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Liu Y, Zhao Z, Song Y, Yin Y, Wu F, Jiang H. Usage of Cell-Free Protein Synthesis in Post-Translational Modification of μ-Conopeptide PIIIA. Mar Drugs 2023; 21:421. [PMID: 37623702 PMCID: PMC10455749 DOI: 10.3390/md21080421] [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: 05/08/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The post-translational modifications of conopeptides are the most complicated modifications to date and are well-known and closely related to the activity of conopeptides. The hydroxylation of proline in conopeptides affects folding, structure, and biological activity, and prolyl 4 hydroxylase has been characterized in Conus literatus. However, the hydroxylation machinery of proline in conopeptides is still unclear. In order to address the hydroxylation mechanism of proline in μ-PIIIA, three recombinant plasmids encoding different hybrid precursors of μ-PIIIA were constructed and crossly combined with protein disulfide isomerase, prolyl 4 hydroxylase, and glutaminyl cyclase in a continuous exchange cell-free protein system. The findings showed that prolyl 4 hydroxylase might recognize the propeptide of μ-PIIIA to achieve the hydroxylation of proline, while the cyclization of glutamate was also formed. Additionally, in Escherichia coli, the co-expression plasmid encoding prolyl 4 hydroxylase and the precursor of μ-PIIIA containing pro and mature regions were used to validate the continuous exchange cell-free protein system. Surprisingly, in addition to the two hydroxyproline residues and one pyroglutamyl residue, three disulfide bridges were formed using Trx as a fusion tag, and the yield of the fusion peptide was approximately 20 mg/L. The results of electrophysiology analysis indicated that the recombinant μ-PIIIA without C-terminal amidate inhibited the current of hNaV1.4 with a 939 nM IC50. Our work solved the issue that it was challenging to quickly generate post-translationally modified conopeptides in vitro. This is the first study to demonstrate that prolyl 4 hydroxylase catalyzes the proline hydroxylation through recognition in the propeptide of μ-PIIIA, and it will provide a new way for synthesizing multi-modified conopeptides with pharmacological activity.
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Affiliation(s)
| | | | | | | | | | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
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2
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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3
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Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations. Mar Drugs 2020; 18:md18100503. [PMID: 33019526 PMCID: PMC7601563 DOI: 10.3390/md18100503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
Marine cone snails belonging to the Conidae family make use of neuroactive peptides in their venom to capture prey. Here we report the proteome profile of the venom duct of Conus eburneus, a cone snail belonging to the Tesseliconus clade. Through tandem mass spectrometry and database searching against the C. eburneus transcriptome and the ConoServer database, we identified 24 unique conopeptide sequences in the venom duct. The majority of these peptides belong to the T and M gene superfamilies and are disulfide-bonded, with cysteine frameworks V, XIV, VI/VII, and III being the most abundant. All seven of the Cys-free peptides are conomarphin variants belonging to the M superfamily that eluted out as dominant peaks in the chromatogram. These conomarphins vary not only in amino acid residues in select positions along the backbone but also have one or more post-translational modifications (PTMs) such as proline hydroxylation, C-term amidation, and γ-carboxylation of glutamic acid. Using molecular dynamics simulations, the conomarphin variants were predicted to predominantly have hairpin-like or elongated structures in acidic pH. These two structures were found to have significant differences in electrostatic properties and the inclusion of PTMs seems to complement this disparity. The presence of polar PTMs (hydroxyproline and γ-carboxyglutamic acid) also appear to stabilize hydrogen bond networks in these conformations. Furthermore, these predicted structures are pH sensitive, becoming more spherical and compact at higher pH. The subtle conformational variations observed here might play an important role in the selection and binding of the peptides to their molecular targets.
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Jimenez EC. Bromotryptophan and its Analogs in Peptides from Marine Animals. Protein Pept Lett 2019; 26:251-260. [PMID: 30663557 DOI: 10.2174/0929866526666190119170020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 01/29/2023]
Abstract
Bromotryptophan is a nonstandard amino acid that is rarely incorporated in ribosomally synthesized and post-translationally modified peptides (ribosomal peptides). Bromotryptophan and its analogs sometimes occur in non-ribosomal peptides. This paper presents an overview of ribosomal and non-ribosomal peptides that are known to contain bromotryptophan and its analogs. This work further covers the biological activities and therapeutic potential of some of these peptides.
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Affiliation(s)
- Elsie C Jimenez
- Department of Physical Sciences, College of Science, University of the Philippines Baguio, Baguio City 2600, Philippines
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5
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Rajesh RP, Franklin JB, Badsha I, Arjun P, Jain RP, Vignesh MS, Kannan RR. Proteome based de novo sequencing of novel conotoxins from marine molluscivorous cone snail Conus amadis and neurological activities of its natural venom in zebrafish model. Protein Pept Lett 2019; 26:819-833. [PMID: 31203793 DOI: 10.2174/0929866526666190614144006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/09/2019] [Accepted: 04/19/2019] [Indexed: 11/22/2022]
Abstract
Conus amadis is a carnivorous snail found abundantly in coastal waters of India. They are equipped with potent chemical arsenal made of neurotoxic peptide concoction used for predation and competition. In this study, we have identified 19 novel conotoxins containing 1, 2 & 3 disulfides, belonging to different classes, from a molluscivorous cone snail Conus amadis using proteome based MALDI-TOF and LC-MS-MS analysis. Among them, 2 novel contryphans, 3 T-superfamily conotoxin, 2 A-superfamily conotoxins and 2 Mini M-Superfamily conotoxins were sequenced to its amino acid level from the fragmented spectrum of singly and doubly charged parent ions using de novo sequencing strategies. ama1054, a contryphan peptide toxin, possesses post translationally modified bromo tryptophan at its seventh position. Except ama1251, all the sequenced peptide toxins possess modified C-terminal amidation. Moreover, we have screened the crude venom for the presence of biological function in zebrafish model. Crude venom exhibited anticonvulsant properties in pentylenetetrazole-induced seizure in zebrafish larvae which suggested anti-epileptic properties of the venom cocktail. Acetyl cholinesterase activity was also identified in the venom complex.
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Affiliation(s)
- R P Rajesh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012. India
| | - Jayaseelan Benjamin Franklin
- Andaman and Nicobar Centre for Ocean Science and Technology, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103. India
| | - Iffath Badsha
- Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119. India
| | - P Arjun
- Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119. India
| | - Ruchi P Jain
- Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119. India
| | - M S Vignesh
- Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119. India
| | - R Rajesh Kannan
- Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119. India
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6
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Vijayasarathy M, Balaram P. Cone snail prolyl-4-hydroxylase α-subunit sequences derived from transcriptomic data and mass spectrometric analysis of variable proline hydroxylation in C. amadis venom. J Proteomics 2019; 194:37-48. [DOI: 10.1016/j.jprot.2018.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
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7
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Moitra P. A combinatorial approach of structure-based virtual screening and molecular dynamics simulation towards the discovery of a highly selective inhibitor for VP9 coat protein of Banna virus. Bioorg Chem 2019; 86:15-27. [PMID: 30684859 DOI: 10.1016/j.bioorg.2019.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/06/2019] [Accepted: 01/09/2019] [Indexed: 12/16/2022]
Abstract
Structure based virtual screening of two libraries containing 27,628 numbers of antiviral compounds was used to discover a few of the potent inhibitor molecules against Banna virus (BAV). Cross-docking studies with many common interfering proteins provided five of the highly selective inhibitor for BAV. Analyses of the leading molecules with ADME-Tox filtering tool and atomistic molecular dynamics simulation studies finally discovered a benzoxazolone derivative as one of the most promising molecules towards the highly selective inhibition of BAV. The theoretical calculations are also supported by the experimental evidences where the interactions between the hit ligand and a model peptide sequence, mimicking the VP9 protein of BAV, were studied. Overall the development of a personalized therapeutic towards the highly selective inhibition of BAV is discussed herein for the first time in literature.
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Affiliation(s)
- Parikshit Moitra
- Technical Research Centre, Indian Association for the Cultivation of Science, 2A & 2B Raja SC Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.
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Gao B, Peng C, Zhu Y, Sun Y, Zhao T, Huang Y, Shi Q. High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail ( Conus quercinus) by Transcriptome Sequencing. Int J Mol Sci 2018; 19:ijms19123901. [PMID: 30563163 PMCID: PMC6321112 DOI: 10.3390/ijms19123901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The primary objective of this study was to realize the large-scale discovery of conotoxin sequences from different organs (including the venom duct, venom bulb and salivary gland) of the vermivorous Oak cone snail, Conus quercinus. Using high-throughput transcriptome sequencing, we identified 133 putative conotoxins that belong to 34 known superfamilies, of which nine were previously reported while the remaining 124 were novel conotoxins, with 17 in new and unassigned conotoxin groups. A-, O1-, M-, and I2- superfamilies were the most abundant, and the cysteine frameworks XIII and VIII were observed for the first time in the A- and I2-superfamilies. The transcriptome data from the venom duct, venom bulb and salivary gland showed considerable inter-organizational variations. Each organ had many exclusive conotoxins, and only seven of all the inferred mature peptides were common in the three organs. As expected, most of the identified conotoxins were synthesized in the venom duct at relatively high levels; however, a number of conotoxins were also identified in the venom bulb and the salivary gland with very low transcription levels. Therefore, various organs have different conotoxins with high diversity, suggesting greater contributions from several organs to the high-throughput discovery of new conotoxins for future drug development.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Herbs, College of Pharmacy, Hainan Medical University, Haikou 571199, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yabing Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yuhui Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Tian Zhao
- Chemistry Department, College of Art and Science, Boston University, Boston, MA 02215, USA.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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Vijayasarathy M, Basheer SM, Balaram P. Cone Snail Glutaminyl Cyclase Sequences from Transcriptomic Analysis and Mass Spectrometric Characterization of Two Pyroglutamyl Conotoxins. J Proteome Res 2018; 17:2695-2703. [DOI: 10.1021/acs.jproteome.8b00132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Marimuthu Vijayasarathy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Soorej M. Basheer
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- Department of Molecular Biology, Kannur University, Nileshwaram Campus, Kasargod 671314, Kerala, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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