Nástroj LoopGrafter
| Title in English | LoopGrafter software tool |
|---|---|
| Authors | |
| Year of publication | 2022 |
| MU Faculty or unit | |
| Citation | |
| Description | Loop transplantation between structurally related proteins is a promising method to improve the activity, specificity and stability of proteins and enzymes. However, despite the structural and functional importance of looped protein regions, currently available loop-based rational protein design methods are scarce in protein engineering. One of the specific challenges related to loop engineering is their unique dynamics, which allows them to exert e.g. allosteric control over the catalytic function of enzymes. Thus, when loops between two different proteins are engineered to be transplanted, such dynamics must be taken into account in the context of the protein structure. The second practical challenge is the identification of sites suitable for transplantation, finding the ideal length of the transferred loop, etc. In Loschmidt's MU laboratories, we are developing a software tool called LoopGrafter, which specifically guides the loop grafting process between structurally related proteins. The server provides an interactive step-by-step procedure in which the user can sequentially identify loops in two input proteins, calculate their geometries, assess their similarities and dynamics, and select the number of loops to transplant. All possible different chimeric proteins derived from any existing recombination point are calculated and 3D models are constructed and energetically evaluated for each. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses. |
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