Protein scaffolds for antibody mimics and other binding proteins

Abstract

Disclosed herein are proteins that include an immunoglobulin fold and that can be used as scaffolds. Also disclosed herein are nucleic acids encoding such proteins and the use of such proteins in diagnostic methods and in methods for evolving novel compound-binding species and their ligands.

What is claimed is: 
     
         1 - 43 . (canceled) 
     
     
         44 . An isolated protein comprising a domain derived from the tenth module of the human fibronectin type III ( 10 Fn3) comprising an amino acid sequence that
 (a) comprises seven beta strands distributed between two antiparallel beta-sheets;   (b) comprises BC, DE and FG loops which connect the beta strands, wherein one, two or three of said loops are mutated;   (c) lacks an integrin binding motif; and   (d) is at least 70% identical to the wild-type human  10 Fn3 domain,   
       wherein said derivative  10 Fn3 domain binds with a Kd at least as tight as 1 μM to an antigen. 
     
     
         45 . The protein of  claim 44 , wherein said protein is a monomer under physiological conditions. 
     
     
         46 . The protein of  claim 44 , wherein said protein is a dimer under physiological conditions. 
     
     
         47 . The protein of  claim 44 , wherein said protein is fused to a second protein domain. 
     
     
         48 . An array comprising a library of proteins comprising a domain derived from the tenth module of the human fibronectin type III ( 10 Fn3) comprising an amino acid sequence that
 (a) comprises seven beta strands distributed between two antiparallel beta-sheets;   (b) comprises BC, DE and FG loops which connect the beta strands, wherein one, two or three of said loops are mutated;   (c) lacks an integrin binding motif; and   (d) is at least 70% identical to the wild-type human  10 Fn3 domain.   
     
     
         49 . A nucleic acid encoding an isolated protein comprising a domain derived from the tenth module of the human fibronectin type III ( 10 Fn3) comprising an amino acid sequence that
 (a) comprises seven beta strands distributed between two antiparallel beta-sheets;   (b) comprises BC, DE and FG loops which connect the beta strands, wherein one, two or three of said loops are mutated;   (c) lacks an integrin binding motif; and   (d) is at least 70% identical to the wild-type human  10 Fn3 domain.   
     
     
         50 . A method of obtaining a protein comprising a domain derived from the tenth module of the wild-type human fibronectin type III ( 10 Fn3) which binds to an antigen, the method comprising:
 (a) providing a wild-type  10 Fn3 domain; to t   (b) generating mutated derivatives of the wild-type  10 Fn3 domain, thereby producing a library of  10 Fn3 domain derivatives;   (c) contacting the library with the antigen;   (d) selecting from the library at least one derivative protein which binds to the antigen with a Kd at least as tight as 1 μM; and   (e) optionally repeating steps (b)-(d).   
     
     
         51 . A method of isolating a protein comprising a domain derived from the tenth module of the wild-type human fibronectin type III ( 10 Fn3) which binds to an antigen, the method comprising:
 (a) contacting the antigen with a candidate protein comprising a mutated derivative of the wild-type  10 Fn3 domain which binds with a Kd at least as tight as 1 μM the antigen under conditions that allow antigen-protein complex formation; and   (b) obtaining the  10 Fn3 derivative protein from the complex.   
     
     
         52 . A method of detecting an antigen in a sample, said method comprising:
 (a) contacting said sample with a protein comprising a domain derived from the tenth module of the wild-type human fibronectin type III ( 10 Fn3) which binds to the antigen with a Kd at least as tight as 1 μM the antigen under conditions that allow antigen-protein complex formation; and   (b) detecting the complex;   
       wherein the detection of the complex indicates the presence of the antigen in the sample. 
     
     
         53 . A pharmaceutical composition comprising the protein of  claim 44 .