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Haghdoust F, Molakarimi M, Mirshahi M, Sajedi RH. Engineering aequorin to improve thermostability through rigidifying flexible sites. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Nemati R, Molakarimi M, Mohseni A, Taghdir M, Khalifeh K, H. Sajedi R. Thermostability of Ctenophore and Coelenterate Ca 2+-Regulated Apo-photoproteins: A Comparative Study. ACS Chem Biol 2021; 16:1538-1545. [PMID: 34181382 DOI: 10.1021/acschembio.1c00401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stabilities of Ca2+-regulated ctenophore and coelenterate apo-photoproteins, apo-mnemiopsin (apo-Mne) and apo-aequorin (apo-Aeq), respectively, were compared biochemically, biophysically, and structurally. Despite high degrees of structural and functional conservation, drastic variations in stability and structural dynamics were found between the two proteins. Irreversible thermoinactivation experiments were performed upon incubation of apo-photoproteins at representative temperatures. The inactivation rate constants (kinact) at 50 °C were determined to be 0.001 and 0.004 min-1 for apo-Mne and apo-Aeq, respectively. Detailed analysis of the inactivation process suggests that the higher thermostability of apo-Mne is due to the higher activation energy (Ea) and subsequently higher values of ΔH* and ΔG* at a given temperature. According to molecular dynamics simulation studies, the higher hydrogen bond, electrostatic, and van der Waals energies in apo-Mne can validate the relationship between the thermal adaptation of apo-Mne and the energy barrier for the inactivation process. Our results show that favorable residues for protein thermostability such as hydrophobic, charged, and adopted α-helical structure residues are more frequent in the apo-Mne structure. Although the effect of acrylamide on fluorescence quenching suggests that the local flexibility in regions around Trp and Tyr residues of apo-Aeq is higher than that of apo-Mne, which results in it having a better ability to penetrate acrylamide molecules, the root-mean-square fluctuation of helix A in apo-Mne is higher than that in apo-Aeq. It seems that the greater flexibility of apo-Mne in these regions may be considered as a determining factor, affecting the thermal stability of apo-Mne through a balance between structural rigidity and flexibility.
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Affiliation(s)
- Robabeh Nemati
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan 45371-38791, Iran
| | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
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Tomilin FN, Rogova AV, Burakova LP, Tchaikovskaya ON, Avramov PV, Fedorov DG, Vysotski ES. Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory. Photochem Photobiol Sci 2021; 20:10.1007/s43630-021-00039-5. [PMID: 33834429 DOI: 10.1007/s43630-021-00039-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460-470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein-substrate complex was optimized using a linear scaling quantum-mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified.
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Affiliation(s)
- Felix N Tomilin
- Kirensky Institute of Physics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/38, Krasnoyarsk, 660036, Russia
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Anastasia V Rogova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
| | - Ludmila P Burakova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia
| | - Olga N Tchaikovskaya
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Pavel V Avramov
- Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia.
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Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019; 15:4535-4546. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | | | - Michael Sahlin
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | - François Dehez
- Laboratoire de Physique et Chimie Théorique , UMR 7019, Faculté des Sciences et Technique , Campus Aiguillettes , 54506 Vandoeuvre-les-Nancy , France
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Dipartimento di Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , via A. Moro 2 , 53100 Siena , Italy
| | - Nicolas Ferré
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
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Burakova LP, Vysotski ES. Recombinant Ca 2+-regulated photoproteins of ctenophores: current knowledge and application prospects. Appl Microbiol Biotechnol 2019; 103:5929-5946. [PMID: 31172204 DOI: 10.1007/s00253-019-09939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022]
Abstract
Bright bioluminescence of ctenophores is conditioned by Ca2+-regulated photoproteins. Although they share many properties characteristic of hydromedusan Ca2+-regulated photoproteins responsible for light emission of marine animals belonging to phylum Cnidaria, a substantial distinction still exists. The ctenophore photoproteins appeared to be extremely sensitive to light-they lose the ability for bioluminescence on exposure to light over the entire absorption spectrum. Inactivation is irreversible because keeping the inactivated photoprotein in the dark does not recover its activity. The capability to emit light can be restored only by incubation of inactivated photoprotein with coelenterazine in the dark at alkaline pH in the presence of oxygen. Although these photoproteins were discovered many years ago, only the cloning of cDNAs encoding these unique bioluminescent proteins in the early 2000s has provided a new impetus for their studies. To date, cDNAs encoding Ca2+-regulated photoproteins from four different species of luminous ctenophores have been cloned. The amino acid sequences of ctenophore photoproteins turned out to completely differ from those of hydromedusan photoproteins (identity less than 29%) though also similar to them having three EF-hand Ca2+-binding sites. At the same time, these photoproteins reveal the same two-domain scaffold characteristic of hydromedusan photoproteins. This review is an attempt to systemize and critically evaluate the data scattered through various articles regarding the structural features of recombinant light-sensitive Ca2+-regulated photoproteins of ctenophores and their bioluminescent and physicochemical properties as well as to compare them with those of hydromedusan photoproteins. In addition, we also discuss the prospects of their biotechnology applications.
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Affiliation(s)
- Lyudmila P Burakova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia.
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Molakarimi M, Gorman MA, Mohseni A, Pashandi Z, Taghdir M, Naderi-Manesh H, Sajedi RH, Parker MW. Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. J Biol Chem 2019; 294:20-27. [PMID: 30420427 PMCID: PMC6322872 DOI: 10.1074/jbc.ra118.006053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 11/06/2022] Open
Abstract
Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca2+-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd2+-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Michael A Gorman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
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