Abstract
Conventional oligopeptide synthesis techniques involve environmentally harmful procedures and materials. In addition, the efficient accumulation of oligopeptides under Hadean Earth environments regarding the origin of life remains still unclear. In these processes, the formation of diketopiperazine is a big issue due to the strong inhibition for further elongation beyond dipeptides. Hydrothermal media enables environmentally friendly oligopeptide synthesis. However, hydrothermal oligopeptide synthesis produces large amounts of diketopiperazine (DKP), due to its thermodynamic stability. DKP inhibits dipeptide elongation and also constitutes an inhibitory pathway in conventional oligopeptide synthesis. Here, we show an efficient pathway for oligopeptide formation using a specially designed experimental setup to run both thermal and non-thermal discharge plasma, generated by nano-pulsed electric discharge with 16–23 kV voltage and 300–430 A current within ca. 500 ns. DKP (14%) was converted to dipeptides and higher oligopeptides in an aqueous solution containing alanine-DKP at pH 4.5, after 20 min of 50 pps thermal plasma irradiation. This is the first study to report efficient oligopeptide synthesis in aqueous medium using nano-pulsed plasma (with thermal plasma being more efficient than non-thermal plasma) via DKP ring-opening. This unexpected finding is implicative to evaluate the pathway how the oligopeptides could have accumulated in the primitive Earth with high-energy plasma sources such as thunder as well as to facilitate the green synthesis of oligopeptides.
This is a preview of subscription content, log in via an institution to check access.
Explore related subjects
Discover the latest articles, news and stories from top researchers in related subjects.References
Baross JA, Hoffman SE (1985) Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. Origins Life Evol Biospheres 15:327–345. https://doi.org/10.1007/BF01808177
Cleaves HJ, Aubrey AD, Bada JL (2009) An evaluation of the critical parameters for abiotic peptide synthesis in submarine hydrothermal systems. Origins Life Evol Biospheres 39:109–126. https://doi.org/10.1007/s11084-008-9154-1
Coin I, Beyermann M, Bienert M (2007) Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences. Nat Protoc 2:3247–3256. https://doi.org/10.1038/nprot.2007.454
Flavel BS, Nambiar M, Shapter JG (2011) Electrochemical detection of copper using a Gly-Gly-His modified carbon nanotube biosensor. Silicon 3:163–171. https://doi.org/10.1007/s12633-011-9080-0
Fuchida S, Naraoka H, Masuda H (2017) Formation of diastereoisomeric piperazine-2,5-dione from DL-alanine in the presence of olivine and water. Origins Life Evol Biospheres 47:83–92. https://doi.org/10.1007/s11084-016-9500-7
Hayashi Y, Wahyudiono MS, Takada N, Kanda N, Sasaki K, Goto M (2014) Decomposition of methyl orange using pulsed discharge plasma at atmospheric pressure: effect of different electrodes. Jpn J Appl Phys 53:010212. https://doi.org/10.7567/JJAP.53.010212
Hayashi Y, Takada N, Wahyudiono KH, Goto M (2017) Synthesis of hydrophilic carbon nanoparticles from amino acids by pulsed arc discharge over aqueous solution in argon under near-critical pressure. J Supercrit Fluids 120:403–407. https://doi.org/10.1016/j.supflu.2016.07.088
Hirose Y, Ohmuro K, Saigoh M, Nakayama T, Yamagata Y (1990) Synthesis of biomolecules from N2, CO, and H2O by electric discharge. Origins Life Evol Biospheres 20:471–481. https://doi.org/10.1007/BF01808195
Holm NG, Andersson EM (1995) Abiotic synthesis of organic compounds under the conditions of submarine hydrothermal systems: a perspective. Planet Space Sci 43:153–159. https://doi.org/10.1016/0032-0633(93)e0043-c
Imai E, Honda H, Hatori K, Matsuno K (1999) Autocatalytic synthesis of oligoglycine in a simulated submarine hydrothermal system. Orig Life Evol Biosph 29:249–259. https://doi.org/10.1023/a:1006545711889
Ishizaki J, Waki Y, Takahashi-Nishioka T, Yokogawa K, Miyamoto K (2009) Selective drug delivery to bone using acidic oligopeptides. J Bone Miner Metab 27:1–8. https://doi.org/10.1007/s00774-008-0004-z
Jiang N, GuoL SK, Lu N, Li J, Wu Y (2017) Discharge and optical characterizations of nanosecond pulse sliding dielectric barrier discharge plasma for volatile organic compound degradation. J Phys d: Appl Phys 50:155206. https://doi.org/10.1088/1361-6463/aa5fe9
Kawamura K, Shimahashi M (2008) One-step formation of oligopeptide-like molecules from Glu and Asp in hydrothermal environments. Naturwissenschaften 95:449–454. https://doi.org/10.1007/s00114-008-0342-7
Kawamura K, Nishi T, Sakiyama T (2005) Consecutive elongation of alanine oligopeptides at the second time range under hydrothermal conditions using a microflow reactor system. J Am Chem Soc 127:522–523. https://doi.org/10.1021/ja0447917
Kawamura K, Takeya H, Kushibe T, Koizumi Y (2011) Mineral-enhanced hydrothermal oligopeptide formation at the second time scale. Astrobiology 11:461–469. https://doi.org/10.1089/ast.2011.0620
Kiyan T, Sasaki M, Ihara T, Namihira T, Hara M, Goto M, Akiyama H (2009) Pulsed breakdown and plasma-aided phenol polymerization in supercritical carbon dioxide and sub-critical water. Plasma Processes Polym 6:778–785. https://doi.org/10.1002/ppap.200900030
Lambert JF, Jaber M, Georgelin T, Stievano L (2013) A comparative study of the catalysis of peptide bond formation by oxide surfaces. Phys Chem Chem Phys 15:13371–13380. https://doi.org/10.1039/C3CP51282G
Li Y, Kojtari A, Friedman G, Brooks AD, Fridman A, Ji HF (2014) Decomposition of L-valine under nonthermal dielectric barrier discharge plasma. J Phys Chem B 118:1612–1620. https://doi.org/10.1021/jp411440k
Liu G, Nguyen TQ, Chow E, Böcking T, Hibbert BD, Gooding JJ (2006) Study of factors affecting the performance of voltammetric copper sensors based on Gly-Gly-His modified glassy carbon and gold electrodes. Electroanalysis 18:1141–1151. https://doi.org/10.1002/elan.200603546
Liu Y, Crittenden JC, Wang L, Liu P (2016) Dechlorination and decomposition of chloroform induced by glow discharge plasma in an aqueous solution. J Hazard Mater 308:84–90. https://doi.org/10.1016/j.jhazmat.2016.01.013
Locke BR, Shih KY (2011) Review of the methods to form hydrogen peroxide in electrical discharge plasma with liquid water. Plasma Sources Sci Technol 20:034006. https://doi.org/10.1088/0963-0252/20/3/034006
Miller SLA (1953) Production of amino acids under possible primitive earth conditions. Science 117:528–529. https://doi.org/10.10126/science.117.3046.528
Mizuno T (1998) Properties and application of supercritical water. Zairyo-to-Kankyo 47:298–305. https://doi.org/10.3323/jcorr1991.47.298
Munegumi T (2014) Chemical evolution of simple amino acids to asparagine under discharge onto the primitive hydrosphere: simulation experiments using contact glow discharge. Bull Chem Soc Jpn 87:1208–1215. https://doi.org/10.1246/bcsj.20140164
Nagayama M, Takaoka O, Inomata K, Yamagata Y (1990) Diketopiperazine-mediated peptide formation in aqueous solution. Origins Life Evol Biospheres 20:249–257. https://doi.org/10.1007/BF01808107
Nazrul IMd, Kaneko T, Kobayashi K (2003) Reaction of amino acids in a supercritical water-flow reactor simulating submarine hydrothermal systems. Bull Chem Soc Jpn 76:1171–1178. https://doi.org/10.1246/bcsj.76.1171
Nishiyama H, Niinuma K, Shinoki S, Takana H (2015) Decomposition of acetic acid using multiple bubble jets with pulsed electrical discharge. Plasma Chem Plasma Process 35:339–354. https://doi.org/10.1007/s11090-014-9607-4
Parker ET, Cleaves HJ, Dworkin JP, Glavin DP, Callahan M, Aubrey A, Lazcano A, Bada JL (2011) Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proc Natl Acad Sci USA 108:5526–5531. https://doi.org/10.1073/pnas.1019191108
Plankensteiner K, Reiner H, Schranz B, Rode BM (2004) Prebiotic formation of amino acids in a neutral atmosphere by electric discharge. Angew Chem, Int Ed Engl 43:1886–1888. https://doi.org/10.1002/anie.200353135
Plankensteiner K, Reiner H, Rode BM (2006) Amino acids on the rampant primordial Earth: electric discharges and the hot salty ocean. Mol Diversity 10:3–7. https://doi.org/10.1007/s11030-006-7009-0
Puiu M, Bala C (2018) Peptide-based biosensors: from self-assembled interfaces to molecular probes in electrochemical assays. Bioelectrochemistry 120:66–75. https://doi.org/10.1016/j.bioelechem.2017.11.009
Reddy PMK, Subrahmanyam Ch (2012) Green approach for wastewater treatment-degradation and mineralization of aqueous organic pollutants by discharge plasma. Ind Eng Chem Res 51:11097–11103. https://doi.org/10.1021/ie301122/10.1021/ie301122p
Santis ED, Ryadnov MD (2015) Peptide self-assembly for nanomaterials: the old new kid on the block. Chem Soc Rev 44:8288–8300. https://doi.org/10.1039/c5cs00470e
Silva BM, Casal S, Andrade PB, Seabra RM, Oliveira MB, Ferreira MA (2004) Free amino acid composition of quince (Cydonia oblonga Miller) fruit (pulp and peel) and jam. J Agric Food Chem 52:1201–1206. https://doi.org/10.1021/jf030564x
Wang Y, Yuan B, Ji Y, Li H (2013) Hydrolysis of hemicellulose to produce fermentable monosaccharides by plasma acid. Carbohydr Polym 97:518–522. https://doi.org/10.1016/j.carbpol.2013.05.017
Wang T, Qu G, Sun Q, Liang D, Hu S (2015) Evaluation of the potential of P-nitrophenol degradation in dredged sediment by pulsed discharge. Plasma Water Res 84:18–24. https://doi.org/10.1016/j.watres.2015.07.022
Wang J, Liu K, Xing R, Yan X (2016) Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev 45:5589–5604. https://doi.org/10.1039/c6cs00176a
Funding
This research was continuously supported by the Collaborative Research Project of the Institute of Pulsed Power Science (IPPS) at Kumamoto University since 2010 and the Institute of Industrial Nanomaterials (IINa) at Kumamoto University since 2020. This research was financially supported by the MEXT Grant-in-Aid for Scientific Research (B), grant number JP19H02017.
Author information
Authors and Affiliations
Contributions
Mitsuru Sasaki and Kunio Kawamura contributed to the management, leadership, and coordination of the research activity planning and execution; they also contributed with the review and editing of the original draft, specifically with the critical review, commentary, and revision. Yuji Miyagawa, Kouki Nonaka, and Ryota Miyanomae contributed by conducting the research and investigation process, specifically performing the experiments and data collection. Furthermore, they contributed with the preparation and writing of the original draft. Armand T. Quitain contributed immensely with the product analysis by HPLC. Tetsuya Kida contributed with the oversight of the research activity planning, including mentorship external to the core team. Motonobu Goto contributed with the development of methodology in the initial stages of the study. Tetsuo Homma contributed with the product analysis by MALDI-TOF/MS and LC/MS. Tomohiro Furusato contributed with the development of the pulsed arc discharge equipment.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Communicated by: Addy Pross
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Sasaki, M., Miyagawa, Y., Nonaka, K. et al. Nano-pulsed discharge plasma-induced abiotic oligopeptide formation from diketopiperazine. Sci Nat 109, 33 (2022). https://doi.org/10.1007/s00114-022-01803-y
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00114-022-01803-y