Resumen de Computer-Aided Protein Design for Engineering Enzymes to Recognize Specific Peptide and DNA Sequences
This dissertation focuses on the design of two enzymes, the Tobacco Etch Virus "Nuclear inclusion a" (NIa) endoprotease (TEV protease) and the Chlamydomonas reinhardtii I-CreI homing endonuclease (I-CreI meganuclease). For this purpose Foldx was used, a protein design algorithm developed in our laboratory, which is based on physical and empirical parameters and which uses the protein structure to perform mutations and theoretical energy calculations.
The TEV protease recognizes and cuts specifically a canonical amino acid sequence, and is commonly used as a molecular tool in protein purification. The aim was to change the recognition site of this enzyme in order to direct the cleavage to specific sequences of interest, thus increasing its applicability.
Secondly, meganucleases are sequence specific dimeric endonucleases with large palindromic cleavage targets.
The meganuclease I-CreI was designed to avoid the formation of homodimers and to favour the formation of obligate heterodimers. This approach enormously increases the repertoire of non-palindromic unique target sites on the genome that can be recognised by artificial enzymes. Such redesigned enzymes could be used in a wide range of applications, including the correction of mutations responsible for inherited monogenic diseases.
In summary, this thesis snows that computer-aided protein design is an effective tool in developing enzymes "a la carte" and has great potential for providing new molecular tools and biotherapies.
