The proteolytic cleavage of TLR8 Z-loop by furin protease - molecular recognition, reaction mechanism and role of water molecules

Abstract Understanding the mechanisms underlying the immune response is crucial for advancing our knowledge of an organism’s defence. One such mechanism is the proteolytic cleavage of the Z-loop in some members of the Toll-like receptor (TLR) family. This process is essential for several reasons: it allows proper receptor dimerisation, facilitates its activation, and introduces a control mechanism by preventing inappropriate or excessive immune reactions. In our study, we focused on investigating the proteolytic cleavage of TLR8 by furin protease, for which the mechanism of this process has not been widely investigated. We employed various computational methods not only to propose the reaction pathway but also to explore the role of water molecules within the reaction site. Those included AI-based structure prediction, molecular dynamics simulations, quantum mechanics and quantum mechanics/molecular mechanics calculations, as well as small-molecule tracking combined with local-distribution methods.