Methods of identifying target polypeptides

Abstract

The present invention provides methods for identifying and/or rank ordering target polypeptides that interact with a candidate polypeptide. Potential targets for the candidate polypeptide are identified using an interaction assay. A set of mutants are derived from the candidate polypeptide and a functional profile is obtained for the set of mutants and the candidate polypeptide. Also, for each identified potential target, an interaction profile is obtained for the set of mutants and the candidate polypeptide. The interaction profiles are compared to the functional profile and based on the degree of correspondence between the profiles, the potential targets are identified and/or rank ordered as target polypeptides that interact to the candidate polypeptide.

What is claimed is:  
     
         1 . A method of rank ordering potential targets of a candidate polypeptide, comprising: 
 (a) comparing a functional profile for a set of polypeptides, wherein said set of polypeptides comprises the candidate polypeptide and a set of mutants derived therefrom, and a plurality of interaction profiles for the set of polypeptides to identify those interaction profiles that correspond to said functional profile, wherein each interaction profile corresponds to a potential target for the candidate polypeptide; and    (b) creating a rank order of said potential targets based upon the degree of correspondence between each interaction profile and functional profile, wherein the rank order of a potential target identifies the likelihood of interaction between the potential target and candidate polypeptide.    
     
     
         2 . The method of  claim 1 , wherein comparing comprises: 
 (a) from the functional profile, obtaining a difference between each mutant functional value and candidate polypeptide functional value to obtain a series of functional difference values;    (b) from the interaction profile of each potential target, obtaining a difference between each mutant interaction value and candidate polypeptide interaction value to obtain a series of interaction difference values; and    (c) for each potential target, producing a set of difference values, wherein each difference value is the difference between the functional difference value and corresponding interaction difference value, thereby identifying those interaction profiles that correspond to the functional profile based on the difference values.    
     
     
         3 . The method of  claim 2 , wherein (c) comprises: 
 determining the statistical difference between the functional difference values and corresponding interaction difference values.    
     
     
         4 . The method of  claim 1 , wherein comparing comprises: 
 selecting those interaction profiles that correspond to the functional profile based on visual comparison of the functional values in the functional profile with corresponding interaction values in the interaction profile of each potential target.    
     
     
         5 . The method of  claim 1 , further comprising identifying the candidate polypeptide in a functional assay.  
     
     
         6 . The method of  claim 5  further comprising identifying the candidate polypeptide in an interleukin-4 activity assay.  
     
     
         7 . The method of  claim 5 , wherein the mutants are dual alanine mutants; the interaction profiles are identified in a yeast two hybrid assay; and the functional assay is an interleukin-4 activity assay.  
     
     
         8 . The method of  claim 1 , wherein the mutants comprising the set of mutants are dual alanine mutants.  
     
     
         9 . The method of  claim 1 , wherein the set of mutants comprises at least two mutants selected from the group consisting of loss of function, reduction of function, and increase of function mutants.  
     
     
         10 . The method of  claim 1 , wherein the set of mutants comprises scrambled sequence and reversed peptide sequence mutants.  
     
     
         11 . A method of rank ordering potential targets of a candidate polypeptide comprising: 
 (a) generating a functional profile for a set of polypeptides comprising the candidate polypeptide and a set of mutants derived therefrom;    (b) generating a plurality of interaction profiles for the set of polypeptides, wherein each interaction profile corresponds to a potential target for the candidate polypeptide; and    (c) creating a rank order of the potential targets based upon the degree of correspondence between each interaction profile and functional profile, wherein the rank order of a potential target identifies the likelihood of interaction between the potential target and candidate polypeptide.    
     
     
         12 . The method of  claim 11 , further comprising identifying the potential targets in an interaction assay.  
     
     
         13 . The method of  claim 11 , further comprising identifying the candidate polypeptide in a functional assay.  
     
     
         14 . The method of  claim 13 , further comprising identifying the candidate polypeptide in an interleukin-4 activity assay.  
     
     
         15 . The method of  claim 13 , wherein the mutants are dual alanine mutants; the interaction profiles are identified in a yeast two hybrid assay; and the functional assay is an interleukin-4 activity assay.  
     
     
         16 . The method of  claim 11 , wherein the mutants comprising the set of mutants are dual alanine mutants.  
     
     
         17 . The method of  claim 11 , wherein the set of mutants comprises at least two mutants selected from the group consisting of loss of function, reduction of function, and increase of function mutants.  
     
     
         18 . The method of  claim 11 , wherein the set of mutants comprises scrambled sequence and reversed peptide sequence mutants.  
     
     
         19 . The method of  claim 11 , wherein the interaction profiles are identified in a yeast two hybrid assay.  
     
     
         20 . A method of rank ordering potential targets of a candidate polypeptide, comprising: 
 (a) identifying a set of potential targets for the candidate polypeptide in an interaction assay;    (b) generating a functional profile for a set of polypeptides comprising the candidate polypeptide and a set of mutants derived therefrom;    (c) for each potential target identified in (a), generating an interaction profile for the set of polypeptides;    (d) selecting those interaction profiles that correspond to the functional profile; and    (e) creating a rank order of said potential targets based upon the degree of correspondence between each interaction profile and functional profile, wherein the rank order of a potential target identifies the likelihood of interaction between the potential target and candidate polypeptide.    
     
     
         21 . The method of  claim 20 , wherein selecting comprises: 
 (a) from the functional profile, obtaining a difference between each mutant functional value and candidate polypeptide functional value to obtain a series of functional difference values;    (b) from the interaction profile of each potential target, obtaining a difference between each mutant interaction value and candidate polypeptide interaction value to obtain a series of interaction difference values; and    (c) for each potential target, producing a set of difference values, wherein each difference value is the difference between the functional difference value and corresponding interaction difference value, thereby identifying those interaction profiles that correspond to the functional profile based on the difference values.    
     
     
         22 . The method of  claim 21 , wherein (c) comprises: 
 determining the statistical difference between the functional difference values and their respective interaction difference values.    
     
     
         23 . The method of  claim 20 , wherein selecting comprises: 
 selecting those interaction profiles that correspond to the functional profile based on visual comparison of the functional values in the functional profile with corresponding interaction values in the interaction profile of each target.    
     
     
         24 . The method of  claim 20 , further comprising identifying the candidate polypeptide in a functional assay.  
     
     
         25 . The method of  claim 24 , further comprising identifying the candidate polypeptide in an interleukin-4 activity assay.  
     
     
         26 . The method of  claim 24 , wherein the mutants are dual alanine mutants; the interaction profiles are identified in a yeast two hybrid assay; and the functional assay is an interleukin-4 activity assay.  
     
     
         27 . The method of  claim 20 , wherein the mutants comprising the set of mutants are dual alanine mutants.  
     
     
         28 . The method of  claim 20 , wherein the set of mutants comprises at least two mutants selected from the group consisting of loss of function, reduction of function, and increase of function mutants.  
     
     
         29 . The method of  claim 20 , wherein the set of mutants comprises scrambled sequence and reversed peptide sequence mutants.  
     
     
         30 . The method of  claim 20 , wherein the interaction assay is a yeast two hybrid assay.  
     
     
         31 . A method of identifying a target of a candidate polypeptide comprising: 
 (a) identifying a set of potential targets for the candidate polypeptide in an interaction assay;    (b) generating a functional profile for a set of polypeptides comprising the candidate polypeptide and a set of mutants derived therefrom;    (c) for each potential target identified in (a), generating an interaction profile for the set of polypeptides;    (d) identifying an interaction profile that corresponds closely to the functional profile, thereby identifying the potential target that corresponds to the identified interaction profile as being a target of the candidate polypeptide.    
     
     
         32 . The method of  claim 31 , further comprising identifying the candidate polypeptide in a functional assay.  
     
     
         33 . The method of  claim 32 , further comprising identifying the candidate polypeptide in an interleukin-4 activity assay.  
     
     
         34 . The method of  claim 32 , wherein the mutants are dual alanine mutants; the interaction profiles are identified in a yeast two hybrid assay; and the functional assay is an interleukin-4 activity assay.  
     
     
         35 . The method of  claim 31 , wherein the mutants comprising the set of mutants are dual alanine mutants.  
     
     
         36 . The method of  claim 31 , wherein the set of mutants comprises at least two mutants selected from the group consisting of loss of function, reduction of function, and increase of function mutants.  
     
     
         37 . The method of  claim 31 , wherein the set of mutants comprises scrambled sequence and reversed peptide sequence mutants.  
     
     
         38 . The method of  claim 31 , wherein the interaction assay is a yeast two hybrid assay.  
     
     
         39 . A computer implemented method of rank ordering potential targets of a candidate polypeptide, comprising: 
 (a) comparing a functional profile for a set of polypeptides, wherein said set of polypeptides comprises the candidate polypeptide and a set of mutants derived therefrom, and a plurality of interaction profiles for the set of polypeptides to identify those interaction profiles that correspond to said functional profile, wherein each interaction profile corresponds to a potential target for the candidate polypeptide; and    (b) creating a rank order of said potential targets based upon the degree of correspondence between each interaction profile and functional profile, wherein the rank order of a potential target identifies the likelihood of interaction between the potential target and candidate polypeptide.    
     
     
         40 . The method of  claim 39 , wherein comparing comprises: 
 (a) from the functional profile, obtaining a difference between each mutant functional value and candidate polypeptide functional value to obtain a series of functional difference values;    (b) from the interaction profile of each potential target, obtaining a difference between each mutant interaction value and candidate polypeptide interaction value to obtain a series of interaction difference values; and    (c) for each potential target, producing a set of difference values, wherein each difference value is the difference between the functional difference value and corresponding interaction difference value, thereby identifying those interaction profiles that correspond to the functional profile based on the difference values.    
     
     
         41 . The method of  claim 40 , wherein (c) comprises: 
 determining the statistical difference between the functional difference values and corresponding interaction difference values.