The core aim of this project is the development of a comprehensive model of the transport cycle of the human dopamine transporter (DAT) and of the bacterial small amino acid transporter LeuT. While LeuT has been crystallised in three conformations, no crystal or cyro-EM structures of the human DAT is available. The availability of structures of the closely related human serotonin transporter and the drosophila DAT allow for building reliable models.
First, DAT models will be evaluated using structure quality assessment methods. These will then be tested against modern force fields using extensive molecular dynamics (MD) simulations, as is was shown that simulation are able to detect also small structural deficiencies. Simulations will be carried out in close collaboration with the Projects of NeuroTrans, which are experimentally investigating on the same transporter. Access to HPC clusters allows for extensive use of advanced simulation techniques. DAT and LeuT will be studied in parallel, because sharing the transport mechanics. Comparison allows for separating transporter specific properties from general valid principles. The main objective of Project 9 are: