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Moroz LL. Brief History of Ctenophora. Methods Mol Biol 2024; 2757:1-26. [PMID: 38668961 DOI: 10.1007/978-1-0716-3642-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Ctenophores are the descendants of the earliest surviving lineage of ancestral metazoans, predating the branch leading to sponges (Ctenophore-first phylogeny). Emerging genomic, ultrastructural, cellular, and systemic data indicate that virtually every aspect of ctenophore biology as well as ctenophore development are remarkably different from what is described in representatives of other 32 animal phyla. The outcome of this reconstruction is that most system-level components associated with the ctenophore organization result from convergent evolution. In other words, the ctenophore lineage independently evolved as high animal complexities with the astonishing diversity of cell types and structures as bilaterians and cnidarians. Specifically, neurons, synapses, muscles, mesoderm, through gut, sensory, and integrative systems evolved independently in Ctenophora. Rapid parallel evolution of complex traits is associated with a broad spectrum of unique ctenophore-specific molecular innovations, including alternative toolkits for making an animal. However, the systematic studies of ctenophores are in their infancy, and deciphering their remarkable morphological and functional diversity is one of the hot topics in biological research, with many anticipated surprises.
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Affiliation(s)
- Leonid L Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
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Su J, Sun T, Wang Y, Shen Y. Conformational Dynamics of Glucagon-like Peptide-2 with Different Electric Field. Polymers (Basel) 2022; 14:polym14132722. [PMID: 35808767 PMCID: PMC9269336 DOI: 10.3390/polym14132722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022] Open
Abstract
Molecular dynamics (MD) simulation was used to study the influence of electric field on Glucagon-like Peptide-2 (GLP-2). Different electric field strengths (0 V/nm ≤ E ≤ 1 V/nm) were mainly carried out on GLP-2. The structural changes in GLP-2 were analyzed by the Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA), Secondary Structure and the number of hydrogen bonds. The stable α—helix structure of GLP-2 was unwound and transformed into an unstable Turn and Coil structure since the stability of the GLP-2 protein structure was reduced under the electric field. Our results show that the degree of unwinding of the GLP-2 structure was not linearly related to the electric field intensity. E = 0.5 V/nm was a special point where the degree of unwinding of the GLP-2 structure reached the maximum at this electric field strength. Under a weak electric field, E < 0.5 V/nm, the secondary structure of GLP-2 becomes loose, and the entropy of the chain increases. When E reaches a certain value (E > 0.5 V/nm), the electric force of the charged residues reaches equilibrium, along the z-direction. Considering the confinement of moving along another direction, the residue is less free. Thus, entropy decreases and enthalpy increases, which enhance the interaction of adjacent residues. It is of benefit to recover hydrogen bonds in the middle region of the protein. These investigations, about the effect of an electric field on the structure of GLP-2, can provide some theoretical basis for the biological function of GLP-2 in vivo.
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Affiliation(s)
| | - Tingting Sun
- Correspondence: (T.S.); (Y.W.); Tel.: +86-571-8507-0705 (T.S. & Y.W.)
| | - Yan Wang
- Correspondence: (T.S.); (Y.W.); Tel.: +86-571-8507-0705 (T.S. & Y.W.)
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Hub Proteins Involved in RAW 264.7 Macrophages Exposed to Direct Current Electric Field. Int J Mol Sci 2020; 21:ijms21124505. [PMID: 32599940 PMCID: PMC7352442 DOI: 10.3390/ijms21124505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
At present, studies on macrophage proteins mainly focus on biological stimuli, with less attention paid to the responses of macrophage proteins to physical stimuli, such as electric fields. Here, we exploited the electric field-sensitive hub proteins of macrophages. RAW 264.7 macrophages were treated with a direct current electric field (dcEF) (200 mV/mm) for four hours, followed by RNA-Seq analysis. Differentially expressed genes (DEGs) were obtained, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and protein–protein interaction (PPI) analysis. Eight qPCR-verified DEGs were selected. Subsequently, three-dimensional protein models of DEGs were modeled by Modeller and Rosetta, followed by molecular dynamics simulation for 200 ns with GROMACS. Finally, dcEFs (10, 50, and 500 mV/mm) were used to simulate the molecular dynamics of DEG proteins for 200 ns, followed by trajectory analysis. The dcEF has no obvious effect on RAW 264.7 morphology. A total of 689 DEGs were obtained, and enrichment analysis showed that the steroid biosynthesis pathway was most affected by the dcEF. Moreover, the three-dimensional protein structures of hub proteins were constructed, and trajectory analysis suggested that the dcEF caused an increase in the atomic motion of the protein in a dcEF-intensity-dependent manner. Overall, we provide new clues and a basis for investigating the hub proteins of macrophages in response to electric field stimulation.
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Ahmed G, Raziq F, Hanif M, Khan J, Munawar KS, Wu M, Cao X, Liu Z. Oxygen-Cluster-Modified Anatase with Graphene Leads to Efficient and Recyclable Photo-Catalytic Conversion of CO 2 to CH 4 Supported by the Positron Annihilation Study. Sci Rep 2019; 9:13103. [PMID: 31511596 PMCID: PMC6739302 DOI: 10.1038/s41598-019-49694-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/20/2019] [Indexed: 01/06/2023] Open
Abstract
Anatase TiO2 hollow nanoboxes were synthesized and combined with the graphene oxide to get nanocomposite of TiO2/rGO (TG). Graphene oxide was used to modify the Oxygen-Clusters and bulk to surface defects. Anatase and TG composite were characterized with the positron annihilation, XPS, EPR, EIS and photocurrent response analysis. The relative affects of defects on the photocatalytic reduction (CO2 to CH4) were studied. The TG composites showed highest photo-catalytic activity after GO coupling (49 µmol g-1 h-1), 28.6 times higher photocurrent yields much higher quantum efficiency (3.17%@400 nm) when compared to the TiO2 nanoboxes. The mechanism of enhanced photo-catalytic CO2 conversion to CH4 elucidated through electrochemical and photo-catalytic experiments with traceable isotope containing carbon dioxide (13CO2). For the first time we discovered that diminishing the comparative concentration ratio of anatase from the bulk to surface defects could significantly increase the conversion of CO2 to CH4.
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Affiliation(s)
- Gulzar Ahmed
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, P.R. China.
- University of Sargodha Sub Campus Mianwali, 42200, Punjab, Pakistan.
| | - Fazal Raziq
- School of Physics, University of Electronic Science and Technology of China, Chengdu, 610054, P.R. China
| | - Muddasir Hanif
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, P.R. China.
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640, P.R. China.
| | - Javid Khan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | | | - Mingmei Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Xingzhong Cao
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Zhongwu Liu
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, P.R. China.
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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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