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Quan Z, Ohmiya Y, Liu YJ. Chemical Mechanism of Fireworm Bioluminescence - A Theoretical Proposition. J Phys Chem A 2023; 127:10851-10859. [PMID: 38103213 DOI: 10.1021/acs.jpca.3c07409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Odontosyllis undecimdonta is a marine worm, commonly known as a fireworm, that exhibits bluish-green bioluminescence (BL). The luciferin (L) and oxyluciferin (OL) during fireworm BL have been experimentally identified in vitro. The L and OL are the respective starting point and ending point of a series of complicated chemical reactions in the BL. However, the chemical mechanism of the fireworm BL remains largely unknown. Before the experiments provided strong evidence for the mechanism, based on our previously successful studies on several bioluminescent systems, we theoretically proposed the chemical mechanism of the fireworm BL in this article. By means of the spin-flip and time-dependent density functional calculations, we clearly described the complete process from L to OL: under the catalysis of luciferase, L undergoes deprotonation and reacts with 3O2 to form a dioxetanone anion via the single-electron transfer mechanism; the dioxetanone anion decomposes into the OL at the first singlet excited state (S1) by the gradually reversible charge-transfer-induced luminescence mechanism; and the S1-OL emits light and deexcites to OL in the ground state.
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Affiliation(s)
- Zhuo Quan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yoshihiro Ohmiya
- Osaka Institute of Technology (OIT), 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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Sineshchekov OA, Govorunova EG, Spudich JL. Probing Channelrhodopsin Electrical Activity in Algal Cell Populations. Methods Mol Biol 2021; 2191:85-96. [PMID: 32865740 PMCID: PMC10641915 DOI: 10.1007/978-1-0716-0830-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Photoelectric recording from populations of phototactic flagellate algae provides a means to study channelrhodopsin functions in vivo. Technical simplicity, versatility, high sensitivity, and reproducibility are the advantages of this assay over recording from individual algal cells by the suction pipette technique. Here we describe the principles and procedures of this assay.
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Affiliation(s)
- Oleg A Sineshchekov
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Elena G Govorunova
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John L Spudich
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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Ito S, Iwaki M, Sugita S, Abe-Yoshizumi R, Iwata T, Inoue K, Kandori H. Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution. J Phys Chem B 2017; 122:165-170. [PMID: 29215887 DOI: 10.1021/acs.jpcb.7b11064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein function is coupled to its structural changes, for which stimulus-induced difference Fourier-transform infrared (FTIR) spectroscopy is a powerful method. By optimizing the attenuated total reflection (ATR)-FTIR analysis on sodium-pumping rhodopsin KR2 in aqueous solution, we first measured the accurate difference spectra upon sodium binding in the whole IR region (4000-1000 cm-1). The new spectral window allows the analysis of not only the fingerprint region (1800-1000 cm-1) but also the hydrogen-bonding donor region (4000-1800 cm-1), revealing an unusually strong hydrogen bond of Tyr located in the sodium binding site of KR2. Progress in ATR-FTIR difference spectroscopy provides an approach to investigating stimulus-induced structural changes of membrane proteins under physiological aqueous conditions.
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Affiliation(s)
| | | | | | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Iwata T, Nozaki D, Yamamoto A, Koyama T, Nishina Y, Shiga K, Tokutomi S, Unno M, Kandori H. Hydrogen Bonding Environment of the N3-H Group of Flavin Mononucleotide in the Light Oxygen Voltage Domains of Phototropins. Biochemistry 2017; 56:3099-3108. [PMID: 28530801 DOI: 10.1021/acs.biochem.7b00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The light oxygen voltage (LOV) domain is a flavin-binding blue-light receptor domain, originally found in a plant photoreceptor phototropin (phot). Recently, LOV domains have been used in optogenetics as the photosensory domain of fusion proteins. Therefore, it is important to understand how LOV domains exhibit light-induced structural changes for the kinase domain regulation, which enables the design of LOV-containing optogenetics tools with higher photoactivation efficiency. In this study, the hydrogen bonding environment of the N3-H group of flavin mononucleotide (FMN) of the LOV2 domain from Adiantum neochrome (neo) 1 was investigated by low-temperature Fourier transform infrared spectroscopy. Using specifically 15N-labeled FMN, [1,3-15N2]FMN, the N3-H stretch was identified at 2831 cm-1 for the unphotolyzed state at 150 K, indicating that the N3-H group forms a fairly strong hydrogen bond. The N3-H stretch showed temperature dependence, with a shift to lower frequencies at ≤200 K and to higher frequencies at ≥250 K from the unphotolyzed to the intermediate states. Similar trends were observed in the LOV2 domains from Arabidopsis phot1 and phot2. By contrast, the N3-H stretch of the Q1029L mutant of neo1-LOV2 and neo1-LOV1 was not temperature dependent in the intermediate state. These results seemed correlated with our previous finding that the LOV2 domains show the structural changes in the β-sheet region and/or the adjacent Jα helix of LOV2 domain, but that such structural changes do not take place in the Q1029L mutant or neo1-LOV1 domain. The environment around the N3-H group was also investigated.
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Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Dai Nozaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Atsushi Yamamoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Takayuki Koyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Yasuzo Nishina
- Department of Molecular Physiology, Graduate School of Medical Sciences, Kumamoto University , Honjo, Kumamoto 860-8556, Japan
| | - Kiyoshi Shiga
- Department of Physiology, School of Health Sciences, Kumamoto University , Kuhonji, Kumamoto 862-0976, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University , Sakai, Osaka 599-8531, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University , Saga 840-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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Harris A, Ljumovic M, Bondar AN, Shibata Y, Ito S, Inoue K, Kandori H, Brown LS. A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1518-29. [PMID: 26260121 DOI: 10.1016/j.bbabio.2015.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
One of the main functions of microbial rhodopsins is outward-directed light-driven proton transport across the plasma membrane, which can provide sources of energy alternative to respiration and chlorophyll photosynthesis. Proton-pumping rhodopsins are found in Archaea (Halobacteria), multiple groups of Bacteria, numerous fungi, and some microscopic algae. An overwhelming majority of these proton pumps share the common transport mechanism, in which a proton from the retinal Schiff base is first transferred to the primary proton acceptor (normally an Asp) on the extracellular side of retinal. Next, reprotonation of the Schiff base from the cytoplasmic side is mediated by a carboxylic proton donor (Asp or Glu), which is located on helix C and is usually hydrogen-bonded to Thr or Ser on helix B. The only notable exception from this trend was recently found in Exiguobacterium, where the carboxylic proton donor is replaced by Lys. Here we describe a new group of efficient proteobacterial retinal-binding light-driven proton pumps which lack the carboxylic proton donor on helix C (most often replaced by Gly) but possess a unique His residue on helix B. We characterize the group spectroscopically and propose that this histidine forms a proton-donating complex compensating for the loss of the carboxylic proton donor.
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Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, ON, Canada
| | | | | | - Yohei Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan; PRESTO, Japan Science and Technology Agency, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.
| | - Leonid S Brown
- Department of Physics, University of Guelph, ON, Canada.
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Alafeefy AM, Bakht MA, Ganaie MA, Ansarie MN, El-Sayed NN, Awaad AS. Synthesis, analgesic, anti-inflammatory and anti-ulcerogenic activities of certain novel Schiff's bases as fenamate isosteres. Bioorg Med Chem Lett 2014; 25:179-83. [PMID: 25522819 DOI: 10.1016/j.bmcl.2014.11.088] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/28/2014] [Indexed: 11/30/2022]
Abstract
A series of certain novel Schiff bases as fenamate isosteres (VI:a-k) were synthesized to locate analgesic, anti-inflammatory agent with minimal ulcerogenic potential. The structures of the newly synthesized compounds were elucidated on the basis of their elemental analysis as well as IR, and NMR and mass spectroscopic data. All the compounds were evaluated for their anti-inflammatory activity by carrageenan induced paw oedema method. The compounds possessing good anti-inflammatory activity were further tested for analgesic, ulcerogenic, lipid peroxidation potentials and liver toxicity. Compounds (VI-c), (VI-f), (VI-h) and (VI-i) showed the best anti-inflammatory and significant analgesic activities at doses comparable to that of the standard drug Indomethacin. However, compounds (VI-c) and (VI-f) could be considered the most potent anti-inflammatory and analgesic molecules with maximum reduction in gastro-intestinal ulceration with no hepatocyte necrosis or liver degeneration.
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Affiliation(s)
- Ahmed M Alafeefy
- Department of Pharmaceutical Chemistry, College of Pharmacy, Salman Bin Abdulaziz University, PO Box 173, Alkharj 11942, Saudi Arabia.
| | - Mohammed A Bakht
- Department of Pharmaceutical Chemistry, College of Pharmacy, Salman Bin Abdulaziz University, PO Box 173, Alkharj 11942, Saudi Arabia
| | - Majid A Ganaie
- Department of Pharmacology and Toxicology, College of Pharmacy, Salman Bin Abdulaziz University, PO Box 173, Alkharj 11942, Saudi Arabia
| | - Mohd N Ansarie
- Department of Pharmacology and Toxicology, College of Pharmacy, Salman Bin Abdulaziz University, PO Box 173, Alkharj 11942, Saudi Arabia
| | - Nahed N El-Sayed
- Department of Chemistry, College of Science, "Girls Section", King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia; National Organization for Drug Control and Research, Giza 35521, Egypt
| | - Amani S Awaad
- Department of Pharmacognosy, College of Pharmacy 'Girls Section', Salman Bin Abdulaziz University, PO Box 173, Alkharj 11942, Saudi Arabia
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