Bioluminescence can be found across a wide range of life forms. It occurs when the oxidation of a substrate molecules called luciferins results in light emission facilitated by enzymes called luciferases. Different luciferases are actively studied and utilized in bioluminescence imaging, diagnostic assays, drug development, and many more. Therefore, the need for a sustainable and cost-effective source of luciferin substrates for bioluminescent reactions is a pressing issue that directly impacts the practical applications of luciferases.

This bachelor thesis will study a putative luciferin synthase using molecular dynamics (adaptive sampling in HTMD) and molecular docking (AutoDock Vina) methods. The C-terminus of this protein contains a phenylalanine-tyrosine-tyrosine (FYY) tripeptide, which is believed to be crucial for luciferin biosynthesis and is present exclusively in bioluminescent species across various homologs. The primary objective of the simulations is to shed light onto the dynamic behavior of the protein, with a secondary focus on the C-terminal helix bearing the FYY tripeptide, which was observed to adopt two distinct conformational states. This protein may play a vital role in bioluminescence by producing coelenterazine, a luciferin often used by marine luciferases, including Renilla, Amphiura, and NanoLuc luciferases. Therefore, it is essential to thoroughly analyse the behavior of the FYY protein.