Orthogonal protein heterodimers

Abstract

Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

We claim: 
     
         1 - 116 . (canceled) 
     
     
         117 . A designed heterodimer protein, comprising a monomer A polypeptide and a monomer B polypeptide, wherein:
 (a) the monomer A polypeptide and the monomer B polypeptide together comprise 4 alpha helices that interact to form the designed heterodimer protein; and   (b) central repeat units of each of the monomer A polypeptide and the monomer B polypeptide comprise a buried, asymmetric hydrogen bond network connecting all four alpha helices;   
       wherein:
 (i) the monomer A polypeptide is a non-naturally occurring polypeptide comprising 2 alpha helices connected by an amino acid linker, and the monomer B polypeptide is a non-naturally occurring polypeptide comprising 2 alpha helices connected by an amino acid linker; or 
 (ii) the monomer A polypeptide is a non-naturally occurring polypeptide comprising 1 alpha helix, and the monomer B polypeptide is a non-naturally occurring polypeptide comprising 3 alpha helices connected by amino acid linkers. 
 
     
     
         118 . The designed heterodimer protein of  claim 117  wherein the monomer A polypeptide is a non-naturally occurring polypeptide comprising 2 alpha helices connected by an amino acid linker, and the monomer B polypeptide is a non-naturally occurring polypeptide comprising 2 alpha helices connected by an amino acid linker. 
     
     
         119 . The designed heterodimer protein of  claim 117  wherein the monomer A polypeptide is a non-naturally occurring polypeptide comprising 1 alpha helix, and the monomer B polypeptide is a non-naturally occurring polypeptide comprising 3 alpha helices connected by amino acid linkers. 
     
     
         120 . The designed heterodimer protein of  claim 117  wherein the monomer A polypeptide and the monomer B polypeptide have an interaction specificity determined by four hydrogen bond networks. 
     
     
         121 . The designed heterodimer protein of  claim 117  wherein the monomer A polypeptide and the monomer B polypeptide each comprise an effector polypeptide domain. 
     
     
         122 . The designed heterodimer protein of  claim 121  wherein each of the effector polypeptide domains is independently selected from the group consisting of a nucleic acid binding protein, a transcription factor, a receptor binding protein, a split enzyme, and an effector of membrane receptors. 
     
     
         123 . The designed heterodimer protein of  claim 117  wherein the monomer A polypeptide comprises a region that binds to a target A and the monomer B polypeptide comprises a region that binds to a target B. 
     
     
         124 . The designed heterodimer protein of  claim 123  wherein a binding affinity of the monomer A polypeptide for target A is approximately equal to a binding affinity of the monomer B polypeptide for target B. 
     
     
         125 . The designed heterodimer protein of  claim 123  wherein a binding affinity of the monomer A polypeptide for target A and a binding affinity of the monomer B polypeptide for target B are greater than a binding affinity of target A for target B. 
     
     
         126 . A cell comprising the designed heterodimer protein of  claim 117 . 
     
     
         127 . The cell of  claim 126  wherein assembly of the designed heterodimer protein regulates a biological function of the cell. 
     
     
         128 . The cell of  claim 126  wherein the monomer A polypeptide and the monomer B polypeptide selectively form a cognate pair and avoid binding to other non-cognate monomers of the cell. 
     
     
         129 . A biological cell comprising a protein logic gate comprising the designed heterodimer protein of  claim 117  as a component of the protein logic gate. 
     
     
         130 . The protein logic gate of  claim 129  provided as an AND, OR, NOT, XOR, NAND, NOR or XNOR logic gate. 
     
     
         131 . A transcriptional network comprising the designed heterodimer protein of  claim 117  as a component of the transcriptional network.