Computational Design of an Ammonium Bionanosensor

We have an ongoingproject entitled, “A Generalized Computational Methodology for the Design of Genetically Encoded Fluorescent Biosensors” with Professors Emrah Eroğlu and Ali Rana Atılgan. The project aims to develop a holistic process that eliminates experimental trial and error stages in biosensor design, takes into account not only the binding region but rather the whole protein structure, and therefore puts more emphasis on the computational steps while also including experimental measurements. For details, please see the related GazeteSU article [1].Within the scope of this PURE project, we wish to enhance the ammonium binding properties of a potassium probe developed experimentally in the Emrah Eroglu lab.We have previously generated several binding site mutants which showed promising results. We will look further into ammonium binding/dissocation events of these mutants with classical and steered molecular dynamics simulations. With this Project, we aim to design double mutants to achieve stronger binding. Our main computational tool will be the VMD/NAMD suite of programs [2, 3].
 
[1] https://gazetesu.sabanciuniv.edu/node/9854
[2] https://www.ks.uiuc.edu/Research/vmd/
[3] http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html