Engineered heterodimeric protein domains

Abstract

The present invention provides an engineered multidomain protein including at least two nonidentical engineered domains, each of which contains a protein-protein interaction interface containing amino acid sequence segments derived from two or more existing homologous parent domains, thereby conferring on the engineered domains assembly specificities distinct from assembly specificities of the parent domains. In particular, the engineered domains form heterodimers with one another preferentially over forming homodimers. Methods of designing and using the engineered proteins are also included.

What is claimed is: 
     
         1 - 30 . (canceled) 
     
     
         31 . A method of designing a multidomain protein with domains that preferentially heterodimerize, the method comprising the steps of:
 (a) selecting a first polypeptide, a second polypeptide, a third polypeptide and a fourth polypeptide, wherein the first and third polypeptides dimerize with each other, but not with the second or fourth polypeptide, and wherein said second and fourth polypeptides dimerize with each other,   (b) composing an amino acid sequence of a first domain from the first and the second polypeptides comprising at least one assembly element from the first polypeptide, and   (c) composing an amino acid sequence of a second domain from the third and fourth polypeptides comprising at least one assembly element from the third polypeptide, such that the assembly elements from the first and third polypeptides assemble with each other, thereby promoting heterodimerization of the first and second domains.   
     
     
         32 . The method of  claim 31 , wherein the first domain further comprises an assembly element from the second polypeptide and the second domain further comprises a assembly element from the fourth polypeptide such that the assembly elements from the second and fourth polypeptides bind assemble with other promoting heterodimerization of the first and second domains. 
     
     
         33 . The method of  claim 31 , wherein step (b) or step (c) comprises comparing three-dimensional structures of two or more of the first, second, third or fourth polypeptides. 
     
     
         34 . The method of  claim 31 , wherein the first and third polypeptides are identical. 
     
     
         35 . The method of  claim 34 , wherein the second and fourth polypeptides are identical.