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Andersen HM, Tai HC, Rubakhin SS, Yau PM, Sweedler JV. A novel series of metazoan L/D peptide isomerases. J Biol Chem 2024; 300:107458. [PMID: 38857862 PMCID: PMC11277431 DOI: 10.1016/j.jbc.2024.107458] [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: 11/30/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
The function of endogenous cell-cell signaling peptides relies on their interactions with cognate receptors, which in turn are influenced by the peptides' structures, necessitating a comprehensive understanding of the suite of post-translational modifications of the peptide. Herein, we report the initial characterization of putative peptide isomerase enzymes extracted from R. norvegicus, A. californica, and B. taurus tissues. These enzymes are both tissue and substrate-specific across all three organisms. Notably, the lungs of the mammalian species, and the central nervous system of the mollusk displayed the highest isomerase activity among the examined tissues. In vitro enzymatic conversion was observed for several endogenous peptides, such as the tetrapeptide GFFD in A. californica, and mammalian neuropeptide FF in R. norvegicus and B. taurus. To understand their mode of action, we explored the effects of several inhibitors on these enzymes, which suggest common active site residues. While further characterization of these enzymes is required, the investigations emphasize a widespread and overlooked enzyme activity related to the creation of bioactive peptides.
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Affiliation(s)
- Harvey M Andersen
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Hua-Chia Tai
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Stanislav S Rubakhin
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M Yau
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Beckman Institute, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA.
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2
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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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3
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Mast DH, Checco JW, Sweedler JV. Advancing d-amino acid-containing peptide discovery in the metazoan. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140553. [PMID: 33002629 DOI: 10.1016/j.bbapap.2020.140553] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022]
Abstract
The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the homochirality of animal proteins while simultaneously revealing new analytical challenges in the structural and functional characterization of peptides. Most known DAACPs have been identified though laborious activity-guided purification studies or by homology to previously identified DAACPs. Peptide characterization experiments are increasingly dominated by high throughput mass spectrometry-based peptidomics, with stereochemistry rarely considered due to the technical challenges of identifying l/d isomerization. This review discusses the prevalence of enzyme-derived DAACPs among animals and the physiological consequences of peptide isomerization. Also highlighted are the analytical methods that have been applied for structural characterization/discovery of DAACPs, including results of several recent studies using non-targeted discovery methods for revealing novel DAACPs, strongly suggesting that more DAACPs remain to be uncovered.
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Affiliation(s)
- David H Mast
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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4
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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5
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Ollivaux C, Soyez D, Toullec JY. Biogenesis of d
-amino acid containing peptides/proteins: where, when and how? J Pept Sci 2014; 20:595-612. [DOI: 10.1002/psc.2637] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Céline Ollivaux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
| | - Daniel Soyez
- Sorbonne Universités, UPMC Univ Paris 06, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
- CNRS, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
| | - Jean-Yves Toullec
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
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‘Chiral compartmentation’ in metabolism: Enzyme stereo-specificity yielding evolutionary options. FEBS Lett 2013; 587:2790-7. [DOI: 10.1016/j.febslet.2013.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
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7
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Morishita F, Furukawa Y, Matsushima O. Molecular cloning of two distinct precursor genes of NdWFamide, a d-tryptophan-containing neuropeptide of the sea hare, Aplysia kurodai. Peptides 2012; 38:291-301. [PMID: 23000476 DOI: 10.1016/j.peptides.2012.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/22/2012] [Accepted: 08/22/2012] [Indexed: 10/27/2022]
Abstract
NdWFamide (NdWFa) is a D-tryptophan-containing cardioexcitatory neuropeptide in gastropod mollusks, such as Aplysia kurodai and Lymanea stagnalis. In this study, we have cloned two cDNA encoding distinct precursors for NdWFa from the abdominal ganglion of A. kurodai. One of the predicted precursor proteins consisted of 90 amino acids (NWF90), and the other consisted of 87 amino acids (NWF87). Both of the predicted precursor proteins have one NWFGKR sequence preceded by the N-terminal signal peptide. Sequential double staining by in situ hybridization (ISH) and immunostaining with anti-NdWFa antibody suggested that NdWFa-precursor and NdWFa peptide co-exist in neurons located in the right-upper quadrant region of the abdominal ganglion. In ISH, NWF90-specific signal and NWF87-specific one were found in different subsets of neurons in the abdominal ganglia of Aplysia. The expression level of NWF90 gene estimated by RT-PCR is much higher than that of NWF87 gene. These results suggest that NWF90 precursor is the major source of NdWFa in Aplysia ganglia.
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Affiliation(s)
- Fumihiro Morishita
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
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Kita M. Bioorganic Studies on the Key Natural Products from Venomous Mammals and Marine Invertebrates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaki Kita
- Division of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba
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9
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Detection of platypus-type l/d-peptide isomerase activity in aqueous extracts of papaya fruit. Biotechnol Lett 2012; 34:1659-65. [DOI: 10.1007/s10529-012-0941-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/25/2012] [Indexed: 10/28/2022]
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Ligabue-Braun R, Verli H, Carlini CR. Venomous mammals: a review. Toxicon 2012; 59:680-95. [PMID: 22410495 DOI: 10.1016/j.toxicon.2012.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/19/2012] [Accepted: 02/21/2012] [Indexed: 01/09/2023]
Abstract
The occurrence of venom in mammals has long been considered of minor importance, but recent fossil discoveries and advances in experimental techniques have cast new light into this subject. Mammalian venoms form a heterogeneous group having different compositions and modes of action and are present in three classes of mammals, Insectivora, Monotremata, and Chiroptera. A fourth order, Primates, is proposed to have venomous representatives. In this review we highlight recent advances in the field while summarizing biochemical characteristics of these secretions and their effects upon humans and other animals. Historical aspects of venom discovery and evolutionary hypothesis regarding their origin are also discussed.
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Affiliation(s)
- Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Department of Biophysics-IB, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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11
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Gehmayr V, Mollay C, Reith L, Müller N, Jilek A. Tight binding of transition-state analogues to a peptidyl-aminoacyl-L/D-isomerase from frog skin. Chembiochem 2011; 12:1996-2000. [PMID: 21739559 PMCID: PMC3195878 DOI: 10.1002/cbic.201100203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Verena Gehmayr
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Christa Mollay
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
| | - Lorenz Reith
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Norbert Müller
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
| | - Alexander Jilek
- Chair of Bioinformatics, Department of Biotechnology, University of Natural Resources and Life SciencesMuthgasse 18, 1190 Vienna (Austria)
- Institute of Organic Chemistry, Johannes Kepler University LinzAltenberger Strasse 69, 4040 Linz (Austria)
- Institute of Molecular Biology, Austrian Academy of SciencesBillrothstrasse 11, 5020 Salzburg (Austria)
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12
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Experimental strategies for the analysis of D-amino acid containing peptides in crustaceans: a review. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3102-7. [PMID: 21497143 DOI: 10.1016/j.jchromb.2011.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/10/2011] [Accepted: 03/17/2011] [Indexed: 11/23/2022]
Abstract
Detection of D-amino acids in natural peptides has been, and remains a challenging task, as peptidyl isomerization is a peculiar and subtle posttranslational modification that does not induce any change in primary sequence or in physicochemical properties of the molecule such as molecular mass or pI. Therefore, the presence of a D-amino acid residue in a peptide chain is generally transparent to classical methods of peptide analysis (electrophoresis, chromatography, mass spectrometry, molecular biology). In this article, we will review the various experimental strategies and analytical techniques, which have been used to characterize and to study D-amino acid containing peptides in crustaceans.
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13
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Jilek A, Mollay C, Lohner K, Kreil G. Substrate specificity of a peptidyl-aminoacyl-L/D-isomerase from frog skin. Amino Acids 2011; 42:1757-64. [PMID: 21424715 PMCID: PMC3325411 DOI: 10.1007/s00726-011-0890-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/09/2011] [Indexed: 12/14/2022]
Abstract
In the skin of fire-bellied toads (Bombina species), an aminoacyl-l/d-isomerase activity is present which catalyses the post-translational isomerization of the l- to the d-form of the second residue of its substrate peptides. Previously, this new type of enzyme was studied in some detail and genes potentially coding for similar polypeptides were found to exist in several vertebrate species including man. Here, we present our studies to the substrate specificity of this isomerase using fluorescence-labeled variants of the natural substrate bombinin H with different amino acids at positions 1, 2 or 3. Surprisingly, this enzyme has a rather low selectivity for residues at position 2 where the change of chirality at the alpha-carbon takes place. In contrast, a hydrophobic amino acid at position 1 and a small one at position 3 of the substrate are essential. Interestingly, some peptides containing a Phe at position 3 also were substrates. Furthermore, we investigated the role of the amino-terminus for substrate recognition. In view of the rather broad specificity of the frog isomerase, we made a databank search for potential substrates of such an enzyme. Indeed, numerous peptides of amphibia and mammals were found which fulfill the requirements determined in this study. Expression of isomerases with similar characteristics in other species can therefore be expected to catalyze the formation of peptides containing d-amino acids.
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Affiliation(s)
- Alexander Jilek
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenberger Str. 69, 4040, Linz, Austria.
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Abstract
The monotremes (the echidnas and the platypus) display both mammalian and reptilian features. Male monotremes have a bilateral crural gland that is connected via a duct to a spur on each hind limb. Male echidnas appear not to use their spurs as weapons in aggressive acts, but the crural system may have a role in reproductive behaviour because it appears only to be active during the breeding season. The secretions produced by the echidna’s crural gland have not hitherto been biochemically or pharmacologically characterised. We used reverse-phase high-performance liquid chromatography (RP-HPLC) to separate the components of echidna venom and compared the chromatograms with those from platypus venom. The echidna venom appears to contain fewer proteins and peptides than platypus venom; however, it appears to have defensin-like peptides that behave similarly on RP-HPLC to those in platypus venom. Like platypus venom, echidna venom has peptidyl aminoacyl l/d-peptide isomerase activity. An RP-HPLC-based assay showed that the second amino acid residue, of a probe synthetic hexapeptide, was converted into the d-form, when incubated with echidna venom.
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