Polypeptide structural motifs associated with cell signaling activity

Abstract

Isolated polypeptides comprising or consisting essentially of specific structural motifs (e.g., three β-sheets and two α-helices) are provided, wherein the polypeptides exhibit at least one cell signaling and/or other non-canonical activity of biological relevance. Also provided are polynucleotides encoding such polypeptides, binding agents that bind such polypeptides, analogs, variants and fragments of such polypeptides, etc., as well as compositions and methods of identifying and using any of the foregoing.

1 . An isolated polypeptide consisting essentially of three β-sheets and two α-helices, wherein the polypeptide exhibits a cell signaling or other non-canonical activity. 
     
     
         2 . The isolated polypeptide of  claim 1 , wherein the polypeptide consists essentially of three antiparallel β-sheets flanked at each end by an α-helix. 
     
     
         3 . The isolated polypeptide of  claim 1 , wherein the polypeptide comprises about 60 to 200 amino acid residues. 
     
     
         4 . The isolated polypeptide of  claim 1 , wherein the polypeptide comprises a contiguous fragment of a human protein, or a sequence having at least 80% identity to said contiguous fragment. 
     
     
         5 . The isolated polypeptide of  claim 1 , wherein the polypeptide comprises at least two non-contiguous fragments of a human protein, or sequences having at least 80% identity to said non-contiguous fragments. 
     
     
         6 . The isolated polypeptide of  claim 1 , wherein the polypeptide is
 a) a GlyRS polypeptide comprising residues 345-438 of SEQ ID NO: 1 or an active fragment or variant thereof;   b) an AspRS polypeptide comprising residues 367-448 of SEQ ID NO: 2 or an active fragment or variant thereof;   c) a HisRS polypeptide comprising residues 294-372 of SEQ ID NO: 3 or an active fragment or variant thereof;   d) a ThrRS polypeptide comprising residues 469-586 of SEQ ID NO: 4 or an active fragment or variant thereof;   e) a GluProRS polypeptide comprising residues 1171-1253 of SEQ ID NO: 5 or an active fragment or variant thereof;   f) a SerRS polypeptide comprising residues 325-410 of SEQ ID NO: 6 or an active fragment or variant thereof;   g) a PheRS polypeptide comprising residues 380-449 of SEQ ID NO: 7 or an active fragment or variant thereof;   h) a LysRS polypeptide comprising residues 425-523 of SEQ ID NO: 8 or an active fragment or variant thereof;   i) a AsnRS polypeptide comprising residues 416-494 of SEQ ID NO: 9 or an active fragment or variant thereof;   j) a AlaRS polypeptide comprising residues 148-258 of SEQ ID NO: 10 or an active fragment or variant thereof;   k) a thioredoxin polypeptide comprising residues 20-105 of SEQ ID NO: 11 or an active fragment or variant thereof;   l) a macrophage inhibitory factor polypeptide comprising residues 1-90 of SEQ ID NO: 12 or an active fragment or variant thereof; and/or   m) a peroxiredoxin 5 isoform B polypeptide comprising residues 32-68 and 125-161 of SEQ ID NO: 13 or an active fragment or variant thereof.   
     
     
         7 .- 18 . (canceled) 
     
     
         19 . The isolated polypeptide of  claim 1 , wherein the polypeptide has chemokine activity. 
     
     
         20 . A pharmaceutical composition comprising a polypeptide according to  claim 1 . 
     
     
         21 . An a) isolated polynucleotide encoding a polypeptide according to  claim 1 , b) vector comprising an isolated polynucleotide of a), or c) host cell comprising a vector of b). 
     
     
         22 - 23 . (canceled) 
     
     
         24 . A method for identifying a polypeptide fragment having a cell signaling activity, comprising the steps of identifying a protein sequence containing a structural motif comprised of two α-helices and three β-sheets, determining the amino acid residue boundaries of the structural motif within said protein, and thereby identifying a polypeptide fragment having cell signaling activity. 
     
     
         25 . The method of  claim 24 , wherein the structural motif consists essentially of at least three antiparallel β-sheets flanked at each end by an α-helix. 
     
     
         26 . The method of  claim 24 , wherein the polypeptide fragment comprises about 60 to 200 amino acids of the protein. 
     
     
         27 . The method of  claim 24 , wherein the step of identifying a protein sequence containing a structural motif comprised of two α-helices and three anti-parallel β-sheets is performed using a secondary structure prediction method. 
     
     
         28 . The method of  claim 24 , wherein the step of identifying a protein sequence containing a structural motif comprised of two α-helices and three anti-parallel β-sheets is performed using a secondary structure prediction method selected from the group consisting of PHDsec, NSSP, SOPM, DSC, SSPRED, MultiPredict, PSA, NNPREDICT, APSSP, GOR, HNN, HTMSRAP, Jpred, JUFO, nnPredict, Porter, PredictProtein, Prof, PSIpred, SOPMA, SSpro and DLP-SVM. 
     
     
         29 . A method for modulating cell signaling comprising contacting a cell with an effective amount of a composition comprising:
 a) a polypeptide according to  claim 1 ;   b) a polynucleotide according to  claim 21 ; and/or   c) an antibody or antigen-binding fragment thereof that specifically binds a polypeptide according to  claim 1 .   
     
     
         30 . The method of  claim 29 , wherein the method is a method of:
 a) modulating chemokine activity;   b) modulating TNF-α secretion;   c) inducing TNF-α secretion;   d) modulating immune cell chemotaxis; and/or   e) inducing monocyte chemotaxis.   
     
     
         31 .- 34 . (canceled) 
     
     
         35 . A screening method for identifying a modulator of cell signaling, comprising the steps of:
 (a) forming a reaction mixture including:
 (i) a component selected from the group consisting of a polypeptide according to  claim 1 ; a polynucleotide according to  claim 21 ; and/or an antibody or antigen-binding fragment thereof that specifically binds a polypeptide according to  claim 1 ; 
 (ii) a binding partner, cellular effector and/or cell type known to be bound and/or modulated by said component; and 
 (iii) a test compound; and 
   (b) detecting an interaction of said component with the binding partner, cellular effector and/or cell type, wherein a change in the interaction in the presence of test compound, relative to the interaction in the absence of the test compound, thereby identifies a modulator of cell signaling.