In silico characterization of phenylacetaldehyde synthases of selected orchids / Amin Nur Husna Binti Airol Azamir

Faculty of Industrial Sciences and Technology

Final Year Report (Bachelor of Applied Science in Industrial Biotechnology) -- Universiti Malaysia Pahang Al-Sultan Abdullah - 2025

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Phenylacetaldehyde synthase (PAAS) is an enzyme essential for producing phenylacetaldehyde, a key component of floral scent. It acts as a bifunctional enzyme, efficiently coupling phenylalanine decarboxylation to oxidation. This process yields phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in precise stoichiometric amounts. Despite its importance, the presence and characteristics of PAAS in various flowers remain underexplored. This study investigated the phenylacetaldehyde synthase (PAAS) and its homologous proteins in five orchid species: Vanda Mimi Palmer, Phalaenopsis equestris, Dendrobium nobile, Dendrobium candidum, and Iris pallida, using an in silico approach. Amino acid sequences available in the NCBI GenBank were utilized to perform homology modeling and predict PAAS's three-dimensional (3D) structures and related proteins. The reliability of these structural models was validated using VERIFY 3D, PROCHECK, and ERRAT tools. This study aims to predict the 3Dprotein structure of selected orchids’ phenylacetaldehyde synthase and homologous proteins using a homology modeling approach and to investigate the binding positions of potential ligands to the 3D structure of the selected orchids’ phenylacetaldehyde synthases by molecular docking. Active pocket regions (R1 and R2) were identified using CASTp, whereas R1 is the predicted pocket binding site of the selected orchid phenylacetaldehyde synthase and homologous proteins while R2 is the predicted pocket binding site of the 6eem, and molecular docking experiments were conducted to evaluate the binding sites and affinities of potential substrates (phenylalanine, tryptophan, and tyrosine) and their products (phenylacetaldehyde, tryptamine, and tyramine). Finally, protein-ligand docking studies were conducted with Autodock Vina to predict the orientation of a ligand bound to the protein and compare it with the predicted active site pocket analysis. This study contributes to a deeper understanding of PAAS's molecular and functional properties and its homologous proteins in orchids. These insights enhance knowledge of floral scent biosynthesis, particularly the enzymatic pathways involving phenylacetaldehyde synthase, and provide valuable information for potential applications in horticulture, the fragrance industry, and related fields