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Rational de novo design of proteins with specific 3-d structures


The de novo design of an artificial protein of the B or A/B class is envisaged. The designed protein will use the topology of a SH3 domain (B) or a IgG binding protein G (A/B) as templates, two small proteins ( 60 residues) extensively studied in the group of L. Serrano at the EMBL. The procedure employed for the design will combine the most recent methods of molecular modelling with experimental methods for the structural characterization of the artificial protein synthesised (CD, NMR). The design procedure will be based on the assembling of structurally related building block from various proteins whose 3-D structure is known. A particular attention will be paid to optimise the packing of amino acids in the interior of the protein since this aspect has been shown to be essential to obtain a well-defined 3-D structure.

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