Prediction and Characterization of Antimicrobial Peptides from Sea Cucumbers (Holothuria sp.) in Papuan Waters, Indonesia

Antimicrobial Peptides (AMPs) are compounds with low molecular weight that play a role in human defense system. However; the bioactive peptides do not always exist in their natural state and they can be liberated from the parent protein structure through hydrolysis. Research on AMPs in sea cucumbers has been limited to only a few specific species. Thus, this research aims to determine the characteristics of the hydrolysates of fresh, boiled, and smoked sea cucumbers, and their antimicrobial activity as well as to predict and characterize the AMPs in the hydrolysates. Hydrolysis of fresh, boiled, and smoked sea cucumbers was carried out by bromelain 5% or papain 5%. The degree of hydrolysis of the sea cucumber hydrolysate was analyzed by soluble nitrogen-TCA method, while their protein content with the Bradford method. The antimicrobial activity of the sea cucumber hydrolysate toward Staphylococcus aureus , Bacillus cereus , and Escherichia coli was done using disk diffusion method. The molecular weight of the peptides in the hydrolysate was determined by SDS-PAGE. Peptides with potential antimicrobial activity (< 5 kDa) were sequenced by LC-MS/MS and analyzed using bioinformatics Mascot, BLASTp, CAMP _R4 , APD3, PepDraw, and PEP-FOLD. Fresh sea cucumbers hydrolyzed with bromelain for 4 hours resulted in hydrolysates with the most degree of hydrolysis, protein content, and antimicrobial activity against the test pathogenic bacteria. Sea cucumbers hydrolysate had stronger antimicrobial activity toward Gram positive bacteria ( S. aureus and B. cereus ) than Gram negative ( E. coli ). This research reported for the first time four AMP sequences from sea cucumber Holothuria atra , i.e. LALGIPLPQLK, IGLFGGAGVGK, INLTLK, and LSLSPFK. The AMPs were characterized by a sequence length of 6–11 amino acids, molecular weight of less than 5 kDa (0.70–1.16 kDa), helical structure, net charge + 1, rich in hydrophobic amino acids with hydrophobicity of + 7.09 to + 12.41 kcal/mol and pI 10.14–10.15.