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.

Description

1. FIELD OF THE INVENTION[0001] The present invention relates to methods for identifying and / or rank ordering target polypeptides that interact with a candidate polypeptide. Specifically, the methods identify and / or rank order target polypeptides by performing functional and interaction assays and comparing the functional and interaction profiles obtained from these assays.2. BACKGROUND OF THE INVENTION[0002] Proteins and protein-protein interactions play a central role in various essential biological processes. For example, these interactions are evident in the interaction of hormones with their respective receptors, in the intracellular and extracellular signalling events mediated by proteins, in enzyme substrate interactions, in intracellular protein trafficking, in the formation of complex structures like ribosomes, viral coat proteins, and filaments, and in antigen-antibody interactions.[0003] Abnormal or disease states can be the direct result of aberrant protein-protein inter...

AI Technical Summary

Benefits of technology

0012] In its broadest sense, the method involves comparing interaction profiles of a set of polypeptides with a functional profile of the set of polypeptides to identify those interaction profiles that correspond to the functional profile. The set of polypeptides comprises a candidate polypeptide for which interaction partner is desired and a set of mutants derived therefrom. In one embodiment, the set of polypeptides includes, in addition to the candidate polypeptide, at least one mutant from each of four different categories: (i) a neutral mutant (N); (ii) a reduction-of-function mutant (ROF or R); (iii) a loss-of-function mutant (LOF or L); and (iv) an increase-of-function (IOF or I) mutant. The functional profile comprises quantitative functional information for each polypeptide of the set, which is typically obtained by assaying each polypeptide of the set in the same functional assay. The interaction profiles comprise quantitative interaction information for each polypeptide of the set, which is typically obtained by assaying each polypeptide in an interaction assay that assesses the ability of the polypeptide to interact with a potential target polypeptide. The degree of correspondence observed between the interaction profiles and functional profiles can be used to rank-order the potential target polypeptides and/or to identify a target polypeptide that interacts with the candidate polypeptide. For rank-ordering, the potential target polypeptides are ordered based upon the degree of correspondence between their respective interaction profiles and functional profile, from highest correspondence to lowest correspondence. The rank-ordering represents the likelihood that a particular potential polypeptide represents an actual target polypeptide for the candidate polypeptide in a biological system. Target polypeptides are identified by selecting those interaction profiles that correspond with the functional profile to a specified degree.

0013] The functional and

Problems solved by technology

The traditional techniques have several drawbacks, the main one being that many of the identified potential target polypeptides are not biologically relevant in a cellular environment.

These traditional techniques have the capability to identify polypeptides that interact with each other, however, more often than not the identified interacting polypeptides do not perform any biologically relevant function in a cellular environment.

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