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Mei S, Yao S, Mo J, Wang Y, Tang J, Li W, Wu T. Integration of cloud-based molecular networking and docking for enhanced umami peptide screening from Pixian douban. Food Chem X 2024; 21:101098. [PMID: 38229673 PMCID: PMC10790023 DOI: 10.1016/j.fochx.2023.101098] [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: 10/15/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
This study presents an innovative cloud-based approach, using Pixian Douban, a well-known Chinese fermented seasoning, as a case study, to improve the identification of umami peptides and explore their interactions with the T1R1/T1R3 receptor. A feature-based molecular networking method was utilized to rapidly identify a total of eighteen peptides, including seven previously unrecorded ones. Notably, the umami threshold of QIVK in an aqueous solution was determined to be 0.3215 mmol/L, surpassing the majority of peptides reported in the past three years. Molecular docking analysis further revealed the strong binding of QIVK to T1R3 receptor residues through hydrogen bonds, as well as interactions via salt bridges and electrostatic attractions. As a result, this research significantly contributes to the efficient screening of umami peptides and the elucidation of the molecular basis of umami sensory perception in complex food systems.
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Affiliation(s)
- Sen Mei
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
| | - Shanshan Yao
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
| | - Jingjing Mo
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
| | - Yi Wang
- Xi'an Jiaotong University, No. 28 Xinning West Road, Xi'an, Shaanxi, 710049, China
| | - Jie Tang
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
| | - Weili Li
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
| | - Tao Wu
- Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, No.999 Guangchang Road, Chengdu 610039, China
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Kotimoole CN, Ramya VK, Kaur P, Reiling N, Shandil RK, Narayanan S, Flo TH, Prasad TSK. Discovery of Species-Specific Proteotypic Peptides To Establish a Spectral Library Platform for Identification of Nontuberculosis Mycobacteria from Mass Spectrometry-Based Proteomics. J Proteome Res 2024; 23:1102-1117. [PMID: 38358903 DOI: 10.1021/acs.jproteome.3c00850] [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: 02/17/2024]
Abstract
Nontuberculous mycobacteria are opportunistic bacteria pulmonary and extra-pulmonary infections in humans that closely resemble Mycobacterium tuberculosis. Although genome sequencing strategies helped determine NTMs, a common assay for the detection of coinfection by multiple NTMs with M. tuberculosis in the primary attempt of diagnosis is still elusive. Such a lack of efficiency leads to delayed therapy, an inappropriate choice of drugs, drug resistance, disease complications, morbidity, and mortality. Although a high-resolution LC-MS/MS-based multiprotein panel assay can be developed due to its specificity and sensitivity, it needs a library of species-specific peptides as a platform. Toward this, we performed an analysis of proteomes of 9 NTM species with more than 20 million peptide spectrum matches gathered from 26 proteome data sets. Our metaproteomic analyses determined 48,172 species-specific proteotypic peptides across 9 NTMs. Notably, M. smegmatis (26,008), M. abscessus (12,442), M. vaccae (6487), M. fortuitum (1623), M. avium subsp. paratuberculosis (844), M. avium subsp. hominissuis (580), and M. marinum (112) displayed >100 species-specific proteotypic peptides. Finally, these peptides and corresponding spectra have been compiled into a spectral library, FASTA, and JSON formats for future reference and validation in clinical cohorts by the biomedical community for further translation.
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Affiliation(s)
- Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Vadageri Krishnamurthy Ramya
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - Radha Krishan Shandil
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Shridhar Narayanan
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, Øya 424.04.035, Norway
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Zuo T, Xie Q, Liu J, Yang J, Shi J, Kong D, Wang Y, Zhang Z, Gao H, Zeng DB, Wang X, Tao P, Wei W, Wang J, Li Y, Long Q, Li C, Chang L, Ning H, Li Y, Cui C, Ge X, Wu J, Li G, Hong X, Yang X, Dai E, He F, Wu J, Ruan Y, Lu S, Xu P. Macrophage-Derived Cathepsin S Remodels the Extracellular Matrix to Promote Liver Fibrogenesis. Gastroenterology 2023; 165:746-761.e16. [PMID: 37263311 DOI: 10.1053/j.gastro.2023.05.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND & AIMS Liver fibrosis is an intrinsic wound-healing response to chronic injury and the major cause of liver-related morbidity and mortality worldwide. However, no effective diagnostic or therapeutic strategies are available, owing to its poorly characterized molecular etiology. We aimed to elucidate the mechanisms underlying liver fibrogenesis. METHODS We performed a quantitative proteomic analysis of clinical fibrotic liver samples to identify dysregulated proteins. Further analyses were performed on the sera of 164 patients with liver fibrosis. Two fibrosis mouse models and several biochemical experiments were used to elucidate liver fibrogenesis. RESULTS We identified cathepsin S (CTSS) up-regulation as a central node for extracellular matrix remodeling in the human fibrotic liver by proteomic screening. Increased serum CTSS levels efficiently predicted liver fibrosis, even at an early stage. Secreted CTSS cleaved collagen 18A1 at its C-terminus, releasing endostatin peptide, which directly bound to and activated hepatic stellate cells via integrin α5β1 signaling, whereas genetic ablation of Ctss remarkably suppressed liver fibrogenesis via endostatin reduction in vivo. Further studies identified macrophages as the main source of hepatic CTSS, and splenectomy effectively attenuated macrophage infiltration and CTSS expression in the fibrotic liver. Pharmacologic inhibition of CTSS ameliorated liver fibrosis progression in the mouse models. CONCLUSIONS CTSS functions as a novel profibrotic factor by remodeling extracellular matrix proteins and may represent a promising target for the diagnosis and treatment of liver fibrosis.
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Affiliation(s)
- Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Qi Xie
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China; Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jinfang Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Degang Kong
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, Key Laboratory of Digital Hepatobiliary Surgery, Chinese People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yin Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Huixia Gao
- Second Department of Internal Medicine, Shijiazhuang Fifth Hospital, Shijiazhuang, China
| | - Dao-Bing Zeng
- Bejing You-An Hospital, Capital Medical University, Beijing, China
| | - Xinxin Wang
- Bejing You-An Hospital, Capital Medical University, Beijing, China
| | - Ping Tao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; Bejing You-An Hospital, Capital Medical University, Beijing, China
| | - Wei Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Jun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Long
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Chonghui Li
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, Key Laboratory of Digital Hepatobiliary Surgery, Chinese People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Huimin Ning
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Chunping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Xinlan Ge
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, Key Laboratory of Digital Hepatobiliary Surgery, Chinese People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jushan Wu
- Bejing You-An Hospital, Capital Medical University, Beijing, China
| | - Guangming Li
- Bejing You-An Hospital, Capital Medical University, Beijing, China
| | - Xuechuan Hong
- TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Erhei Dai
- Second Department of Internal Medicine, Shijiazhuang Fifth Hospital, Shijiazhuang, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Junzhu Wu
- TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
| | - Yuanyuan Ruan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Shichun Lu
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, Key Laboratory of Digital Hepatobiliary Surgery, Chinese People's Liberation Army Medical School, Chinese People's Liberation Army General Hospital, Beijing, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics and Research and Development of New Drug, Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China; TaiKang Medical School (School of Basic Medical Sciences), Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Guizhou University, School of Medicine, Guiyang, China.
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