Web application for predicting of “hot spot” sites for mutagenesis experiments

Web application HotSpot Wizard offers a possibility of structural and evolutionary analysis to predict "hot sites" for targeted mutagenesis of proteins.

Protein Engineering Group from Institute of Experimental Biology at Masaryk University, Brno, Czech Republic has launched a web application for structural and evolutionary analysis of proteins. HotSpot Wizard is a tool integrating informations obatained from bioinformatics databases and computational tools. Output of this application is a structure of protein with mapped sites most suitable for mutagenesis, which is available for direct display in an internet browser or can be downloaded for offline visualization. This tool will serve for scientific purposes to i.e. improve catalytic properties of enzymes.

Targeted mutagenesis is similar to evolution, but with difference that is done targeted and in short time period. Scientists use it to improve or obtain new properties of proteins. For purpose to effectivaly mutate a protein is essential to find suitable amino acid to change. During "classical" evolution in proteins are selected aminoacids, which are crucial for protein structure or function. These stay unchange and are called conserved. Amino acids, which specifity is not essential for protein proper function, are called variable, can be and are suitable for change by another amino acids.

If such amino acid is located for example in the catalytic site, participates on binding of the substrate, stabilization of the reaction intermediates or can facilitate product release, is possible that change into another amino acid will influence reaction rate, substrate specifity and enantioselectivity.

HotSpot Wizard can find such amino acids. As input is required a PDB file of protein structure. In first step are foound amino acids essential for functio. Consequently HotSpot Wizard searches for important amino acids, identifies cavity of active site and calculate tunnel connecting burried cavities with protein surface. Finally is determined evolutionary conservation of indivdual amino acids. Output is a list of amino acids sorted by predicted mutability and with information of conservation level and potential function.

HotSpot Wizard offers easy to use structural and evolutionary analysis even for users without further knowledge of computer modeling. Application can be found at http://loschmidt.chemi.muni.cz/hotspotwizard/.

Autor: Jiri Polinek