1
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Claereboudt EJS, Dandamudi M, Longueville L, Harb HY, Lynagh T. Flipped binding modes for the same agonist in closely related neuropeptide-gated ion channels. Biophys J 2025; 124:1049-1057. [PMID: 39801005 PMCID: PMC11993918 DOI: 10.1016/j.bpj.2025.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 12/06/2024] [Accepted: 01/10/2025] [Indexed: 01/31/2025] Open
Abstract
Neuropeptides are inter-cellular signaling molecules occurring throughout animals. Most neuropeptides bind and activate G-protein-coupled receptors, but some also activate ionotropic receptors (or "ligand-gated ion channels"). This is exemplified by the tetra-peptide H-Phe-Met-Arg-Phe-NH2 (FMRFamide (FMRFa)), which activates mollusk and annelid FMRFa-gated sodium channels (FaNaCs) from the trimeric degenerin/epithelial sodium channel superfamily. Here, we explored the structure-activity relationships determining FMRFa potency at mollusk and annelid FaNaCs in the light of emerging structural data, using synthetic neuropeptide analogs, heterologous expression, and two-electrode voltage clamp. Substitutions of the FMRFa N-terminal phenylalanine residue (F1) and methionine residue (M2) decreased or abolished FMRFa potency at mollusk Aplysia kurodai FaNaC but had little effect at annelid Malacoceros fuliginosus FaNaC1. Conversely, F4 substitutions had little effect on FMRFa potency at A. kurodai FaNaC but either abolished, strongly decreased, or slightly increased potency at M. fuliginosus FaNaC1. Accordingly, recently published high-resolution FaNaC structures show that F1 and F4 residues orient deep into the neuropeptide-binding pockets of A. kurodai FaNaC and M. fuliginosus FaNaC1, respectively. We also use noncanonical amino acid substitutions in A. kurodai FaNaC to describe the physico-chemical determinants of FMRFa F1 binding to A. kurodai FaNaC aromatic side chains. Our results show that the "deeper" of the two FMRFa phenylalanine residues in the binding pocket is crucial for FMRFa potency despite the peptide orienting very differently into the homologous binding sites of two closely related receptors.
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Affiliation(s)
| | | | | | - Hassan Y Harb
- Concept Life Sciences Limited, Chapel-en-le-Frith, UK
| | - Timothy Lynagh
- Michael Sars Centre, University of Bergen, Bergen, Norway.
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2
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Hashemi S, Vosough P, Taghizadeh S, Savardashtaki A. Therapeutic peptide development revolutionized: Harnessing the power of artificial intelligence for drug discovery. Heliyon 2024; 10:e40265. [PMID: 39605829 PMCID: PMC11600032 DOI: 10.1016/j.heliyon.2024.e40265] [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: 02/20/2024] [Revised: 10/07/2024] [Accepted: 11/07/2024] [Indexed: 11/29/2024] Open
Abstract
Due to the spread of antibiotic resistance, global attention is focused on its inhibition and the expansion of effective medicinal compounds. The novel functional properties of peptides have opened up new horizons in personalized medicine. With artificial intelligence methods combined with therapeutic peptide products, pharmaceuticals and biotechnology advance drug development rapidly and reduce costs. Short-chain peptides inhibit a wide range of pathogens and have great potential for targeting diseases. To address the challenges of synthesis and sustainability, artificial intelligence methods, namely machine learning, must be integrated into their production. Learning methods can use complicated computations to select the active and toxic compounds of the drug and its metabolic activity. Through this comprehensive review, we investigated the artificial intelligence method as a potential tool for finding peptide-based drugs and providing a more accurate analysis of peptides through the introduction of predictable databases for effective selection and development.
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Affiliation(s)
- Samaneh Hashemi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parisa Vosough
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Taghizadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Watteyne J, Chudinova A, Ripoll-Sánchez L, Schafer WR, Beets I. Neuropeptide signaling network of Caenorhabditis elegans: from structure to behavior. Genetics 2024; 228:iyae141. [PMID: 39344922 PMCID: PMC11538413 DOI: 10.1093/genetics/iyae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/19/2024] [Indexed: 10/01/2024] Open
Abstract
Neuropeptides are abundant signaling molecules that control neuronal activity and behavior in all animals. Owing in part to its well-defined and compact nervous system, Caenorhabditis elegans has been one of the primary model organisms used to investigate how neuropeptide signaling networks are organized and how these neurochemicals regulate behavior. We here review recent work that has expanded our understanding of the neuropeptidergic signaling network in C. elegans by mapping the evolutionary conservation, the molecular expression, the receptor-ligand interactions, and the system-wide organization of neuropeptide pathways in the C. elegans nervous system. We also describe general insights into neuropeptidergic circuit motifs and the spatiotemporal range of peptidergic transmission that have emerged from in vivo studies on neuropeptide signaling. With efforts ongoing to chart peptide signaling networks in other organisms, the C. elegans neuropeptidergic connectome can serve as a prototype to further understand the organization and the signaling dynamics of these networks at organismal level.
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Affiliation(s)
- Jan Watteyne
- Department of Biology, University of Leuven, Leuven 3000, Belgium
| | | | - Lidia Ripoll-Sánchez
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Psychiatry, Cambridge University, Cambridge CB2 0SZ, UK
| | - William R Schafer
- Department of Biology, University of Leuven, Leuven 3000, Belgium
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Isabel Beets
- Department of Biology, University of Leuven, Leuven 3000, Belgium
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4
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Mao RT, Guo SQ, Zhang G, Li YD, Xu JP, Wang HY, Fu P, Liu CP, Wu SQ, Chen P, Mei YS, Jin QC, Liu CY, Zhang YCF, Ding XY, Liu WJ, Romanova EV, Zhou HB, Cropper EC, Checco JW, Sweedler JV, Jing J. Two C-terminal isoforms of Aplysia tachykinin-related peptide receptors exhibit phosphorylation-dependent and phosphorylation-independent desensitization mechanisms. J Biol Chem 2024; 300:107556. [PMID: 39002683 PMCID: PMC11365428 DOI: 10.1016/j.jbc.2024.107556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/27/2024] [Accepted: 06/30/2024] [Indexed: 07/15/2024] Open
Abstract
Diversity, a hallmark of G protein-coupled receptor (GPCR) signaling, partly stems from alternative splicing of a single gene generating more than one isoform for a receptor. Additionally, receptor responses to ligands can be attenuated by desensitization upon prolonged or repeated ligand exposure. Both phenomena have been demonstrated and exemplified by the deuterostome tachykinin signaling system, although the role of phosphorylation in desensitization remains a subject of debate. Here, we describe the signaling system for tachykinin-related peptides (TKRPs) in a protostome, mollusk Aplysia. We cloned the Aplysia TKRP precursor, which encodes three TKRPs (apTKRP-1, apTKRP-2a, and apTKRP-2b) containing the FXGXR-amide motif. In situ hybridization and immunohistochemistry showed predominant expression of TKRP mRNA and peptide in the cerebral ganglia. TKRPs and their posttranslational modifications were observed in extracts of central nervous system ganglia using mass spectrometry. We identified two Aplysia TKRP receptors (apTKRPRs), named apTKRPR-A and apTKRPR-B. These receptors are two isoforms generated through alternative splicing of the same gene and differ only in their intracellular C termini. Structure-activity relationship analysis of apTKRP-2b revealed that both C-terminal amidation and conserved residues of the ligand are critical for receptor activation. C-terminal truncates and mutants of apTKRPRs suggested that there is a C-terminal phosphorylation-independent desensitization for both receptors. Moreover, apTKRPR-B also exhibits phosphorylation-dependent desensitization through the phosphorylation of C-terminal Ser/Thr residues. This comprehensive characterization of the Aplysia TKRP signaling system underscores the evolutionary conservation of the TKRP and TK signaling systems, while highlighting the intricacies of receptor regulation through alternative splicing and differential desensitization mechanisms.
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Affiliation(s)
- Rui-Ting Mao
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Shi-Qi Guo
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Guo Zhang
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
| | - Ya-Dong Li
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ju-Ping Xu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Hui-Ying Wang
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ping Fu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Cui-Ping Liu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Shao-Qian Wu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Ping Chen
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yu-Shuo Mei
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Qing-Chun Jin
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Cheng-Yi Liu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yan-Chu-Fei Zhang
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xue-Ying Ding
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Wei-Jia Liu
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hai-Bo Zhou
- School of Electronic Science and Engineering, Nanjing University, Nanjing, Jiangsu, China; Peng Cheng Laboratory, Shenzhen, China.
| | - Elizabeth C Cropper
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jian Jing
- Department of Neurology and Medical Psychology, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Peng Cheng Laboratory, Shenzhen, China; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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5
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Hai-Na Z, Jun-Jie J, Guang-Meng X. Peptides derived from growth factors: Exploring their diverse impact from antimicrobial properties to neuroprotection. Biomed Pharmacother 2024; 176:116830. [PMID: 38824833 DOI: 10.1016/j.biopha.2024.116830] [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: 01/29/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024] Open
Abstract
Growth factor-derived peptides are bioactive molecules that play a crucial role in various physiological processes within the human body. Over the years, extensive research has revealed their diverse applications, ranging from antimicrobial properties to their potential in neuroprotection and treating various diseases. These peptides exhibit innate immune responses and have been found to possess potent antimicrobial properties against a wide range of pathogens. Growth factor-derived peptides have demonstrated the ability to promote neuronal survival, prevent cell death, and stimulate neural regeneration. As a result, they hold immense promise in the treatment of various neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis, as well as in the management of traumatic brain injuries. Moreover, growth factor-derived peptides have shown potential for supporting tissue repair and wound healing processes. By enhancing cell proliferation and migration, these peptides contribute to the regeneration of damaged tissues and promote a more efficient healing response. The applications of growth factor-derived peptides extend beyond their therapeutic potential in health; they also have a role in various disease conditions. For example, researchers have explored their influence on cancer cells, where some peptides have demonstrated anti-cancer properties, inhibiting tumor growth and promoting apoptosis in cancer cells. Additionally, their immunomodulatory properties have been investigated for potential applications in autoimmune disorders. Despite the immense promise shown by growth factor-derived peptides, some challenges need to be addressed. Nevertheless, ongoing research and advancements in biotechnology offer promising avenues to overcome these obstacles. The review summarizes the foundational biology of growth factors and the intricate signaling pathways in various physiological processes as well as diseases such as cancer, neurodegenerative disorders, cardiovascular ailments, and metabolic syndromes.
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Affiliation(s)
- Zhang Hai-Na
- Department of Rehabilitation, The Second Hospital of Jilin University, Changchun 130000, PR China
| | - Jiang Jun-Jie
- Department of Rehabilitation, The Second Hospital of Jilin University, Changchun 130000, PR China
| | - Xu Guang-Meng
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun 130000, PR China.
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6
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Sharma S, Naldrett MJ, Gill MJ, Checco JW. Affinity-Driven Aryl Diazonium Labeling of Peptide Receptors on Living Cells. J Am Chem Soc 2024; 146:13676-13688. [PMID: 38693710 PMCID: PMC11149697 DOI: 10.1021/jacs.4c04672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Peptide-receptor interactions play critical roles in a wide variety of physiological processes. Methods to link bioactive peptides covalently to unmodified receptors on the surfaces of living cells are valuable for studying receptor signaling, dynamics, and trafficking and for identifying novel peptide-receptor interactions. Here, we utilize peptide analogues bearing deactivated aryl diazonium groups for the affinity-driven labeling of unmodified receptors. We demonstrate that aryl diazonium-bearing peptide analogues can covalently label receptors on the surface of living cells using both the neurotensin and the glucagon-like peptide 1 receptor systems. Receptor labeling occurs in the complex environment of the cell surface in a sequence-specific manner. We further demonstrate the utility of this covalent labeling approach for the visualization of peptide receptors by confocal fluorescence microscopy and for the enrichment and identification of labeled receptors by mass spectrometry-based proteomics. Aryl diazonium-based affinity-driven receptor labeling is attractive due to the high abundance of tyrosine and histidine residues susceptible to azo coupling in the peptide binding sites of receptors, the ease of incorporation of aryl diazonium groups into peptides, and the relatively small size of the aryl diazonium group. This approach should prove to be a powerful and relatively general method to study peptide-receptor interactions in cellular contexts.
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Affiliation(s)
- Sheryl Sharma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Michael J Naldrett
- Proteomics and Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Makayla J Gill
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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7
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Park SB, Yang Y, Bang SI, Kim TS, Cho D. AESIS-1, a Rheumatoid Arthritis Therapeutic Peptide, Accelerates Wound Healing by Promoting Fibroblast Migration in a CXCR2-Dependent Manner. Int J Mol Sci 2024; 25:3937. [PMID: 38612747 PMCID: PMC11012285 DOI: 10.3390/ijms25073937] [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: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
In patients with autoimmune disorders such as rheumatoid arthritis (RA), delayed wound healing is often observed. Timely and effective wound healing is a crucial determinant of a patient's quality of life, and novel materials for skin wound repair, such as bioactive peptides, are continuously being studied and developed. One such bioactive peptide, AESIS-1, has been studied for its well-established anti-rheumatoid arthritis properties. In this study, we attempted to use the anti-RA material AESIS-1 as a therapeutic wound-healing agent based on disease-modifying antirheumatic drugs (DMARDs), which can help restore prompt wound healing. The efficacy of AESIS-1 in wound healing was assessed using a full-thickness excision model in diabetic mice; this is a well-established model for studying chronic wound repair. Initial observations revealed that mice treated with AESIS-1 exhibited significantly advanced wound repair compared with the control group. In vitro studies revealed that AESIS-1 increased the migration activity of human dermal fibroblasts (HDFs) without affecting proliferative activity. Moreover, increased HDF cell migration is mediated by upregulating chemokine receptor expression, such as that of CXC chemokine receptor 2 (CXCR2). The upregulation of CXCR2 through AESIS-1 treatment enhanced the chemotactic reactivity to CXCR2 ligands, including CXC motif ligand 8 (CXCL8). AESIS-1 directly activates the ERK and p38 mitogen-activated protein kinase (MAPK) signaling cascades, which regulate the migration and expression of CXCR2 in fibroblasts. Our results suggest that the AESIS-1 peptide is a strong wound-healing substance that increases the movement of fibroblasts and the expression of CXCR2 by turning on the ERK and p38 MAPK signaling cascades.
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Affiliation(s)
- Seung Beom Park
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Yoolhee Yang
- Kine Sciences, 6F, 24, Eonju-ro85gil, Gangnam-gu, Seoul 06221, Republic of Korea; (Y.Y.); (D.C.)
| | - Sa Ik Bang
- Department of Plastic Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Gangnam-gu, Seoul 06351, Republic of Korea;
| | - Tae Sung Kim
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Daeho Cho
- Kine Sciences, 6F, 24, Eonju-ro85gil, Gangnam-gu, Seoul 06221, Republic of Korea; (Y.Y.); (D.C.)
- Institute of Convergence Science, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 02841, Republic of Korea
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8
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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9
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Beets I, Zels S, Vandewyer E, Demeulemeester J, Caers J, Baytemur E, Courtney A, Golinelli L, Hasakioğulları İ, Schafer WR, Vértes PE, Mirabeau O, Schoofs L. System-wide mapping of peptide-GPCR interactions in C. elegans. Cell Rep 2023; 42:113058. [PMID: 37656621 PMCID: PMC7615250 DOI: 10.1016/j.celrep.2023.113058] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/19/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
Neuropeptides and peptide hormones are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many peptides remain elusive, as our insight into peptide-receptor interactions is limited and many peptide GPCRs are still orphan receptors. Here we report a genome-wide peptide-GPCR interaction map in Caenorhabditis elegans. By reverse pharmacology screening of over 55,384 possible interactions, we identify 461 cognate peptide-GPCR couples that uncover a broad signaling network with specific and complex combinatorial interactions encoded across and within single peptidergic genes. These interactions provide insights into peptide functions and evolution. Combining our dataset with phylogenetic analysis supports peptide-receptor co-evolution and conservation of at least 14 bilaterian peptidergic systems in C. elegans. This resource lays a foundation for system-wide analysis of the peptidergic network.
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Affiliation(s)
- Isabel Beets
- Department of Biology, KU Leuven, 3000 Leuven, Belgium.
| | - Sven Zels
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | | | - Jonas Demeulemeester
- The Francis Crick Institute, London NW1 1AT, UK; VIB - KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Jelle Caers
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Esra Baytemur
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Amy Courtney
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Petra E Vértes
- Department of Psychiatry, Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, UK
| | - Olivier Mirabeau
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Inserm U1224, Brain-Immune Communication Lab, 75015 Paris, France
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10
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Wang HY, Yu K, Liu WJ, Jiang HM, Guo SQ, Xu JP, Li YD, Chen P, Ding XY, Fu P, Zhang YCF, Mei YS, Zhang G, Zhou HB, Jing J. Molecular Characterization of Two Wamide Neuropeptide Signaling Systems in Mollusk Aplysia. ACS Chem Neurosci 2023. [PMID: 37339428 DOI: 10.1021/acschemneuro.3c00158] [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: 06/22/2023] Open
Abstract
Neuropeptides with the C-terminal Wamide (Trp-NH2) are one of the last common ancestors of peptide families of eumetazoans and play various physiological roles. In this study, we sought to characterize the ancient Wamide peptides signaling systems in the marine mollusk Aplysia californica, i.e., APGWamide (APGWa) and myoinhibitory peptide (MIP)/Allatostatin B (AST-B) signaling systems. A common feature of protostome APGWa and MIP/AST-B peptides is the presence of a conserved Wamide motif in the C-terminus. Although orthologs of the APGWa and MIP signaling systems have been studied to various extents in annelids or other protostomes, no complete signaling systems have yet been characterized in mollusks. Here, through bioinformatics, molecular and cellular biology, we identified three receptors for APGWa, namely, APGWa-R1, APGWa-R2, and APGWa-R3. The EC50 values for APGWa-R1, APGWa-R2, and APGWa-R3 are 45, 2100, and 2600 nM, respectively. For the MIP signaling system, we predicted 13 forms of peptides, i.e., MIP1-13 that could be generated from the precursor identified in our study, with MIP5 (WKQMAVWa) having the largest number of copies (4 copies). Then, a complete MIP receptor (MIPR) was identified and the MIP1-13 peptides activated the MIPR in a dose-dependent manner, with EC50 values ranging from 40 to 3000 nM. Peptide analogs with alanine substitution experiments demonstrated that the Wamide motif at the C-terminus is necessary for receptor activity in both the APGWa and MIP systems. Moreover, cross-activity between the two signaling systems showed that MIP1, 4, 7, and 8 ligands could activate APGWa-R1 with a low potency (EC50 values: 2800-22,000 nM), which further supported that the APGWa and MIP signaling systems are somewhat related. In summary, our successful characterization of Aplysia APGWa and MIP signaling systems represents the first example in mollusks and provides an important basis for further functional studies in this and other protostome species. Moreover, this study may be useful for elucidating and clarifying the evolutionary relationship between the two Wamide signaling systems (i.e., APGWa and MIP systems) and their other extended neuropeptide signaling systems.
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Affiliation(s)
- Hui-Ying Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ke Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wei-Jia Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hui-Min Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shi-Qi Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ju-Ping Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ya-Dong Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xue-Ying Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ping Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan-Chu-Fei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yu-Shuo Mei
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Guo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hai-Bo Zhou
- Peng Cheng Laboratory, Shenzhen 518000, China
- School of Electronic Science and Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
- Peng Cheng Laboratory, Shenzhen 518000, China
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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11
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Fu P, Mei YS, Liu WJ, Chen P, Jin QC, Guo SQ, Wang HY, Xu JP, Zhang YCF, Ding XY, Liu CP, Liu CY, Mao RT, Zhang G, Jing J. Identification of three elevenin receptors and roles of elevenin disulfide bond and residues in receptor activation in Aplysia californica. Sci Rep 2023; 13:7662. [PMID: 37169790 PMCID: PMC10175484 DOI: 10.1038/s41598-023-34596-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
Neuropeptides are ubiquitous intercellular signaling molecules in the CNS and play diverse roles in modulating physiological functions by acting on specific G-protein coupled receptors (GPCRs). Among them, the elevenin signaling system is now believed to be present primarily in protostomes. Although elevenin was first identified from the L11 neuron of the abdominal ganglion in mollusc Aplysia californica, no receptors have been described in Aplysia, nor in any other molluscs. Here, using two elevenin receptors in annelid Platynereis dumerilii, we found three putative elevenin GPCRs in Aplysia. We cloned the three receptors and tentatively named them apElevR1, apElevR2, and apElevR3. Using an inositol monophosphate (IP1) accumulation assay, we demonstrated that Aplysia elevenin with the disulfide bond activated the three putative receptors with low EC50 values (ranging from 1.2 to 25 nM), supporting that they are true receptors for elevenin. In contrast, elevenin without the disulfide bond could not activate the receptors, indicating that the disulfide bond is required for receptor activity. Using alanine substitution of individual conserved residues other than the two cysteines, we showed that these residues appear to be critical to receptor activity, and the three different receptors had different sensitivities to the single residue substitution. Finally, we examined the roles of those residues outside the disulfide bond ring by removing these residues and found that they also appeared to be important to receptor activity. Thus, our study provides an important basis for further study of the functions of elevenin and its receptors in Aplysia and other molluscs.
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Affiliation(s)
- Ping Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Yu-Shuo Mei
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Wei-Jia Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Qing-Chun Jin
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Shi-Qi Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Hui-Ying Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Ju-Ping Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Yan-Chu-Fei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Xue-Ying Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Cui-Ping Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Cheng-Yi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Rui-Ting Mao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Guo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China.
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medical Psychology and Neurology, Nanjing Drum Tower Hospital, Institute for Brain Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China.
- Peng Cheng Laboratory, Shenzhen, 518000, China.
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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12
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Xu JP, Ding XY, Guo SQ, Wang HY, Liu WJ, Jiang HM, Li YD, Fu P, Chen P, Mei YS, Zhang G, Zhou HB, Jing J. Characterization of an Aplysia vasotocin signaling system and actions of posttranslational modifications and individual residues of the ligand on receptor activity. Front Pharmacol 2023; 14:1132066. [PMID: 37021048 PMCID: PMC10067623 DOI: 10.3389/fphar.2023.1132066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
The vasopressin/oxytocin signaling system is present in both protostomes and deuterostomes and plays various physiological roles. Although there were reports for both vasopressin-like peptides and receptors in mollusc Lymnaea and Octopus, no precursor or receptors have been described in mollusc Aplysia. Here, through bioinformatics, molecular and cellular biology, we identified both the precursor and two receptors for Aplysia vasopressin-like peptide, which we named Aplysia vasotocin (apVT). The precursor provides evidence for the exact sequence of apVT, which is identical to conopressin G from cone snail venom, and contains 9 amino acids, with two cysteines at position 1 and 6, similar to nearly all vasopressin-like peptides. Through inositol monophosphate (IP1) accumulation assay, we demonstrated that two of the three putative receptors we cloned from Aplysia cDNA are true receptors for apVT. We named the two receptors as apVTR1 and apVTR2. We then determined the roles of post-translational modifications (PTMs) of apVT, i.e., the disulfide bond between two cysteines and the C-terminal amidation on receptor activity. Both the disulfide bond and amidation were critical for the activation of the two receptors. Cross-activity with conopressin S, annetocin from an annelid, and vertebrate oxytocin showed that although all three ligands can activate both receptors, the potency of these peptides differed depending on their residue variations from apVT. We, therefore, tested the roles of each residue through alanine substitution and found that each substitution could reduce the potency of the peptide analog, and substitution of the residues within the disulfide bond tended to have a larger impact on receptor activity than the substitution of those outside the bond. Moreover, the two receptors had different sensitivities to the PTMs and single residue substitutions. Thus, we have characterized the Aplysia vasotocin signaling system and showed how the PTMs and individual residues in the ligand contributed to receptor activity.
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Affiliation(s)
- Ju-Ping Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Xue-Ying Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Shi-Qi Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Hui-Ying Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Wei-Jia Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Hui-Min Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Ya-Dong Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Ping Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Yu-Shuo Mei
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Guo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
| | - Hai-Bo Zhou
- School of Electronic Science and Engineering, Nanjing University, Nanjing, Jiangsu, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Chemistry and Biomedicine Innovation Center, Institute for Brain Sciences, Advanced Institute for Life Sciences, School of Life Sciences, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, Nanjing University, Nanjing, Jiangsu, China
- Peng Cheng Laboratory, Shenzhen, China
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Satake H. Kobayashi Award 2021: Neuropeptides, receptors, and follicle development in the ascidian, Ciona intestinalis Type A: New clues to the evolution of chordate neuropeptidergic systems from biological niches. Gen Comp Endocrinol 2023; 337:114262. [PMID: 36925021 DOI: 10.1016/j.ygcen.2023.114262] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Ciona intestinalis Type A (Ciona robusta) is a cosmopolitan species belonging to the phylum Urochordata, invertebrate chordates that are phylogenetically the most closely related to the vertebrates. Therefore, this species is of interest for investigation of the evolution and comparative physiology of endocrine, neuroendocrine, and nervous systems in chordates. Our group has identified>30 Ciona neuropeptides (80% of all identified ascidian neuropeptides) primarily using peptidomic approaches combined with reference to genome sequences. These neuropeptides are classified into two groups: homologs or prototypes of vertebrate neuropeptides and novel (Ciona-specific) neuropeptides. We have also identified the cognate receptors for these peptides. In particular, we elucidated multiple receptors for Ciona-specific neuropeptides by a combination of a novel machine learning system and experimental validation of the specific interaction of the predicted neuropeptide-receptor pairs, and verified unprecedented phylogenies of receptors for neuropeptides. Moreover, several neuropeptides were found to play major roles in the regulation of ovarian follicle development. Ciona tachykinin facilitates the growth of vitellogenic follicles via up-regulation of the enzymatic activities of proteases. Ciona vasopressin stimulates oocyte maturation and ovulation via up-regulation of maturation-promoting factor- and matrix metalloproteinase-directed collagen degradation, respectively. Ciona cholecystokinin also triggers ovulation via up-regulation of receptor tyrosine kinase signaling and the subsequent activation of matrix metalloproteinase. These studies revealed that the neuropeptidergic system plays major roles in ovarian follicle growth, maturation, and ovulation in Ciona, thus paving the way for investigation of the biological roles for neuropeptides in the endocrine, neuroendocrine, nervous systems of Ciona, and studies of the evolutionary processes of various neuropeptidergic systems in chordates.
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Affiliation(s)
- Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
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14
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Yussif BM, Blasing CV, Checco JW. Endogenous l- to d-amino acid residue isomerization modulates selectivity between distinct neuropeptide receptor family members. Proc Natl Acad Sci U S A 2023; 120:e2217604120. [PMID: 36877849 PMCID: PMC10089201 DOI: 10.1073/pnas.2217604120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/03/2023] [Indexed: 03/08/2023] Open
Abstract
The l- to d-amino acid residue isomerization of neuropeptides is an understudied post-translational modification found in animals across several phyla. Despite its physiological importance, little information is available regarding the impact of endogenous peptide isomerization on receptor recognition and activation. As a result, the full roles peptide isomerization play in biology are not well understood. Here, we identify that the Aplysia allatotropin-related peptide (ATRP) signaling system utilizes l- to d-residue isomerization of one amino acid residue in the neuropeptide ligand to modulate selectivity between two distinct G protein-coupled receptors (GPCRs). We first identified a novel receptor for ATRP that is selective for the D2-ATRP form, which bears a single d-phenylalanine residue at position 2. Using cell-based receptor activation experiments, we then characterized the stereoselectivity of the two known ATRP receptors for both endogenous ATRP diastereomers, as well as for homologous toxin peptides from a carnivorous predator. We found that the ATRP system displayed dual signaling through both the Gαq and Gαs pathways, and each receptor was selectively activated by one naturally occurring ligand diastereomer over the other. Overall, our results provide insights into an unexplored mechanism by which nature regulates intercellular communication. Given the challenges in detecting l- to d-residue isomerization from complex mixtures de novo and in identifying receptors for novel neuropeptides, it is likely that other neuropeptide-receptor systems may also utilize changes in stereochemistry to modulate receptor selectivity in a manner similar to that discovered here.
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Affiliation(s)
- Baba M. Yussif
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE68588
| | - Cole V. Blasing
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE68588
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE68588
- The Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE68588
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Satake H, Osugi T, Shiraishi A. Impact of Machine Learning-Associated Research Strategies on the Identification of Peptide-Receptor Interactions in the Post-Omics Era. Neuroendocrinology 2023; 113:251-261. [PMID: 34348315 DOI: 10.1159/000518572] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/19/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUNDS Elucidation of peptide-receptor pairs is a prerequisite for many studies in the neuroendocrine, endocrine, and neuroscience fields. Recent omics analyses have provided vast amounts of peptide and G protein-coupled receptor (GPCR) sequence data. GPCRs for homologous peptides are easily characterized based on homology searching, and the relevant peptide-GPCR interactions are also detected by typical signaling assays. In contrast, conventional evaluation or prediction methods, including high-throughput reverse-pharmacological assays and tertiary structure-based computational analyses, are not useful for identifying interactions between novel and omics-derived peptides and GPCRs. SUMMARY Recently, an approach combining machine learning-based prediction of novel peptide-GPCR pairs and experimental validation of the predicted pairs have been shown to breakthrough this bottleneck. A machine learning method, logistic regression for human class A GPCRs and the multiple subsequent signaling assays led to the deorphanization of human class A orphan GPCRs, namely, the identification of 18 peptide-GPCR pairs. Furthermore, using another machine learning algorithm, the support vector machine (SVM), the peptide descriptor-incorporated SVM was originally developed and employed to predict GPCRs for novel peptides characterized from the closest relative of vertebrates, Ciona intestinalis Type A (Ciona robusta). Experimental validation of the predicted pairs eventually led to the identification of 11 novel peptide-GPCR pairs. Of particular interest is that these newly identified GPCRs displayed neither significant sequence similarity nor molecular phylogenetic relatedness to known GPCRs for peptides. KEY MESSAGES These recent studies highlight the usefulness and versatility of machine learning for enabling the efficient, reliable, and systematic identification of novel peptide-GPCR interactions.
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Affiliation(s)
- Honoo Satake
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Tomohiro Osugi
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
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16
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AI protein structure prediction-based modeling and mutagenesis of a protostome receptor and peptide ligands reveal key residues for their interaction. J Biol Chem 2022; 298:102440. [PMID: 36049520 PMCID: PMC9562341 DOI: 10.1016/j.jbc.2022.102440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
The protostome leucokinin (LK) signaling system, including LK peptides and their G protein-coupled receptors, has been characterized in several species. Despite progress in this area, molecular mechanisms governing LK peptide-receptor interactions remain to be elucidated. Previously, we identified a precursor protein for Aplysia leucokinin-like peptides (ALKs) that contains the greatest number of amidated peptides among LK precursors in all species identified so far. Here, we identified the first ALK receptor from Aplysia, ALKR. We used cell-based IP1 activation assays to demonstrate that the two ALK peptides with the most copies, ALK1 and ALK2, activated ALKR with high potencies. Other endogenous ALK-derived peptides bearing the FXXWX-amide motif also activated ALKR to various degrees. Our examination of cross-species activity of ALKs with the Anopheles LKR was consistent with a critical role for the FXXWX-amide motif in receptor activity. Furthermore, we showed, through alanine substitution of ALK1, the highly conserved phenylalanine (F), tryptophan (W), and C-terminal amidation were each essential for receptor activation. Finally, we used an AI-based protein structure prediction server (Robetta) and Autodock Vina to predict the ligand-bound conformation of ALKR. Our model predicted several interactions (i.e., hydrophobic interactions, hydrogen bonds, and amide-pi stacking) between ALK peptides and ALKR, and several of our substitution and mutagenesis experiments were consistent with the predicted model. In conclusion, our results provide important information defining the possible interactions between ALK peptides and their receptors. The workflow utilized here may be useful for studying other ligand-receptor interactions for a neuropeptide signaling system, particularly in protostomes.
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Zhang G, Guo SQ, Yin SY, Yuan WD, Chen P, Kim JI, Wang HY, Zhou HB, Susswein AJ, Kaang BK, Jing J. Exogenous expression of an allatotropin-related peptide receptor increased the membrane excitability in Aplysia neurons. Mol Brain 2022; 15:42. [PMID: 35534865 PMCID: PMC9082908 DOI: 10.1186/s13041-022-00929-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/01/2022] [Indexed: 02/04/2023] Open
Abstract
Neuropeptides act mostly on a class of G-protein coupled receptors, and play a fundamental role in the functions of neural circuits underlying behaviors. However, physiological functions of some neuropeptide receptors are poorly understood. Here, we used the molluscan model system Aplysia and microinjected the exogenous neuropeptide receptor apATRPR (Aplysia allatotropin-related peptide receptor) with an expression vector (pNEX3) into Aplysia neurons that did not express the receptor endogenously. Physiological experiments demonstrated that apATRPR could mediate the excitability increase induced by its ligand, apATRP (Aplysia allatotropin-related peptide), in the Aplysia neurons that now express the receptor. This study provides a definitive evidence for a physiological function of a neuropeptide receptor in molluscan animals.
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Suchak V, Sathyanath S, Kakunje A. Neuropeptides in psychiatry. ARCHIVES OF MEDICINE AND HEALTH SCIENCES 2022. [DOI: 10.4103/amhs.amhs_91_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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