PEPTIDE BIORECEPTOR DESIGN FOR PORCINE (SUS SCROFA) PROTEIN BIOMARKERS IMMOBILIZATION USING IN SILICO METHOD

• Main Author: Ilhamsah, Mashening
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/76543
• Institution: Institut Teknologi Bandung

One of Islam teachings is people should not consume haram products, including food products. One of them is swine and its derivation. Unfortunately, porcine usage as substitution in animal product recently has made consumer worried. Current developed technologies have their own limitation such as it takes a long time to extract swine sample up to 6 hours and lower accuracy when the sample has been processed in high temperature. To solve this issue, peptide as bioreceptor is chosen as recognition element in biosensor because it’s easy to produce and selective while biosensor has been known for its vast application and quick detection time. Myoglobin and ?-hemoglobin are chosen as swine (Sus scrofa) biomarkers because they can maintain stable structure in high temperature. In this study, peptide-based bioreceptor for each swine biomarker is designed using in silico method. The first step is predicting binding site for each biomarker. Initial peptide sequence can be obtained through complementary amino acid pairing principle, using predicted biomarker’s active residues as template. Then, obtained peptide sequence is predicted for its structure, validated, refined if predicted peptide structure doesn’t meet validation requirements, and analyzed its interaction with biomarker through molecular docking. Later, amino acids substitution is done to optimize peptide binding with biomarker. The final peptide bioreceptor sequence obained is GQGGQLGLQDAAQGG for detecting myoglobin biomarker and VLQAVAAPQAQHGLL for detecting ?-hemoglobin biomarker. The designed bioreceptor is also tested for their specificity using biomarker from another species, that is myoglobin from horse (Equus caballus) and ?-hemoglobin from horse (Equus caballus) and bovine (Bos taurus). Interaction stability between biomarker and bioreceptor is analyzed through molecular dynamics simulation. The results showed that the designed peptide bioreceptors can be specifically bonded with swine biomarker based on molecular docking and form stable interaction based on molecular dynamics simulation.