Computational design of proteins with new functions

In Synthetic Biology we are often confronted by the taskof designing new parts and devices composed of proteinswith specified functionalities that are not found in nature.We will discuss the applications of our computationalprotein design methodology to design proteins with newfunctionalities. We have developed an automated compu-tational method that uses high-resolution protein struc-tures together with molecular modelling techniques tosimulate the result of combinatorial mutagenesis anddynamics of protein structures. We use a physical modelof the protein's unfolded and folded states to rank theproteins according to their folding free energy. For that weuse an all-atom force field, a high-resolution proteinstructure and a rotamer library. Our methodology com-bines the sequence and rotamer searches with the dockingproblem into a single combinatorial optimisation proce-dure to generate protein sequences and their structures,able to bind a specified molecular target. Our computa-tional procedure can also be applied to reduce the librarysize in directed evolution experiments. We will discuss theapplications of our methodology to design new syntheticproteins and enzymes. In particular, we have added anesterase activity into a Thioredoxin protein while main-taining its wild-type activity. We verify our predictionswith experimental results.