In Silico Analysis of Bioactive Peptides in Invasive Sea Grass Halophila stipulacea

Kandemır-Cavas, Cagin; Pérez‐Sánchez, Horacio; Mert-Ozupek, Nazli; Çavaş, Levent

doi:10.3390/cells8060557

Cited by 16 publications

(9 citation statements)

References 49 publications

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“…If they are not available, peptides are not taken into account. Simulation of proteolysis using the BIOPEP-UWM database has recently been described by, e.g., Lin et al [85], Yu D. et al [91], and Kandemir-Cavas et al [92]. Data concerning proteolysis simulation may be interpreted together with protein structures [93].…”

Section: Discussionmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

545

397

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The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

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Section: Discussionmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

545

397

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“…Bioactive peptides are obtained via wet lab studies. The bioinformatic tools are also used for discovering of bioactive peptides (Agirbasli & Cavas, 2017;Kandemir-Cavas et al, 2019). In this study, Pvtoxin-a and Pvtoxin-b from P. volitans were studied as model proteins.…”

Section: Discussionmentioning

confidence: 99%

Bioactivities from Novel Toxins of Pterois volitans: A Bioinformatics Approach

Çavaş

Bilgin

2021

Gazi University Journal of Science Part A: Engineering and Innovation

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Pterois volitans (Linnaeus, 1758), native of the Indo-Pacific Ocean, is an invasive fish species in the Western-Atlantic. Due to the very long venomous spines, they increase their populations in newly invaded habitats. No validated eradication method has been existed for this species yet. Therefore, there is an urgent need for alternative utilization methods for this fish species. Bioactive peptides are of great importance for human health since they exhibit excellent inhibitory properties for some medicinally important enzymes in human metabolisms such as angiotensin converting enzyme (ACE) and dipeptidyl peptidase-IV (DPP-IV). In this study, the bioactive peptides in protein-based venom of P. volitans, Pvtoxin-a and Pvtoxin-b, were investigated by using in silico tools. Total number of negatively charged residues (Asp + Glu) for Pvtoxin-a and Pvtoxin-b were found as 21 and 18, respectively. Total number of positively charged residues (Arg + Lys) for Pvtoxin-a and Pvtoxin-b were observed to be 22 and 24, respectively. According to BIOPEP results, AE values for ACE and DPP-IV were found to be 0.0305 and 0.0666 for Pvtoxin-a and Pvtoxin-b as 0.0333 and 0.0569, respectively. It is very interesting to note that AE values related to antioxidant property were observed to be 0.0083 for both Pvtoxin-a and Pvtoxin-b. Although AE value for alpha-glucosidase inhibitor was found to be 0.0014 for Pvtoxin-a, no AE value was obtained for Pvtoxin-b. In conclusion, the BIOPEP results clearly show that after a possible eradication study, protein-based venoms from P. volitans can be evaluated in the production of bioactive peptides. A possible economical value may create a pressure on its increasing population in newly invaded areas.

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“…Also, peptides with this length have a higher resistance to degradation, increasing their bioavailability and, more significantly, bioactivity (52). It has been reported that the determination of binding energy based on in silico experimental methods using HPEPDOCK shows a good correlation with the results obtained experimentally so that these molecules are the ones with the higher antiadipogenic potentiality (53,54). However, concerning the results obtained with Autodock tools, the peptides TTPW, ATSF, ITY, and TSF showed the formation of hydrogen bonds in anti-adipogenic regions of the PPARγ receptor, mainly the three presented bonds with Cys285, which has been since it presents more significant antiadipogenic effects, with binding energies of −5.96, 3.89, −5.91, and −4.68 kcal/mol, respectively (28).…”

Section: In Silico Methodologymentioning

confidence: 97%

Protein Concentrates on Tepary Bean (Phaseolus acutifolius Gray) as a Functional Ingredient: In silico Docking of Tepary Bean Lectin to Peroxisome Proliferator-Activated Receptor Gamma

et al. 2021

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The tepary bean (Phaseolus acutifolius Gray) is a US–Mexico frontier native crop, produces high yields in agriculture, and needs to be reconsidered because of its nutritional and functional properties. This study aimed to determine the technological and nutritional properties of flours and protein concentrates of tepary bean, besides determining an in silico agonist effect of tepary bean lectin to peroxisome proliferator-activated receptor gamma (PPAR-γ). We evaluated the technological properties of raw samples (tepary flour and tepary protein concentrate) and cooked samples (tepary flour and tepary protein concentrate). The flours present a significant difference (p < 0.05) concerning protein concentrates in water absorption and oil absorption capacity. The raw samples' emulsifying capacity was higher than that reported in the literature for other legumes, but not the cooked samples. The samples' foaming capacity had no significant difference in treatments (p > 0.05), and cooked tepary bean protein concentrate presented complete gelation at a lower concentration (2%). Nutritionally, raw samples present a protein percentage of 23.46 ± 0.06 and 71.38 ± 0.44 and cooked samples present a protein percentage of 25.27 ± 0.04 and 62.69 ± 0.14; a chemical score of 72, 86, 82, and 72; in vitro protein digestibility (%) = 48.20 ± 0.31, 49.80 ± 0.80, 61.77 ± 1.70, and 63.61 ± 4.19; and C-PER = 0.86, 1.34, 1.93, and 1.81, respectively. All the samples showed methionine + cysteine as the limiting amino acid. All these nutritional data are very similar to the common bean (Phaseolus vulgaris). SDS-PAGE preserves the lectin fraction in both protein concentrates. The in silico study of tepary lectin (PDB: 6tt9) shows that there were seven peptides that presented values below −120 kcal/mol: PEW, VSVGF, PSQK, TTPW, ATSF, ITY, and TSF, with VSVGF, PSQK, and PEW having the highest affinity for active sites of the PAPRγ receptor (binding energies from −5.32 to −7.04 kcal/mol). These peptides could show antiadipogenic or antidiabetic activity based on the intermolecular bond energies and open an interesting research item.

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In Silico Analysis of Bioactive Peptides in Invasive Sea Grass Halophila stipulacea

Cited by 16 publications

References 49 publications

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Bioactivities from Novel Toxins of Pterois volitans: A Bioinformatics Approach

Protein Concentrates on Tepary Bean (Phaseolus acutifolius Gray) as a Functional Ingredient: In silico Docking of Tepary Bean Lectin to Peroxisome Proliferator-Activated Receptor Gamma

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