Skip to main content

Non-targeted Identification of d-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS

  • Protocol
  • First Online:
Peptidomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1719))

Abstract

d-Amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-l-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide’s mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a non-targeted manner.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.00
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bai L, Sheeley S, Sweedler JV (2009) Analysis of endogenous d-amino acid-containing peptides in Metazoa. Bioanal Rev 1(1):7–24. https://doi.org/10.1007/s12566-009-0001-2

    Article  PubMed  PubMed Central  Google Scholar 

  2. Ollivaux C, Soyez D, Toullec JY (2014) Biogenesis of d-amino acid containing peptides/proteins: where, when and how? J Pept Sci 20(8):595–612. https://doi.org/10.1002/psc.2637

    Article  CAS  PubMed  Google Scholar 

  3. Richter K, Egger R, Kreil G (1987) d-alanine in the frog skin peptide dermorphin is derived from l-alanine in the precursor. Science 238(4824):200–202

    Article  CAS  PubMed  Google Scholar 

  4. Kamatani Y, Minakata H, Kenny PT, Iwashita T, Watanabe K, Funase K, Sun XP, Yongsiri A, Kim KH, Novales-Li P et al (1989) Achatin-I, an endogenous neuroexcitatory tetrapeptide from Achatina fulica Ferussac containing a d-amino acid residue. Biochem Biophys Res Commun 160(3):1015–1020

    Article  CAS  PubMed  Google Scholar 

  5. Ohta N, Kubota I, Takao T, Shimonishi Y, Yasuda-Kamatani Y, Minakata H, Nomoto K, Muneoka Y, Kobayashi M (1991) Fulicin, a novel neuropeptide containing a d-amino acid residue isolated from the ganglia of Achatina fulica. Biochem Biophys Res Commun 178(2):486–493. https://doi.org/10.1016/0006-291X(91)90133-R

    Article  CAS  PubMed  Google Scholar 

  6. Buczek O, Yoshikami D, Bulaj G, Jimenez EC, Olivera BM (2005) Post-translational amino acid isomerization: a functionally important d-amino acid in an excitatory peptide. J Biol Chem 280(6):4247–4253. https://doi.org/10.1074/jbc.M405835200

    Article  CAS  PubMed  Google Scholar 

  7. Ollivaux C, Gallois D, Amiche M, Boscameric M, Soyez D (2009) Molecular and cellular specificity of post-translational aminoacyl isomerization in the crustacean hyperglycaemic hormone family. FEBS J 276(17):4790–4802. https://doi.org/10.1111/j.1742-4658.2009.07180.x

    Article  CAS  PubMed  Google Scholar 

  8. Bai L, Livnat I, Romanova EV, Alexeeva V, Yau PM, Vilim FS, Weiss KR, Jing J, Sweedler JV (2013) Characterization of GdFFD, a d-amino acid-containing neuropeptide that functions as an extrinsic modulator of the Aplysia feeding circuit. J Biol Chem 288(46):32837–32851. https://doi.org/10.1074/jbc.M113.486670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Bai L, Romanova EV, Sweedler JV (2011) Distinguishing endogenous d-amino acid-containing neuropeptides in individual neurons using tandem mass spectrometry. Anal Chem 83(7):2794–2800. https://doi.org/10.1021/ac200142m

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Sachon E, Clodic G, Galanth C, Amiche M, Ollivaux C, Soyez D, Bolbach G (2009) d-amino acid detection in peptides by MALDI-TOF-TOF. Anal Chem 81(11):4389–4396. https://doi.org/10.1021/ac9002886

    Article  CAS  PubMed  Google Scholar 

  11. Koehbach J, Gruber CW, Becker C, Kreil DP, Jilek A (2016) MALDI TOF/TOF-based approach for the identification of d-amino acids in biologically active peptides and proteins. J Proteome Res 15(5):1487–1496. https://doi.org/10.1021/acs.jproteome.5b01067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Sheeley SA, Miao H, Ewing MA, Rubakhin SS, Sweedler JV (2005) Measuring d-amino acid-containing neuropeptides with capillary electrophoresis. Analyst 130(8):1198–1203. https://doi.org/10.1039/b504717j

    Article  CAS  PubMed  Google Scholar 

  13. Jia C, Lietz CB, Yu Q, Li L (2014) Site-specific characterization of d-amino acid containing peptide epimers by ion mobility spectrometry. Anal Chem 86(6):2972–2981. https://doi.org/10.1021/ac4033824

    Article  CAS  PubMed  Google Scholar 

  14. Tao Y, Quebbemann NR, Julian RR (2012) Discriminating d-amino acid-containing peptide epimers by radical-directed dissociation mass spectrometry. Anal Chem 84(15):6814–6820. https://doi.org/10.1021/ac3013434

    Article  CAS  PubMed  Google Scholar 

  15. Livnat I, Tai HC, Jansson ET, Bai L, Romanova EV, Chen TT, Yu K, Chen SA, Zhang Y, Wang ZY, Liu DD, Weiss KR, Jing J, Sweedler JV (2016) A d-amino acid-containing neuropeptide discovery funnel. Anal Chem 88(23):11868–11876. https://doi.org/10.1021/acs.analchem.6b03658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ewing MA, Wang J, Sheeley SA, Sweedler JV (2008) Detecting d-amino acid-containing neuropeptides using selective enzymatic digestion. Anal Chem 80(8):2874–2880. https://doi.org/10.1021/ac7025173

    Article  CAS  PubMed  Google Scholar 

  17. Bhushan R, Bruckner H (2004) Marfey’s reagent for chiral amino acid analysis: a review. Amino Acids 27(3–4):231–247. https://doi.org/10.1007/s00726-004-0118-0

    Article  CAS  PubMed  Google Scholar 

  18. Yang CY, Yu K, Wang Y, Chen SA, Liu DD, Wang ZY, YN Su, Yang SZ, Chen TT, Livnat I, Vilim FS, Cropper EC, Weiss KR, Sweedler JV, Jing J (2016) Aplysia locomotion: network and behavioral actions of GdFFD, a d-amino acid-containing neuropeptide. PLoS One 11(1):e0147335. https://doi.org/10.1371/journal.pone.0147335

    Article  PubMed  PubMed Central  Google Scholar 

  19. Finoulst I, Pinkse M, Van Dongen W, Verhaert P (2011) Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices. J Biomed Biotechnol 2011:245291. https://doi.org/10.1155/2011/245291

    Article  PubMed  PubMed Central  Google Scholar 

  20. Conlon JM (2007) Purification of naturally occurring peptides by reversed-phase HPLC. Nat Protoc 2(1):191–197. https://doi.org/10.1038/nprot.2006.437

    Article  CAS  PubMed  Google Scholar 

  21. Liardon R, Ledermann S, Ott U (1981) Determination of d-amino acids by deuterium labelling and selected ion monitoring. J Chromatogr A 203:385–395. https://doi.org/10.1016/S0021-9673(00)80309-X

    Article  CAS  Google Scholar 

  22. Fountoulakis M, Lahm HW (1998) Hydrolysis and amino acid composition of proteins. J Chromatogr A 826(2):109–134

    Article  CAS  PubMed  Google Scholar 

  23. Turner AJ (2013) Chapter 79—Aminopeptidase N In: Rawling ND, Salvesen G (eds) Handbook of Proteolytic Enzymes. Academic Press, London, pp 397–403. https://doi.org/10.1016/B978-0-12-382219-2.00079-X

  24. Gill SC, von Hippel PH (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182(2):319–326. https://doi.org/10.1016/0003-2697(89)90602-7

  25. Conibear AC, Daly NL, Craik DJ (2012) Quantification of small cyclic disulfide-rich peptides. Biopolymers 98(6):518–524. https://doi.org/10.1002/bip.22121

    Article  CAS  PubMed  Google Scholar 

  26. Anthis NJ, Clore GM (2013) Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm. Protein Sci 22(6):851–858. https://doi.org/10.1002/pro.2253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Murai Y, Wang L, Masuda K, Sakihama Y, Hashidoko Y, Hatanaka Y, Hashimoto M (2013) Rapid and controllable hydrogen/deuterium exchange on aromatic rings of α-amino acids and peptides. Eur J Org Chem 2013(23):5111–5116. https://doi.org/10.1002/ejoc.201300405

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Institutes of Health, Award No. P30 DA018310 from the National Institute on Drug Abuse (NIDA) and Award No. 2 R01NS031609 from the National Institute of Neurological Disorders and Stroke (NINDS). J.W.C. was supported in part by a Beckman Institute Postdoctoral Fellowship, funded by a Beckman Foundation gift to the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jonathan V. Sweedler .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Tai, HC., Checco, J.W., Sweedler, J.V. (2018). Non-targeted Identification of d-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS. In: Schrader, M., Fricker, L. (eds) Peptidomics. Methods in Molecular Biology, vol 1719. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7537-2_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7537-2_7

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7536-5

  • Online ISBN: 978-1-4939-7537-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics