Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Protein Extraction from Supplied Nannochloropsis sp. Biomass
2.3. Xylanase Treatment and Preparation of Molecular Weight Cut Off Permeate Fractions
2.4. Screening and Identification of ACE-1 Inhibitory Activity
2.5. Preparation, Mass Spectrometry Analysis and Identification of Peptides
2.6. In Silico Analysis
2.6.1. Simulated Gastrointestinal (GI) Digestion Using Peptide Cutter
2.6.2. Prediction of Peptide and Peptide Fragment Bioactivities
2.7. Chemical Synthesis, Primary Structure Determination and Theoretical Value Calculation of Peptide Sequences
2.8. Cyclooxygenase Inhibition
2.9. Antimicrobial Screening
3. Results
3.1. Extraction Yields for Protein and Xylanase Treated Permeate Fractions
3.2. Proximate Composition of Whole Alga and Protein Extracts
3.3. ACE-1 Inhibition and Characterisation of Bioactive Peptides Using Mass Spectrometry (MS)
3.4. In Silico Assessment of Identified Peptide Novelity and Additional Bioactivities
3.5. Chemical Synthesis and Confirmation of Bioactivities In Vitro
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Proteins [% DW] | Lipids [% DW] | Carbohydrates [% DW] | Other [% DW] | References |
---|---|---|---|---|---|
Nannochloropsis sp. biomass (this study) Nannochloropsis sp. protein extract (this study) | 27.95 ± 1.42 26.16 + 0.4 | 1.25 ± 0.39 0.38 ± 0.3 | n/d n/d | Ash 23.18 ± 2.59; Moisture 6.37 ± 0.75 27.78 ± 0.13 | This study This study |
Nannochloropsis gaditana | 46.2 ± 0.3 | 31.9 ± 0.6 | 15.8 ± 0.4 | Ash 6.4 ± 0.0 | Verspreet et al., 2021 [6] |
Nannochloropsis oculata | 30.4 ± 1.8 | 20.5 ± 1.2 | 37.1 ± 1.7 | Mineral, fiber, etc. 11.1 ± 0.8 | Qian et al., 2013 [34] |
N. oculata | 31.0 ± 0.0 | 1.3 ± 0.0 | 17.8 ± 0.1 | Ash 32.9 ± 0.0 Fiber 4.4 ± 0.0 | Samarakoon et al., 2013 [35] |
N. oculata | 30.5 | 8.0 | 19.6 | Ash 30.6 | Sanjeewa et al., 2016 [36] |
N. gaditana | 28.0 | 18.4 | 45.0 | - | Nacer et al., 2020 [10] |
Nannochloropsis sp. | 31.7 ± 0.1 | 15.0 ± 0.1 | 9.0 ± 0.4 | Ash 27.3 ± 0.2 | Fithriani et al., 2020 [37] |
Parent Protein Name & UniProt Accession Number | Peptide Single Amino Acid Sequence | Peptide Ranker Value 1 | Novelty (Found in Database 1,2) | Observed Bioactivity In Vitro | Simulated Digestion Using PeptideCutter 3/Peptide Digestion Fragments | Associated Predicted Bioactivities of Peptide Fragments Resulting from Simulated GI Digestion | References |
---|---|---|---|---|---|---|---|
Chlorophyll a-b binding protein, chloroplastic OS = Porphyridium purpureum OX = 35,688 GN = FVE85_6435 PE = 4 SV = 1; Chlorophyll a-b binding protein 1B-21, chloroplastic OS = Porphyridium purpureum OX = 35,688 GN = FVE85_3955 PE = 4 SV = 1 | AGDVGFDPLGF | 0.89 | Novel | ACE-1 inhibitory, Antibacterial activity against E. coli at a concentration of 1 mg/mL | Chymotrypsin–position 6 and 9. Peptide fragments AGDVGF, DPL and GF | No predicted bioactivities associated with any peptide fragments reported in BIOPEP | [26] |
Mannose-6-phosphate isomerase OS = Vibrio sp. SM1977 OX = 2,662,262 GN = manA PE = 3 SV = 1; Uncharacterized protein OS = Porphyridium purpureum OX = 35,688 GN = FVE85_9013 PE = 4 SV = 1; REVERSED p-aminobenzoic acid synthase OS = Ectocarpus siliculosus OX = 2880 GN = PABS PE = 4 SV = 1; REVERSED Uncharacterized protein OS = Gimesia algae OX = 2,527,971 GN = Pan161_23400 PE = 4 SV = 1; REVERSED NADH-ubiquinone oxidoreductase chain 4 OS = Guillardia theta OX = 55,529 GN = nad4 PE = 3 SV = 1; REVERSED NADH-ubiquinone oxidoreductase chain 4 OS = Chroomonas placoidea OX = 173,977 GN = nad4 PE = 3 SV = 1; REVERSED Transcriptional regulator OS = Formosa algae OX = 225,843 GN = BKP44_19185 PE = 4 SV = 1; REVERSED Deoxyguanosine kinase OS = Shewanella algae OX = 38,313 GN = BFS86_13800 PE = 4 SV = 1 | GDVGLF | 0.82 | Novel | ACE-1 | Pepsin position 4, 5, 6, Chymotrypsin position 5 and 6. Peptide fragments GDVG, L, F | No predicted bioactivities associated with peptide fragments reported in BIOPEP | [26] |
Uncharacterized protein OS = Mesonia algae OX = 213,248 GN = LX95_02145 PE = 4 SV = 1 | YANDLLCMPI | 0.77 | Novel | ACE-1; COX-1 and COX-2 inhibition | Pepsin 1, 4, 5, 6 and Chymotrypsin at position 4, 5 and 6. Peptide fragments Y, AND, L, L, CMPI | MPI corresponds to amino acid fragments 2–5 of the antithrombotic peptide DMPIQAFLLYQEPVLGPVR, AND has sequence similarity with peptides NDQF an antiviral peptide and NDPQF a bitterness suppressing peptide but no reported exact matches for AND | [26] |
REVERSED SHR-BD domain-containing protein OS = Ectocarpus siliculosus OX = 2880 GN = Esi_0004_0132 PE = 4 SV = 1 | KGGGSGANGGRL | 0.72 | Novel | ACE-1 | Pepsin, Trypsin and Chymotrypsin cut the peptide at positions 1, 11 and 12. Resulting peptide fragments are K, GGGSGANGGR, L | GGGSGANGGR has sequence similarity in terms of the amino acids GR with peptides GGAAGGR a DPP-IV inhibitory peptide, TKHGGRINTL an antiviral peptide and the ACE inhibitory peptide FPVGRGL | [26] |
Phycocyanin protein, accession number: tr|S5FXR4|S5FXR4_9CYAN | NKFPYTTQ | 0.19 | Novel | ACE-1 inhibition | Trypsin–position 2 Pepsin–position 3 Peptide fragment: NK, F, PYTTQ | NK–ACE-1 inhibitor found previously in Wakame seaweed; TTQ found as an ACE inhibitor previously isolated from bean (Phaseolus vulgaris) | [41,42] |
Protein R-phycocyanin alpha subunit Synechococcus sp. (accession number: P27288 PHCA_SYNPW | VYNKFPYTTQ | 0.18 | Novel | ACE-1 inhibition | Trypsin–position 4 Pepsin–1, 2, 5 Resulting peptide fragments: V, Y, NK, F, PYTTQ | NK–ACE inhibitor found previously in Wakame seaweed; TTQ found as an ACE inhibitor previously isolated from bean (Phaseolus vulgaris) | [43] |
Transcriptor initiation protein from Porphyridium sp. (accession number tr|A0A5J4YUD5|A0A5J4YUD5_PORPP | LVGADAHALGVICS | 0.39 | Novel | ACE-1 inhibition | Pepsin–positions 1 and 8 Resulting peptide fragments: L, VGADAHA, LGIVICS | AHA, also occurs at the C-terminal end of a peptide NGRAHA that has antithrombotic activity; | [44] |
HEAT repeat-containing protein 1 OS = Ectocarpus siliculosus OX = 2880 GN = Esi_0125_0072 PE = 3 SV = 1 (accession number: tr|D7FJ23|D7FJ23_ECTSI) | VVGAVGAADLL | 0.23 | Novel | ACE-1 inhibition | Pepsin at positions 9, 10 and 11 Fragments: VVGAVGAAD, L, L | AAD found at C-terminal end of CAMKII inhibitor KKALRRQEAADAL |
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Hayes, M.; Mora, L.; Lucakova, S. Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis. Biomolecules 2022, 12, 1806. https://doi.org/10.3390/biom12121806
Hayes M, Mora L, Lucakova S. Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis. Biomolecules. 2022; 12(12):1806. https://doi.org/10.3390/biom12121806
Chicago/Turabian StyleHayes, Maria, Leticia Mora, and Simona Lucakova. 2022. "Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis" Biomolecules 12, no. 12: 1806. https://doi.org/10.3390/biom12121806