Method for development of a peptide building block useful for de novo protein design

Abstract

The present invention relates to a top-down symmetric deconstruction approach which provides a novel alternative means to successfully identify a useful polypeptide “building block” for subsequent “bottom-up” de novo design of target protein architecture. The present invention also pertains to a novel peptides isolated by top-down symmetric deconstruction which may be useful for design or directed evolution of novel proteins with novel functionalities.

1 . A top-down symmetric deconstruction method for generating a polypeptide building block for design of a target architecture comprising:
 (a) choosing a protein having the target architecture,   (b) imposing a cumulative symmetric constraint on core, turn and secondary structure by targeted mutagenesis,   (c) retaining symmetric mutations if they are neutral or favorable to protein stability, folding and solubility,   (d) analyzing sequences to identify candidate symmetric mutations,   (e) analyzing the candidate symmetric mutations by molecular modeling   (f) determining a peptide sequence with a complete symmetric deconstruction and   (g) fragmentation of the peptide sequence to determine the polypeptide building block   wherein polypeptide building block is generated for design of the target architecture.   
     
     
         2 . The method of  claim 1 , wherein the target architecture is a β-trefoil. 
     
     
         3 . The method of  claim 1 , wherein the protein is fibroblast growth factor-1 (FGF-1). 
     
     
         4 . The method of  claim 1 , wherein the core is a hydrophobic core. 
     
     
         5 . The method of  claim 1 , wherein the turn is a reverse-turn. 
     
     
         6 . The method of  claim 1 , wherein the secondary structure is a β-strand. 
     
     
         7 . The method of  claim 1 , wherein step (b) comprises application of specific transforms. 
     
     
         8 . The method of  claim 7 , wherein the specific transforms comprise symmetric deconstruction of the core, turn and secondary structure. 
     
     
         9 . The method of  claim 8 , wherein the specific transforms are performed sequentially. 
     
     
         10 . The method of  claim 8 , wherein the core is a hydrophobic core, the turn is a reverse-turn and the secondary structure is a β-strand. 
     
     
         11 . A peptide motif isolated by the method of  claim 1 . 
     
     
         12 . The peptide motif of  claim 11 , wherein the peptide motif is Monofoil-4P.