotonated, preresonance Raman and UV-vis spectra have been interpreted in favor of a protonated Glu181. Previous computational approaches were not able to resolve this issue, providing contradicting data as well. Here, we perform hybrid QM/MM calculations using DFT methods for the electronic ground state, MRCI methods for the electronically excited states, and a polarization model for the MM part in order to investigate this issue systematically. We constructed various active-site models for protonated as well as unprotonated Glu181, which were evaluated by computing NMR, IR, Raman, and UV-vis spectroscopic data. The resulting differences in the UV-vis and Raman spectra between protonated and unprotonated models are very subtle, which has two major consequences. First, the common interpretation of prior Raman and UV-vis experiments in favor of a neutral Glu181 appears questionable, as it is based on the assumption that a charge at the Glu181 location would have a sizable impact. Second, also theoretical results should be interpreted with care. Spectroscopic differences between the structural models must be related to modeling uncertainties and intrinsic methodological errors. Despite a detailed comparison of various rhodopsins and mutants and consistently favorite results with charged Glu181 models, we find merely weak evidence from UV-vis and Raman calculations. On the contrary, difference FTIR and NMR chemical shift measurements on Rh mutants are indicative of the protonation state of Glu181. Supported by our results, they provide strong and independent evidence for a charged Glu181.
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Affiliation(s)
- Jan S Frähmcke
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Str. 10, D-38106 Braunschweig, Germany
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49
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Swiderek K, Paneth P. Importance of the lactate dehydrogenase quaternary structure in theoretical calculations. J Phys Chem B 2010; 114:3393-7. [PMID: 20155895 DOI: 10.1021/jp100026z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using the example of lactate dehydrogenase, we show that enzyme quaternary structure has an important influence on the structure of the active site and that models that comprise all amino acids in the vicinity of an active site, but are missing this structural information, can lead to incorrect results. We also show that binding isotope effects are very sensitive to the geometric parameters, and thus one should be very cautious when interpreting results obtained with models that are too coarse. In terms of the type of hydrogen bonds, our results indicate that binding isotope effects are pronounced only when a hydrogen bond exhibits some covalent character.
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Technical University of Lodz, ulica Zeromskiego 116, 90-924 Lodz, Poland
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50
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Mroginski MA, Kaminski S, Hildebrandt P. Raman Spectra of the Phycoviolobilin Cofactor in Phycoerythrocyanin Calculated by QM/MM Methods. Chemphyschem 2010; 11:1265-74. [DOI: 10.1002/cphc.200900895] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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