Elucidating the role of dynamic tunnels in enzyme catalysis: simulations and fluorescence experiments

Abstract: Enzymes are very efficient and specific natural catalysts. Their active site is often buried inside their core and connected to a solvent via transport pathways – tunnels. Geometry, physico-chemical properties and dynamics of tunnels determine the exchange rates of ligands between the active sites and a solvent that can often limit the overall catalytic efficiency. The project aims to establish new methods to study properties and dynamics of functionally relevant tunnels. First, we will generate molecular dynamics simulations of enzymes with known relevant tunnels. Then we will develop an automated protocol and software for a time-effective analysis of the tunnel dynamics and apply them on a wide range of enzymes. Novel fluorescence approaches to study tunnel relevance and dynamics will be established to provide additional validation of the protocol. Such analyses will expand our knowledge on properties of tunnels governing the transport processes in enzymes. Compiled cases will enable future studies on the role of tunnels in a protein engineering and inhibitor design. Keywords in English: enzyme structure; tunnel; channel; gate; transport pathway; transport process; molecular dynamics; molecular simulation; molecular modeling; mechanism of enzymatic reaction; fluorescence spectroscopy; single molecule microsopy; unnatural aminoacids