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Setlur AS, Karunakaran C, Panhalkar V, Sharma S, Sarkar M, Niranjan V. Multifaceted computational profiling of thymol and geraniol against the human proteome for bio-repellent alternatives: Toxicity predictions, degradation analysis, and quantum mechanical approaches. Acta Trop 2024; 258:107359. [PMID: 39142548 DOI: 10.1016/j.actatropica.2024.107359] [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] [Received: 06/29/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
With growing interest in natural compounds as alternative mosquito repellents, assessing the toxicity and structure of potential repellent naturals like thymol (monoterpene phenol) and geraniol (monoterpene alcohol) is vital for understanding their stability and human impact. This study aimed to determine the structural, toxicity, and binding profiles of thymol and geraniol using computational predictions, xTB metadynamics, quantum mechanics, and principal component analysis. Toxicity studies using Protox-II, T.E.S.T, and SwissADME indicated that thymol and geraniol belong to toxicity class 4 and 5, respectively, with low toxicity predictions in other endpoints. Overall pharmacokinetic profile was generated via pkCSM. Off-target predictions via SwissTarget Predictions, LigTMap, Pharmapper, and SuperPred showed that these molecules can bind to 614 human proteins. The degradation of thymol and geraniol were performed using xTB metadynamics and the outcomes showed that the degradants for both compounds were stable and had lower toxicity profile. Nine tautomers were generated via quantum mechanics for thymol and four for geraniol, with RMSD ranging from 3.8 to 6.3 Å for thymol and 3.6 to 4 Å for geraniol after superimpositions. DFT studies found that HOMO-LUMO values and electronegativity parameters of thymol and geraniol did not differ significantly from their isomers. Binding affinity studies against 614 proteins, analysed via PCA and violin plots, highlighted the probable range of binding. These multifaceted in-silico findings corroborate the stability and potential utility of thymol and geraniol as safer alternatives in repellent applications.
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Affiliation(s)
- Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, Affiliated to Visvesvaraya Technological University (VTU), Belagavi 560018, India
| | - Chandrashekar Karunakaran
- Department of Biotechnology, RV College of Engineering, Bangalore, Affiliated to Visvesvaraya Technological University (VTU), Belagavi 560018, India
| | - Vartul Panhalkar
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana 122001, India
| | - Sonia Sharma
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana 122001, India
| | - Manas Sarkar
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana 122001, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, Affiliated to Visvesvaraya Technological University (VTU), Belagavi 560018, India.
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2
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Nonkhwao S, Leaokittikul D, Patramanon R, Jangpromma N, Daduang J, Daduang S. Revealing the pH-dependent conformational changes in sol g 2.1 protein and potential ligands binding. Sci Rep 2024; 14:21179. [PMID: 39261547 PMCID: PMC11391043 DOI: 10.1038/s41598-024-72014-w] [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] [Received: 04/03/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024] Open
Abstract
Sol g 2, a major protein found in the venom of the tropical fire ant (Solenopsis geminata), is well-known for its ability to bind various hydrophobic molecules. In this study, we investigate the binding activity of recombinant Sol g 2.1 protein (rSol g 2.1) with potential molecules, including (E)-β-Farnesene, α-Caryophyllene, and 1-Octen-3-ol at different pH levels (pH 7.4 and 5.5) using fluorescence competitive binding assays (FCBA). Our results revealed that Sol g 2.1 protein has higher affinity binding with these ligands at neutral pH. Relevance to molecular docking and molecular dynamics simulations were utilized to provide insights into the stability and conformational dynamics of Sol g 2.1 and its ligand complexes. After simulation, we found that Sol g 2.1 protein has higher affinity binding with these ligands as well as high structural stability at pH 7.4 than at an acidic pH level, indicating by RMSD, RMSF, Rg, SASA, and principal component analysis (PCA). Additionally, the Sol g 2.1 protein complexes at pH 7.4 showed significantly lower binding free energy (∆Gbind) and higher total residue contributions, particularly from key non-polar amino acids such as Trp36, Met40, Cys62, and Ile104, compared to the lower pH environment. These explain why they exhibited higher binding affinity than the lower pH. Therefore, we suggested that Sol g 2.1 protein is a pH-responsive carrier protein. These findings also expand our understanding of protein-ligand interactions and offer potential avenues for the development of innovative drug delivery strategies targeting Sol g 2.1 protein.
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Affiliation(s)
- Siriporn Nonkhwao
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Rina Patramanon
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nisachon Jangpromma
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jureerut Daduang
- Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sakda Daduang
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, 40002, Thailand.
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Yi SC, Chen XH, Wu YH, Wu J, Wang JQ, Wang MQ. Identification of odorant-binding proteins and functional analysis of antenna-specific BhorOBP28 in Batocera horsfieldi (Hope). PEST MANAGEMENT SCIENCE 2024; 80:4055-4068. [PMID: 38567786 DOI: 10.1002/ps.8112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/10/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The important wood-boring pest Batocera horsfieldi has evolved a sensitive olfactory system to locate host plants. Odorant-binding proteins (OBPs) are thought to play key roles in olfactory recognition. Therefore, exploring the physiological function of OBPs could facilitate a better understanding of insect chemical communications. RESULTS In this research, 36 BhorOBPs genes were identified via transcriptome sequencing of adults' antennae from B. horsfieldi, and most BhorOBPs were predominantly expressed in chemosensory body parts. Through fluorescence competitive binding and fluorescence quenching assays, the antenna-specific BhorOBP28 was investigated and displayed strong binding affinities forming stable complexes with five volatiles, including (+)-α-Pinene, (+)-Limonene, β-Pinene, (-)-Limonene, and (+)-Longifolene, which could also elicit conformation changes when they were interacting with BhorOBP28. Batocera horsfieldi females exhibited a preference for (-)-Limonene, and a repellent response to (+)-Longifolene. Feeding dsOBP19 produced by a bacteria-expressed system with a newly constructed vector could lead to the knockdown of BhorOBP28, and could further impair B. horsfieldi attraction to (-)-Limonene and repellent activity of (+)-Longifolene. The analysis of site-directed mutagenesis revealed that Leu7, Leu72, and Phe121 play a vital role in selectively binding properties of BhorOBP28. CONCLUSION By modeling the molecular mechanism of olfactory recognition, these results demonstrate that BhorOBP28 is involved in the chemoreception of B. horsfieldi. The bacterial-expressed dsRNA delivery system gains new insights into potential population management strategies. Through the olfactory process concluded that discovering novel behavioral regulation and environmentally friendly control options for B. horsfieldi in the future. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shan-Cheng Yi
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xin-Hui Chen
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Hang Wu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Juan Wu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia-Qing Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Man-Qun Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Park K, Choi H, Han IJ, Asefa WR, Jeong C, Yu S, Jeong H, Choi M, Yoon SE, Kim YJ, Choi MS, Kwon JY. Molecular and cellular organization of odorant binding protein genes in Drosophila. Heliyon 2024; 10:e29358. [PMID: 38694054 PMCID: PMC11058302 DOI: 10.1016/j.heliyon.2024.e29358] [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: 02/22/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Chemosensation is important for the survival and reproduction of animals. The odorant binding proteins (OBPs) are thought to be involved in chemosensation together with chemosensory receptors. While OBPs were initially considered to deliver hydrophobic odorants to olfactory receptors in the aqueous lymph solution, recent studies suggest more complex roles in various organs. Here, we use GAL4 transgenes to systematically analyze the expression patterns of all 52 members of the Obp gene family and 3 related chemosensory protein genes in adult Drosophila, focusing on chemosensory organs such as the antenna, maxillary palp, pharynx, and labellum, and other organs such as the brain, ventral nerve cord, leg, wing, and intestine. The OBPs were observed to express in diverse organs and in multiple cell types, suggesting that these proteins can indeed carry out diverse functional roles. Also, we constructed 10 labellar-expressing Obp mutants, and obtained behavioral evidence that these OBPs may be involved in bitter sensing. The resources we constructed should be useful for future Drosophila OBP gene family research.
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Affiliation(s)
- Keehyun Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyungjun Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - I Joon Han
- Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Wayessa Rahel Asefa
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chaiyoung Jeong
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seungyun Yu
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hanhee Jeong
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minkook Choi
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Sung-Eun Yoon
- Korea Drosophila Resource Center, Gwangju, 61005, Republic of Korea
| | - Young-Joon Kim
- Korea Drosophila Resource Center, Gwangju, 61005, Republic of Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Min Sung Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jae Young Kwon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
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Wang L, Hou M, Liang C, Xu Q, Lu Y, Zhao Z. Role of odorant binding protein C12 in the response of Tribolium castaneum to chemical agents. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105861. [PMID: 38685215 DOI: 10.1016/j.pestbp.2024.105861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 05/02/2024]
Abstract
Tribolium castaneum is a worldwide pest of stored grain that mainly damages flour, and not only causes serious loss of flour quality but also leads to deterioration of flour quality. Chemical detection plays a key role in insect behavior, and the role of odorant-binding proteins (OBPs) in insect chemical detection has been widely studied. OBPs can interact with small molecule compounds and thereby modulate variation in insecticide susceptibility in insects. In this study, a total of 65 small molecule compounds are selected to investigate the bound effect with TcOBP C12. The molecular docking results showed that β-caryophyllene, (-)-catechin, butylated hydroxytoluene, diphenyl phthalate and quercetin were the top five compounds, with docking binding energies of -6.11, -5.25, -5.09, -5.05, and - 5.03 Kcal/mol, respectively. Molecular dynamics analysis indicated that odorant binding protein C12 (TcOBP C12) exhibited high binding affinity to all five tested chemical ligands, evidenced by fluorescence quenching assay in vitro. In addition, the contact toxicity assay results suggested that these chemical agents caused a dose-dependent increase in mortality rate for T. castaneum adults. The TcOBP C12 gene was upregulated >2 times after a 24-h exposure, indicating that OBP C12 may play an important role for T. castaneum in response to these chemical agents. In conclusion, our results provide a theoretical basis for future insecticide experiments and pest management.
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Affiliation(s)
- Lei Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Mingrui Hou
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Chuanqi Liang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Qingfen Xu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Yujie Lu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang 212100, PR China.
| | - Zongpei Zhao
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang 212100, PR China.
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Yin J, Chen HL, Grigsby-Brown A, He Y, Cotten ML, Short J, Dermady A, Lei J, Gibbs M, Cheng ES, Zhang D, Long C, Xu L, Zhong T, Abzalimov R, Haider M, Sun R, He Y, Zhou Q, Tjandra N, Yuan Q. Glia-derived secretory fatty acid binding protein Obp44a regulates lipid storage and efflux in the developing Drosophila brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588417. [PMID: 38645138 PMCID: PMC11030299 DOI: 10.1101/2024.04.10.588417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Glia derived secretory factors play diverse roles in supporting the development, physiology, and stress responses of the central nervous system (CNS). Through transcriptomics and imaging analyses, we have identified Obp44a as one of the most abundantly produced secretory proteins from Drosophila CNS glia. Protein structure homology modeling and Nuclear Magnetic Resonance (NMR) experiments reveal Obp44a as a fatty acid binding protein (FABP) with a high affinity towards long-chain fatty acids in both native and oxidized forms. Further analyses demonstrate that Obp44a effectively infiltrates the neuropil, traffics between neuron and glia, and is secreted into hemolymph, acting as a lipid chaperone and scavenger to regulate lipid and redox homeostasis in the developing brain. In agreement with this essential role, deficiency of Obp44a leads to anatomical and behavioral deficits in adult animals and elevated oxidized lipid levels. Collectively, our findings unveil the crucial involvement of a noncanonical lipid chaperone to shuttle fatty acids within and outside the brain, as needed to maintain a healthy brain lipid environment. These findings could inspire the design of novel approaches to restore lipid homeostasis that is dysregulated in CNS diseases.
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Affiliation(s)
- Jun Yin
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Hsueh-Ling Chen
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Anna Grigsby-Brown
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Yi He
- Fermentation Facility, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Myriam L Cotten
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR
| | - Jacob Short
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Aidan Dermady
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Jingce Lei
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Mary Gibbs
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Ethan S Cheng
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Dean Zhang
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Caixia Long
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Lele Xu
- Advanced Science Research Center, The City University of New York, New York, NY
- Ph.D. Program in Biology, The Graduate Center of the City University of New York, New York, NY
| | - Tiffany Zhong
- Neuroscience Program, Princeton University, Princeton, NJ
| | - Rinat Abzalimov
- Advanced Science Research Center, The City University of New York, New York, NY
| | - Mariam Haider
- Department of Cell and Developmental Biology, Vanderbilt Brain Institute, Center for Structural Biology, Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN
| | - Rong Sun
- Department of Cell and Developmental Biology, Vanderbilt Brain Institute, Center for Structural Biology, Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN
| | - Ye He
- Advanced Science Research Center, The City University of New York, New York, NY
- Ph.D. Program in Biology, The Graduate Center of the City University of New York, New York, NY
| | - Qiangjun Zhou
- Department of Cell and Developmental Biology, Vanderbilt Brain Institute, Center for Structural Biology, Vanderbilt Kennedy Center, Vanderbilt University, Nashville, TN
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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Wang P, Liu M, Lv C, Tian Z, Li R, Li Y, Zhang Y, Liu J. Identifying the Key Role of Plutella xylostella General Odorant Binding Protein 2 in Perceiving a Larval Attractant, ( E, E)-2,6-Farnesol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5690-5698. [PMID: 38447177 DOI: 10.1021/acs.jafc.4c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
There is currently a lack of effective olfaction-based techniques to control diamondback moth (DBM) larvae. Identifying behaviorally active odorants for DBM larvae and exploring their recognition mechanisms can provide insights into olfaction-based larval control strategies. Through the two-choice assay, (E,E)-2,6-farnesol (farnesol) was identified as a compound exhibiting significant attractant activity toward DBM larvae, achieving an attraction index of 0.48 ± 0.13. PxylGOBP1 and PxylGOBP2, highly expressed in the antennae of DBM larvae, both showed high affinity toward farnesol. RNAi technology was used to knock down PxylGOBP1 and PxylGOBP2, revealing that the attraction of DBM larvae to farnesol nearly vanished following the knockdown of PxylGOBP2, indicating its critical role in recognizing farnesol. Further investigation into the PxylGOBP2-farnesol interaction revealed the importance of residues like Thr9, Trp37, and Phe118 in PxylGOBP2's binding to farnesol. This research is significant for unveiling the olfactory mechanisms of DBM larvae and developing larval behavior regulation techniques.
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Affiliation(s)
- Pei Wang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Miao Liu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Changhong Lv
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Tian
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruichi Li
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifan Li
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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8
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Li YJ, Gu FM, Chen HC, Liu ZX, Song WM, Wu FA, Sheng S, Wang J. Binding characteristics of pheromone-binding protein 1 in Glyphodes pyloalis to organophosphorus insecticides: Insights from computational and experimental approaches. Int J Biol Macromol 2024; 260:129339. [PMID: 38218287 DOI: 10.1016/j.ijbiomac.2024.129339] [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] [Received: 06/27/2023] [Revised: 12/27/2023] [Accepted: 01/06/2024] [Indexed: 01/15/2024]
Abstract
Glyphodes pyloalis (Lepidoptera: Pyralidae) is one of the major pests in mulberry production in China, which has developed resistance to various insecticides. Chemoreception is one of the most crucial physiological tactics in insects, playing a pivotal role in recognizing chemical stimuli in the environment, including noxious stimuli such as insecticides. Herein, we obtained recombinant pheromone-binding protein 1 (GpylPBP1) that exhibited antennae-biased expression in G. pyloalis. Ligand-binding assays indicated that GpylPBP1 had the binding affinities to two organophosphorus insecticides, with a higher binding affinity to chlorpyrifos than to phoxim. Computational simulations showed that a mass of nonpolar amino acid residues formed the binding pocket of GpylPBP1 and contributed to the hydrophobic interactions in the bindings of GpylPBP1 to both insecticides. Furthermore, the binding affinities of three GpylPBP1 mutants (F12A, I52A, and F118A) to both insecticides were all significantly reduced compared to those of the GpylPBP1-wild type, suggesting that Phe12, Ile52, and Phe118 residues were crucial binding sites and played crucial roles in the bindings of GpylPBP1 to both insecticides. Our findings can be instrumental in elucidating the effects of insecticides on olfactory recognition in moths and facilitating the development of novel pest management strategies using PBPs as targets based on insect olfaction.
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Affiliation(s)
- Yi-Jiangcheng Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Feng-Ming Gu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Hong-Chao Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Zhi-Xiang Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Wen-Miao Song
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Fu-An Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, PR China
| | - Sheng Sheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, PR China.
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, PR China.
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9
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Huang CW, Lin C, Nguyen MK, Hussain A, Bui XT, Ngo HH. A review of biosensor for environmental monitoring: principle, application, and corresponding achievement of sustainable development goals. Bioengineered 2023; 14:58-80. [PMID: 37377408 DOI: 10.1080/21655979.2022.2095089] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 06/29/2023] Open
Abstract
Human health/socioeconomic development is closely correlated to environmental pollution, highlighting the need to monitor contaminants in the real environment with reliable devices such as biosensors. Recently, variety of biosensors gained high attention and employed as in-situ application, in real-time, and cost-effective analytical tools for healthy environment. For continuous environmental monitoring, it is necessary for portable, cost-effective, quick, and flexible biosensing devices. These benefits of the biosensor strategy are related to the Sustainable Development Goals (SDGs) established by the United Nations (UN), especially with reference to clean water and sources of energy. However, the relationship between SDGs and biosensor application for environmental monitoring is not well understood. In addition, some limitations and challenges might hinder the biosensor application on environmental monitoring. Herein, we reviewed the different types of biosensors, principle and applications, and their correlation with SDG 6, 12, 13, 14, and 15 as a reference for related authorities and administrators to consider. In this review, biosensors for different pollutants such as heavy metals and organics were documented. The present study highlights the application of biosensor for achieving SDGs. Current advantages and future research aspects are summarized in this paper.Abbreviations: ATP: Adenosine triphosphate; BOD: Biological oxygen demand; COD: Chemical oxygen demand; Cu-TCPP: Cu-porphyrin; DNA: Deoxyribonucleic acid; EDCs: Endocrine disrupting chemicals; EPA: U.S. Environmental Protection Agency; Fc-HPNs: Ferrocene (Fc)-based hollow polymeric nanospheres; Fe3O4@3D-GO: Fe3O4@three-dimensional graphene oxide; GC: Gas chromatography; GCE: Glassy carbon electrode; GFP: Green fluorescent protein; GHGs: Greenhouse gases; HPLC: High performance liquid chromatography; ICP-MS: Inductively coupled plasma mass spectrometry; ITO: Indium tin oxide; LAS: Linear alkylbenzene sulfonate; LIG: Laser-induced graphene; LOD: Limit of detection; ME: Magnetoelastic; MFC: Microbial fuel cell; MIP: Molecular imprinting polymers; MWCNT: Multi-walled carbon nanotube; MXC: Microbial electrochemical cell-based; NA: Nucleic acid; OBP: Odorant binding protein; OPs: Organophosphorus; PAHs: Polycyclic aromatic hydrocarbons; PBBs: Polybrominated biphenyls; PBDEs: Polybrominated diphenyl ethers; PCBs: Polychlorinated biphenyls; PGE: Polycrystalline gold electrode; photoMFC: photosynthetic MFC; POPs: Persistent organic pollutants; rGO: Reduced graphene oxide; RNA: Ribonucleic acid; SDGs: Sustainable Development Goals; SERS: Surface enhancement Raman spectrum; SPGE: Screen-printed gold electrode; SPR: Surface plasmon resonance; SWCNTs: single-walled carbon nanotubes; TCPP: Tetrakis (4-carboxyphenyl) porphyrin; TIRF: Total internal reflection fluorescence; TIRF: Total internal reflection fluorescence; TOL: Toluene-catabolic; TPHs: Total petroleum hydrocarbons; UN: United Nations; VOCs: Volatile organic compounds.
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Affiliation(s)
- Chi-Wei Huang
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Chitsan Lin
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
- Ph.D. Program in Maritime Science and Technology, College of Maritime, National Kaohsiung University of Science and TechnologyPh.D. Program in Maritime Science and Technology, Kaohsiung, Taiwan
| | - Minh Ky Nguyen
- Ph.D. Program in Maritime Science and Technology, College of Maritime, National Kaohsiung University of Science and TechnologyPh.D. Program in Maritime Science and Technology, Kaohsiung, Taiwan
| | - Adnan Hussain
- Ph. D. Program of Aquatic Science and Technology, College of Hydrosphere Science, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Xuan-Thanh Bui
- Department Water Science & Technology, Key Laboratory of Advanced Waste Treatment Technology, Ho Chi Minh City University of Technology (HCMUT), Vietnam National University Ho Chi Minh (VNU-HCM), Ho Chi Minh City, Vietnam
- Department Water Science & Technology, Faculty of Environment & Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
| | - Huu Hao Ngo
- Department Water Science & Technology, Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney NSW, Australia
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Wang Y, Bian XK, Zhang L, Chen WY, Lyu QJ, Du SS. The essential oil of Kochia scoparia (L.) Schrad. as a potential repellent against stored-product insects. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:124416-124424. [PMID: 37996575 DOI: 10.1007/s11356-023-31011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Chemical composition of the essential oil from Kochia scoparia (L.) Schrad. (syn. Bassia scoparia (L.) A. J. Scott) was analyzed in quality and quantity by GC-MS and GC-FID. Repellent activities of the essential oil from K. scoparia (KSEO) were evaluated against two common species of stored-product insects Tribolium castaneum Herbst and Liposcelis bostrychophila Badonnel. Results indicated that KSEO mainly consisted of eugenol, β-caryophyllene, and α-humulene, accounting for 75.6%, 8.2%, and 1.4% of the total oil, respectively. KSEO and the three major components were repellent to T. castaneum and L. bostrychophila adults. Notably, KSEO exerted significant effects, comparable to the positive control DEET at 2 and 4 h post-exposure. Eugenol at 63.17-2.53 nL/cm2 exhibited high percentage repellency ranging from 96 to 70% against L. bostrychophila during 4-h exposure. To gain further insights into the repellent activity, molecular docking simulation was performed with eugenol as the ligand and an odorant binding protein TcOBPC12 (gene: TcOBP10B) from the model insect T. castaneum as the receptor. Docking calculation results revealed that TcOBPC12 had binding affinity to eugenol (△G = - 4.52 kcal/mol) along with a hydrogen bond of 0.18 nm (1.8 Å) long forming between them, which could be an important target protein associated with identifying volatile repellent molecules. This work highlights the promising potential of KSEO as a botanical repellent for controlling stored-product insects.
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Affiliation(s)
- Yang Wang
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
- Beijing Key Laboratory of Traditional Chinese Medicine Protection and Utilization, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China.
| | - Xiao-Kun Bian
- Department of Pharmacy, Yancheng No.1 People's Hospital, Yancheng, 224000, Jiangsu, China
| | - Li Zhang
- Department of Nursing, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Wen-Yan Chen
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Qiu-Ju Lyu
- Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Shu-Shan Du
- Beijing Key Laboratory of Traditional Chinese Medicine Protection and Utilization, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
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11
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Deng H, Nakamoto T. Biosensors for Odor Detection: A Review. BIOSENSORS 2023; 13:1000. [PMID: 38131760 PMCID: PMC10741685 DOI: 10.3390/bios13121000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Animals can easily detect hundreds of thousands of odors in the environment with high sensitivity and selectivity. With the progress of biological olfactory research, scientists have extracted multiple biomaterials and integrated them with different transducers thus generating numerous biosensors. Those biosensors inherit the sensing ability of living organisms and present excellent detection performance. In this paper, we mainly introduce odor biosensors based on substances from animal olfactory systems. Several instances of organ/tissue-based, cell-based, and protein-based biosensors are described and compared. Furthermore, we list some other biological materials such as peptide, nanovesicle, enzyme, and aptamer that are also utilized in odor biosensors. In addition, we illustrate the further developments of odor biosensors.
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Affiliation(s)
| | - Takamichi Nakamoto
- Laboratory for Future Interdisciplinary Research of Science and Technology, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori, Yokohama 226-8503, Kanagawa, Japan;
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12
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Chang TW, Wang SH, Chin IS, Li PZ, Lo SC, Hsieh SY, Lin JH, Wei PK. Biomimetic affinity sensor for the ultrasensitive detection of neonicotinoids. Biosens Bioelectron 2023; 239:115630. [PMID: 37634420 DOI: 10.1016/j.bios.2023.115630] [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] [Received: 02/14/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Multiple pesticides are often used in combination to protect crops from pests. This makes rapid on-site detection of pesticide contamination challenging. Herein, we describe a method for simultaneous detection of diverse neonicotinoid pesticides using a sensor that combines neonicotinoid-specific odorant-binding protein 2 (OBP2), which was cloned from an insect chemical sensing protein and modified gold nanoparticles with local surface plasmon resonance (LSPR)-based digital nanoplasmonometry (DiNM). When neonicotinoid pesticides bind to OBP2 on gold nanoparticles, the induced LSPR shift peak wavelength is too small to be measured using conventional LSPR immunoassays. DiNM records and compares the scattered image intensity in two adjacent wavelength bands, A and B, centered on the LSPR peak. It considers both the peak shift and the relative intensity change in these two bands, resulting in a significant LSPR signal enhancement. Then the spectral-image contrast was computed as the signal response. Using this approach, we obtained excellent limits of detection (LODs) of 1.4, 1.5, and 4.5 ppb for the neonicotinoids imidacloprid, acetamiprid, and dinotefuran, respectively. Blind tests demonstrated high positive and negative rates for teas, approximately 85 and 100%, respectively. Recombinant OBP2 produced in E. coli offers several advantages over antibodies, including high yield, time savings, and cost effectiveness. Moreover, this method is highly selective and sensitive to neonicotinoids, making it practical for field use.
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Affiliation(s)
- Ting-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Sheng-Hann Wang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Iuan-Sheau Chin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Zhen Li
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shu-Cheng Lo
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Shu-Yi Hsieh
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan; Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Pei-Kuen Wei
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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13
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Saveleva L, Sima M, Klema J, Krejčík Z, Vartiainen P, Sitnikova V, Belaya I, Malm T, Jalava PI, Rössner P, Kanninen KM. Transcriptomic alterations in the olfactory bulb induced by exposure to air pollution: Identification of potential biomarkers and insights into olfactory system function. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 104:104316. [PMID: 37981204 DOI: 10.1016/j.etap.2023.104316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
This study evaluated how exposure to the ubiquitous air pollution component, ultrafine particles (UFPs), alters the olfactory bulb (OB) transcriptome. The study utilised a whole-body inhalation chamber to simulate real-life conditions and focused on UFPs due to their high translocation and deposition ability in OBs as well as their prevalence in ambient air. Female C57BL/6J mice were exposed to clean air or to freshly generated combustion derived UFPs for two weeks, after which OBs were dissected and mRNA transcripts were investigated using RNA sequencing analysis. For the first time, transcriptomics was applied to determine changes in mRNA expression levels occurring after subacute exposure to UFPs in the OBs. We found forty-five newly described mRNAs to be involved in air pollution-induced responses, including genes involved in odorant binding, synaptic regulation, and myelination signalling pathway, providing new gene candidates for future research. This study provides new insights for the environmental science and neuroscience fields and nominates future research directions.
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Affiliation(s)
- Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Jugoslávských partyzánů 1580/3, Prague 160 00, Czech Republic
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Petra Vartiainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Valeriia Sitnikova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irina Belaya
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pasi I Jalava
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pavel Rössner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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14
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Han WK, Tang FX, Yu N, Zhang YX, Liu ZW. A nonsensory odorant-binding protein plays an important role in the larval development and adult mating of Spodoptera frugiperda. INSECT SCIENCE 2023; 30:1325-1336. [PMID: 36647341 DOI: 10.1111/1744-7917.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Odorant-binding proteins (OBPs) play key roles in the perception of semiochemicals in insects. Several OBPs in insect olfactory systems have been functionally characterized, and they provide excellent targets for pest control. The functions of some OBPs that are highly expressed in the nonsensory organs of insects remain unclear. Here, the physiological function of an OBP (OBP27) that was highly expressed in the nonsensory organs of Spodoptera frugiperda was studied. OBP27 was nested within the Plus-C cluster according to phylogenetic analysis. The transcription of OBP27 steadily increased throughout the development of S. frugiperda, and transcripts of this gene were abundant in the fat body and male reproductive organs. An OBP27 knockout strain with an early frameshift mutation was obtained using the clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated protein 9 (Cas9) system. The development time of OBP27-/- larvae was significantly longer than that of other larvae. Both male and female OBP27-/- pupae weighed significantly less than wild-type (WT) pupae. In crosses of OBP27-/- males or females, the mating rate was lower and the mating duration was longer for OBP27-/- male-WT female pairs than for WT-WT pairs. By contrast, the mating rate, hatching rate, and number of eggs of OBP27-/- female-WT male pairs and WT-WT pairs were similar. These findings indicate that OBP27 plays an important role in the larval development and mating process in male adults. Generally, our findings provide new insights into the physiological roles of nonsensory OBPs.
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Affiliation(s)
- Wei-Kang Han
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng-Xian Tang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Na Yu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yi-Xi Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ze-Wen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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15
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Xiang D, Abdelnabby H, Wang MQ. Predicted structure of odorant-binding protein 12 from Monochamus alternatus (Hope) suggests a mechanism of flexible odorant-binding. Int J Biol Macromol 2023:125152. [PMID: 37270128 DOI: 10.1016/j.ijbiomac.2023.125152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/14/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Odorant-binding proteins (OBPs) are thought to bind and deliver hydrophobic odorants from the environment to receptors on insect sensory neurons, and have been used to screen behaviorally active compounds of insects. In order to screen behaviorally active compounds for Monochamus alternatus by OBPs, we cloned full length of Obp12 coding sequence from M. alternatus and proved secretion property of MaltOBP12, then tested binding affinities of recombinant MaltOBP12 to 12 pine volatiles in vitro. We confirmed MaltOBP12 has binding affinities to 9 pine volatiles. The structure of MaltOBP12 and protein-ligand interactions were further analyzed by homology modeling, molecular docking, site-directed mutagenesis, and ligand-binding assays. These results demonstrated that the binding pocket of MaltOBP12 consists of several large aromatic and hydrophobic residues, and four aromatic residues (Tyr50, Phe109, Tyr112, Phe122) are essential for odorant-binding; ligands adopt extensive hydrophobic interactions with an overlapping subset of residues in the binding pocket. Finally, based on non-directional hydrophobic interactions, MaltOBP12 binds odorants flexibly. These findings will not only help us understand how OBPs flexibly bind odorants but also promote to screen of behaviourally active compounds by computer methods to prevent M. alternatus in the future.
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Affiliation(s)
- Daokun Xiang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hazem Abdelnabby
- Department of Plant Protection, Faculty of Agriculture, Benha University, Banha, Qalyubia 13736, Egypt
| | - Man-Qun Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Silva L, Antunes A. Omics and Remote Homology Integration to Decipher Protein Functionality. Methods Mol Biol 2023; 2627:61-81. [PMID: 36959442 DOI: 10.1007/978-1-0716-2974-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
In the recent years, several "omics" technologies based on specific biomolecules (from DNA, RNA, proteins, or metabolites) have won growing importance in the scientific field. Despite each omics possess their own laboratorial protocols, they share a background of bioinformatic tools for data integration and analysis. A recent subset of bioinformatic tools, based on available templates or remote homology protocols, allow computational fast and high-accuracy prediction of protein structures. The quickly predict of actually unsolved protein structures, together with late omics findings allow a boost of scientific advances in multiple fields such as cancer, longevity, immunity, mitochondrial function, toxicology, drug design, biosensors, and recombinant protein engineering. In this chapter, we assessed methodological approaches for the integration of omics and remote homology inferences to decipher protein functionality, opening the door to the next era of biological knowledge.
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Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
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17
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Yamaguchi M, Tatara Y, Nugraha ED, Sato Y, Miura T, Hosoda M, Syaifudin M, Tokonami S, Kashiwakura I. Serum Proteomic and Oxidative Modification Profiling in Mice Exposed to Total Body X-Irradiation. Antioxidants (Basel) 2022; 11:antiox11091710. [PMID: 36139779 PMCID: PMC9495380 DOI: 10.3390/antiox11091710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/25/2022] Open
Abstract
The details of the dose-dependent response of serum proteins exposed to ionizing radiation, especially the oxidative modification response in amino acid sequences of albumin, the most abundant protein, are unknown. Thus, a proteomic analysis of the serum components from mice exposed to total body X-irradiation (TBI) ranging from 0.5 Gy to 3.0 Gy was conducted using LC-MS/MS. The analysis of oxidative modification sequences of albumin (mOMSA) in TBI mouse serum revealed significant moderate or strong correlations between the X-irradiation exposure dose and modification of 11 mOMSAs (especially the 97th, 267th and 499th lysine residues, 159th methionine residue and 287th tyrosine residues). In the case of X-irradiation of serum alone, significant correlations were also found in the 14 mOMSAs. In addition, a dose-dependent variation in six proteins (Angiotensinogen, Odorant-binding protein 1a, Serine protease inhibitor A3K, Serum paraoxonase/arylesterase 1, Prothrombin and Epidermal growth factor receptor) was detected in the serum of mice exposed to TBI. These findings suggest the possibility that the protein variation and serum albumin oxidative modification responses found in exposed individuals are important indicators for considering the effects of radiation on living organisms, along with DNA damage, and suggests their possible application as biomarkers of radiation dose estimation.
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Affiliation(s)
- Masaru Yamaguchi
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
| | - Yota Tatara
- Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Eka Djatnika Nugraha
- The Research Center for Safety, Metrology, and Nuclear Quality Technology (PRTKMMN), Research Organization for Nuclear Energy, National Research and Innovation Agency of Indonesia (BRIN), JI. Lebak Bulus Raya No. 49, Jakarta Selatan 12440, DKI Jakarta, Indonesia
| | - Yoshiaki Sato
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
| | - Tomisato Miura
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Masahiro Hosoda
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Mukh Syaifudin
- Research Center for Radioisotope, Radiopharmaceutical and Biodosimetry Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, Kw. Puspiptek, Setu, Tangerang Selatan 15312, Banten, Indonesia
| | - Shinji Tokonami
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Ikuo Kashiwakura
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
- Correspondence:
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Wasilewski T, Brito NF, Szulczyński B, Wojciechowski M, Buda N, Melo ACA, Kamysz W, Gębicki J. Olfactory Receptor-based Biosensors as Potential Future Tools in Medical Diagnosis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Coelho CMM, Pereira R, Vieira TF, Teixeira CM, Fernandes MJG, Rodrigues ARO, Pereira DM, Sousa S, Gil Fortes A, Castanheira EMS, T Gonçalves MS. Synthesis, computational and nanoencapsulation studies on eugenol-derived insecticides. NEW J CHEM 2022. [DOI: 10.1039/d2nj01893d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new set of alkoxy alcohols were synthesised by reaction of eugenol oxirane with aliphatic and aromatic alcohols. These eugenol derivatives were evaluated against their effect upon the viability of...
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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