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Abdulbagi M, Di B, Li B. Resolving D-Amino Acid Containing Peptides Using Ion Mobility-Mass Spectrometry: Challenges and Recent Developments. Crit Rev Anal Chem 2023:1-10. [PMID: 37975700 DOI: 10.1080/10408347.2023.2282510] [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: 11/19/2023]
Abstract
Peptides and proteins having D-amino acids in their sequences are now believed to be widespread among different living organisms. Their significance is attributed to the diverse functions of these molecules, such as having a certain pathological implication or enhancing biological activity. Indeed, some peptide molecules with D-amino acids in their structure have already found their way to clinical use such as the antibacterial gramicidin and the antidiabetic nateglinide. Ion mobility mass spectrometry (IM-MS) added an additional dimension of separation as it depends on ions mobility in the space, which is dependent on their shapes, and the shape depends on the orientation of atoms. Thus, D-amino acids containing peptides (DAACPs) will have different mobility and collision cross-section values than those with L-amino acids. Eventually, this will lead to baseline separation of the two peptides. Additionally, ion mobility can precisely locate the position of D-amino acids by analyzing the difference in the arrival times of the fragment ions. The importance of DAACPs, as well as the difficulties in discovering them, were addressed in this review. Similarly, we emphasized how recent developments in IM-MS have improved their detection and analysis. Consequently, the LC-IM-MS/MS platform appears to be promising in isomeric mixture analysis.
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Affiliation(s)
- Mohamed Abdulbagi
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
| | - Bin Di
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Bo Li
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
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Tran P, Crawford T, Ragnarsson L, Deuis JR, Mobli M, Sharpe SJ, Schroeder CI, Vetter I. Structural Conformation and Activity of Spider-Derived Inhibitory Cystine Knot Peptide Pn3a Are Modulated by pH. ACS OMEGA 2023; 8:26276-26286. [PMID: 37521635 PMCID: PMC10373202 DOI: 10.1021/acsomega.3c02664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Numerous spider venom-derived gating modifier toxins exhibit conformational heterogeneity during purification by reversed-phase high-performance liquid chromatography (RP-HPLC). This conformational exchange is especially peculiar for peptides containing an inhibitor cystine knot motif, which confers excellent structural stability under conditions that are not conducive to disulfide shuffling. This phenomenon is often attributed to proline cis/trans isomerization but has also been observed in peptides that do not contain a proline residue. Pn3a is one such peptide forming two chromatographically distinguishable peaks that readily interconvert following the purification of either conformer. The nature of this exchange was previously uncharacterized due to the fast rate of conversion in solution, making isolation of the conformers impossible. In the present study, an N-terminal modification of Pn3a enabled the isolation of the individual conformers, allowing activity assays to be conducted on the individual conformers using electrophysiology. The conformers were analyzed separately by nuclear magnetic resonance spectroscopy (NMR) to study their structural differences. RP-HPLC and NMR were used to study the mechanism of exchange. The later-eluting conformer was the active conformer with a rigid structure that corresponds to the published structure of Pn3a, while NMR analysis revealed the earlier-eluting conformer to be inactive and disordered. The exchange was found to be pH-dependent, arising in acidic solutions, possibly due to reversible disruption and formation of intramolecular salt bridges. This study reveals the nature of non-proline conformational exchange observed in Pn3a and possibly other disulfide-rich peptides, highlighting that the structure and activity of some disulfide-stabilized peptides can be dramatically susceptible to disruption.
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Affiliation(s)
- Poanna Tran
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Theo Crawford
- Centre
for Advanced Imaging, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Lotten Ragnarsson
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R. Deuis
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
| | - Mehdi Mobli
- Centre
for Advanced Imaging, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Sharpe
- Molecular
Medicine Program, Research Institute, The
Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christina I. Schroeder
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
- Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702-1201, United States
- Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Irina Vetter
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
- School
of Pharmacy, The University of Queensland, Brisbane, Queensland 4102, Australia
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A subfraction obtained from the venom of the tarantula Poecilotheria regalis contains inhibitor cystine knot peptides and induces relaxation of rat aorta by inhibiting L-type voltage-gated calcium channels. Toxicon X 2023; 18:100151. [PMID: 36873112 PMCID: PMC9978846 DOI: 10.1016/j.toxcx.2023.100151] [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: 12/20/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Venoms from tarantulas contain low molecular weight vasodilatory compounds whose biological action is conceived as part of the envenomation strategy due to its propagative effects. However, some properties of venom-induced vasodilation do not match those described by such compounds, suggesting that other toxins may cooperate with these ones to produce the observed biological effect. Owing to the distribution and function of voltage-gated ion channels in blood vessels, disulfide-rich peptides isolated from venoms of tarantulas could be conceived into potential vasodilatory compounds. However, only two peptides isolated from spider venoms have been investigated so far. This study describes for the first time a subfraction containing inhibitor cystine knot peptides, PrFr-I, obtained from the venom of the tarantula Poecilotheria regalis. This subfraction induced sustained vasodilation in rat aortic rings independent of vascular endothelium and endothelial ion channels. Furthermore, PrFr-I decreased calcium-induced contraction of rat aortic segments and reduced extracellular calcium influx to chromaffin cells by the blockade of L-type voltage-gated calcium channels. This mechanism was unrelated to the activation of potassium channels from vascular smooth muscle, since vasodilation was not affected in the presence of TEA, and PrFr-I did not modify the conductance of the voltage-gated potassium channel Kv10.1. This work proposes a new envenomating function of peptides from venoms of tarantulas, and establishes a new mechanism for venom-induced vasodilation.
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Key Words
- ACh, acetylcholine
- ADP, adenosine diphosphate
- Cav, voltage-gated calcium channel
- DMEM, Dulbecco's modified eagle's medium
- DRP, disulfide-rich peptide
- EC50, half maximal effective concentration
- Emax, maximum effect
- FBS, fetal bovine serum
- HPLC, high-performance liquid chromatography
- ICK peptide
- ICK, inhibitor cystine knot
- IKCa, intermediate conductance calcium-activated potassium channel
- Kv, voltage-gated potassium channel
- L-type calcium voltage-gated calcium
- LC-MS/MS, liquid chromatography-tandem mass spectrometer
- MALDI, matrix-assisted desorption ionization
- Nav, voltage-gated sodium channel
- Phe, phenylephrine
- Poecilotheria regalis, venom
- RP, reverse phase
- Rat aorta
- SEM, standard error of the mean
- SKCa, small conductance calcium-activated potassium channel
- SNP, sodium nitroprusside
- TEA, tetraethylammonium
- TOF, time of flight
- TRP, transient receptor potential
- Vasodilation
- Vh, holding-voltage
- endothelium-intact (E+), endothelium-denuded (E−)
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The Molecular Composition of Peptide Toxins in the Venom of Spider Lycosa coelestis as Revealed by cDNA Library and Transcriptomic Sequencing. Toxins (Basel) 2023; 15:toxins15020143. [PMID: 36828457 PMCID: PMC9959208 DOI: 10.3390/toxins15020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
In the so-called "struggle for existence" competition, the venomous animals developed a smart and effective strategy, envenomation, for predation and defense. Biochemical analysis revealed that animal venoms are chemical pools of proteinase, peptide toxins, and small organic molecules with various biological activities. Of them, peptide toxins are of great molecular diversity and possess the capacity to modulate the activity of ion channels, the second largest group of drug targets expressed on the cell membrane, which makes them a rich resource for developing peptide drug pioneers. The spider Lycosa coelestis (L. coelestis) commonly found in farmland in China is a dominant natural enemy of agricultural pests; however, its venom composition and activity were never explored. Herein, we conducted cDNA library and transcriptomic sequencing of the venom gland of L. coelestis, which identified 1131 high-quality expressed sequence tags (ESTs), grouped into three categories denoted as toxin-like ESTs (597, 52.79%), cellular component ESTs (357, 31.56%), and non-matched ESTs (177, 15.65%). These toxin-like ESTs encode 98 non-reductant toxins, which are artificially divided into 11 families based on their sequence homology and cysteine frameworks (2-14 cysteines forming 1-7 disulfide bonds to stabilize the toxin structure). Furthermore, RP-HPLC purification combined with off-line MALDI-TOF analysis have detected 147 different peptides physically existing in the venom of L. coelestis. Electrophysiology analysis confirmed that the venom preferably inhibits the voltage-gated calcium channels in rat dorsal root ganglion neurons. Altogether, the present study has added a great lot of new members to the spider toxin superfamily and built the foundation for characterizing novel active peptides in the L. coelestis venom.
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Abstract
Polyphenols constitute a diverse array of naturally occurring secondary metabolites found in plants which, when consumed, have been shown to promote human health. Greater consumption may therefore aid in the fight against diseases such as obesity, diabetes, heart disease, cancer, etc. Tree bark is polyphenol-rich and has potential to be used in food supplements. However, it is important to gain insight into the polyphenol profile of different barks to select the material with greatest concentration and diversity. Ultra-performance liquid chromatography (UPLC) was coupled with an ion mobility time-of-flight high-definition/high-resolution mass spectrometer (UPLC-HDMSE) to profile ethanol extracts of three common tree barks (Pinus contorta, Pinus sylvestris, Quercus robur) alongside a commercial reference (Pycnogenol® extracted from Pinus pinaster). Through the use of Progenesis QI informatics software, 35 high scoring components with reported significance to health were tentatively identified across the three bark extracts following broadly the profile of Pycnogenol®. Scots Pine had generally higher compound abundances than in the other two extracts. Oak bark extract showed the lowest abundances but exhibited higher amounts of naringenin and 3-O-methylrosmarinic acid. We conclude that forestry bark waste provides a rich source of extractable polyphenols suitable for use in food supplements and so can valorise this forestry waste stream.
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