# Patent

## Title
Binding proteins to the constant region of immunoglobulin G

## Abstract

The present invention provides polypeptides that bind to immunoglobulin G and methods for their use.

## Background
CROSS-REFERENCE
This application is a U.S. National Phase of International Application No. PCT/US2013/033721, filed Mar. 25, 2013, which claims priority to U.S. Provisional Application No. 61/615,642, filed Mar. 26, 2012, the disclosures of which are hereby incorporated by reference in their entireties.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
This invention was made with government support under grant number HDTRA1-10-1-0040 awarded by the Defense Threat Reduction Agency. The government has certain rights in the invention.


BACKGROUND
Recombinant monoclonal antibodies and Fc-fusion proteins have become an important class of biological pharmaceuticals and research reagents. Their manufacture typically involves mammalian cells as the expression host and affinity chromatography as a key purification step. While upstream processes such as cell-line development and engineering have significantly enhanced antibody yields, the downstream purification steps remain expensive and reduce productivity. The vast majority of antibody purification pipelines employ a Protein A-based purification step, which contributes to the majority of the raw-material costs1, 2. Antibody elution from a Protein A column is typically achieved by lowering the pH to 3. However, at such low pH, aggregation and denaturation of the antibody and of Fc-fusion proteins can easily occur.
SUMMARY OF THE INVENTION
In a first aspect, the present invention provides polypeptides comprising or consisting of an amino acid sequence of general formula 1 Z1-Z2-Z3 (SEQ ID NO: 1), wherein
Z1 is a peptide with an amino acid sequence according to general formula 2: X1-S-X2 (SEQ ID NO: 2), wherein

    
    
        X1 is any four amino acids; and
        X2 is any nine amino acids;
    
    


Z2 is a peptide of between 17 and 50 amino acid residues; and
Z3 is a peptide with an amino acid amino acid sequence according to general formula 3: B1-Q-B2-F-Y-B3 (SEQ ID NO: 3)

    
    
        B1 is any four amino acids;
        B2 is any two amino acids; and
        B3 is any four amino acids.
    
    


In one embodiment, X2 may be R-X10 (SEQ ID NO: 50), wherein X10 is any 8 amino acids. In another embodiment, X2 may be a peptide of general formula 4: R-J1-V-J2 (SEQ ID NO: 4), wherein

    
    
        J1 is any two amino acids; and
        J2 is any five amino acids.
    
    


In one embodiment, X2 may be RTA(X3)D(A/F)(L/R/K)(K/L)H (SEQ ID NO: 5); wherein X3 is any amino acid.
In a further embodiment, B1 may be (T/S/R/M/P/W/V)(M/F)(E/M/K/L/V)(Q) (SEQ ID NO: 6). In another embodiment, B2 may be (S/A)(F/L/M/I). In a still further embodiment, B3 may be M(B4)(L/W)(R/K) (SEQ ID NO: 7), wherein B4 is any amino acid. In another embodiment, the polypeptides comprise an amino acid sequence of general formula 5, Z4-Z1-Z2-Z3 (SEQ ID NO: 8), wherein Z4 is a peptide of at least between 100-200 amino acids in length.
In another aspect, the invention provides pharmaceutical compositions comprising the polypeptide of any embodiment of the invention and a pharmaceutically acceptable carrier.
In a further aspect, the invention provides compositions, comprising the polypeptide of any embodiment of the invention bound to a solid support.
In another aspect, the present invention provides isolated nucleic acids, encoding the polypeptide of any embodiment of the invention. In a further aspect, the invention provides recombinant expression vectors comprising a nucleic acid of the invention operatively linked to a promoter. In a still further aspect, the invention provides recombinant host cells, comprising the recombinant expression vector of the invention.
In a further aspect, the invention provides methods for purifying antibodies, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to any embodiment of the invention under suitable conditions for binding of antibodies in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) dissociating the antibody from the antibody-polypeptide complexes, to isolate the antibody.
In a still further aspect, the invention provides methods for detection of an antibody in a sample, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to any embodiment of the invention under suitable conditions for binding of antibodies or Fc fusion protein in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) detecting the antibody-polypeptide complexes.



DESCRIPTION OF THE FIGURES
FIG. 1. Design strategy. (A) Phe14 from Protein A (pdb I.D. 116×) with Fc and comparing the binding interactions of Protein A, neonatal Fc receptor (FcRn)19 and a synthetic peptide isolated through phage display. (B) Docked hotspots derived from Phe14. (C) Inverse rotamers of Gln11. (D) Minimized Protein A B domain called Z34C and model of FcB6 bound to the Fc region of IgG1 (based on 116×).
FIG. 2. Summary of the first round of affinity improvement; sequence alignment after 3 selections (SEQ ID NO: 213). Sequence contains HM at the N-terminus and LE at the C-terminus which were part of the cloning sites.
FIGS. 3A and B. Sequence alignments (from top to bottom (FIG. 3A) SEQ ID NOs: 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 199, 200, and 200; and (FIG. 3B) SEQ ID NOs: 188, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 210, 211, and 212) of clones after 4 selections at different pH levels, showing only the sequence stretch that contained mutations from the originally designed sequence.
FIG. 4. Diversity of C-terminal interface helix (epi2 library), here residues 155-179 (SEQ ID NO: 187) are shown. Alignment contains residue combination after 3 rounds of selection, amino acid on top describe the starting diversity. Selections were done around neutral pH. These changes affect binding affinity, but unlikely affect pH sensitivity as this peptide stretch is not the helix peptide stretch next to histidine 433 of the IgG.



DETAILED DESCRIPTION OF THE INVENTION
All references cited are herein incorporated by reference in their entirety. Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.).
As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. “And” as used herein is interchangeably used with “or” unless expressly stated otherwise.
As used herein, the amino acid residues are abbreviated as follows: alanine (Ala; A), asparagine (Asn; N), aspartic acid (Asp; D), arginine (Arg; R), cysteine (Cys; C), glutamic acid (Glu; E), glutamine (Gln; Q), glycine (Gly; G), histidine (His; H), isoleucine (Ile; I), leucine (Leu; L), lysine (Lys; K), methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V).
All embodiments of any aspect of the invention can be used in combination, unless the context clearly dictates otherwise.
Unless the context clearly requires otherwise, throughout the description and the claims, the words ‘comprise’, ‘comprising’, and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of “including, but not limited to”. Words using the singular or plural number also include the plural and singular number, respectively. Additionally, the words “herein,” “above,” and “below” and words of similar import, when used in this application, shall refer to this application as a whole and not to any particular portions of the application.
The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While the specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize.
In a first aspect, the present invention provides polypeptides comprising an amino acid sequence of general formula 1 Z1-Z2-Z3 (SEQ ID NO: 1), wherein
Z1 is a peptide with an amino acid sequence according to general formula 2: X1-S-X2 (SEQ ID NO: 2), wherein

    
    
        X1 is any four amino acids; and
        X2 is any nine amino acids;
    
    


Z2 is a peptide of between 17 and 50 amino acid residues; and
Z3 is a peptide with an amino acid amino acid sequence according to general formula 3: B1-Q-B2-F-Y-B3 (SEQ ID NO: 3)

    
    
        B1 is any four amino acids;
        B2 is any two amino acids; and
        B3 is any four amino acids.
    
    


As demonstrated herein, the inventors have computationally designed and prepared polypeptides according to the invention that bind to the Fc (Fragment, crystallizable) constant region of immunoglobulin G (IgG). The recited polypeptide serves as a module that can bind to the IgG Fc region, and thus can be combined with other polypeptide modules to carry out such binding and to add other functionality to as desired for a given purpose. The IgG Fc-binding of the polypeptides of the present invention permits the use of polypeptides of the invention, for example, as an alternative to Protein A in antibody or Fc fusion protein isolation and other assays. Furthermore, in some embodiments, the polypeptides are thermostable and can be purified through heating bacterial cells expressing them at up to 80° C. Therefore, little to no other physical or chemical step is necessary to release the polypeptides from the cells. Centrifugation eliminates cell debris and aggregates. Thus, production could be much less cumbersome and expensive compared to Protein A. The thermostability of the polypeptides likely results in a longer half-life than the conventional Protein A and possibly less proteolytic cleavage.
In one embodiment, Z1 and Z3 represent two different helices that interact with the Fc region of an IgG and are separated by spacer region Z2.
In one embodiment, the X2 is R-X10 (SEQ ID NO: 50), wherein X10 is any 8 amino acids. In this embodiment, Z1 has the sequence X1-S-R-X10 (SEQ ID NO: 9). As described in more detail in the examples that follow, this embodiment provides the added benefit of pH-dependent binding of the polypeptides of the invention to the IgG Fc region. Thus, the polypeptides bind more strongly to the IgG Fc region at one pH compared to another pH, permitting pH dependent fine control for IgG affinity purification and other uses.
In another embodiment, X2 is a peptide of general formula 4: R-J1-V-J2 (SEQ ID NO: 4), wherein

    
    
        J1 is any two amino acids; and
        J2 is any five amino acids. This embodiment provides improved pH dependent binding to the resulting polypeptides, as described in more detail in the examples that follow.
    
    


In a further embodiment, X1 is EY(A/C)V (SEQ ID NO: 10). In a still further embodiment, X2 is (R/A/T)TA(X3)DA(L/R/K/F)(K/L)(H/L) (SEQ ID NO: 11); wherein X3 is any amino acid. In other embodiments, X2 is RTA(X3)DA(R/K)KH (SEQ ID NO: 12) or RTAVDALKH (SEQ ID NO: 13). Each of these embodiments is found in specific preferred polypeptides described in the examples that follow, or is a genus of amino acid sequences found in such preferred polypeptides.
In other embodiments, Z1 is selected from the group consisting of








EYCVSATAEDALKH;
(SEQ ID NO: 14)


 


EYCVSRTAVDAKKH;
(SEQ ID NO: 15)


 


EYAVSRTAVDALKH;
(SEQ ID NO: 16)


 


EYCVSRTAVDALKH;
(SEQ ID NO: 17)


 


EY(A/C)VSRTA(E/V/L/M/A/I/T)DALKH;
(SEQ ID NO: 18)


 


EY(A/C)VSRTA(E/V/L/R/M/A)DALKH;
(SEQ ID NO: 19)


 


EY(A/C)VSRTA(E/V/M/A/I/T)DALKH;
(SEQ ID NO: 20)


 


EY(A/C)VSRTAVDALKH;
(SEQ ID NO: 21)


 


EY(A/C)VSRTA(V/M)DALKH;
(SEQ ID NO: 22)


 


EY(A/C)VSRTAMDALKH;
(SEQ ID NO: 23)


 


EY(A/C)VSRTAADALKH;
(SEQ ID NO: 24)


 


EY(A/C)VSRTAMDALKH;
(SEQ ID NO: 25)


 


EY(A/C)VSRTALDALKH;
(SEQ ID NO: 26)


 


EY(A/C)VSRTAIDALKH;
(SEQ ID NO: 27)


 


EY(A/C)VSRTATDALKH;
(SEQ ID NO: 28)


 


EY(A/C)VSRTAVDALKH
(SEQ ID NO: 29)


 


EYAVSRTAMDALKH;
(SEQ ID NO: 30)


 


EYAVSRTAADALKH;
(SEQ ID NO: 31)


 


EYAVSRTAMDALKH;
(SEQ ID NO: 32)


 


EYAVSRTALDALKH;
(SEQ ID NO: 33)


 


EYAVSRTAIDALKH;
(SEQ ID NO: 34)


 


EYAVSRTATDALKH;
(SEQ ID NO: 35)


 


EYCVSRTAMDALKH;
(SEQ ID NO: 36)


 


EYCVSRTAADALKH;
(SEQ ID NO: 37)


 


EYCVSRTAMDALKH;
(SEQ ID NO: 38)


 


EYCVSRTALDALKH;
(SEQ ID NO: 39)


 


EYCVSRTAIDALKH;
(SEQ ID NO: 40)


and


 


EYCVSRTATDALKH.
(SEQ ID NO: 41)






Each of these embodiments represents either specific peptide domains in preferred embodiments described herein, or represents consensus sequences of such preferred embodiments. In a further preferred embodiment, Z1 is EYAVSRTAVDALKH (SEQ ID NO: 16) or EYCVSRTAVDALKH (SEQ ID NO: 17).
The polypeptides of general formula 1 as disclosed above include Z3 as a peptide with an amino acid amino acid sequence according to general formula 3: B1-Q-B2-F-Y-B3 (SEQ ID NO: 3)

    
    
        B1 is any four amino acids;
        B2 is any two amino acids; and
        B3 is any four amino acids.
    
    


In one embodiment B1 is (T/S/R/M/P/W/V/E)(M/F)(E/M/K/L/V)Q (SEQ ID NO: 42). In a further embodiment, B1 is (T/S/R/M/P/W/V)(M/F)(E/M/K/L/V)Q (SEQ ID NO: 6). In another embodiment, B1 is TFEQ (SEQ ID NO: 43). In a further embodiment, B2 is (S/A)(F/L/M/I). In a still further embodiment, B2 is selected from the group consisting of SF, SL, AF, and AL. Most preferably, B2 is SF. In another embodiment, B3 is M(B4)(L/W)(R/K) (SEQ ID NO: 7), wherein B4 is any amino acid. In one embodiment, B4 is selected from the group consisting of V, L, M, R, and K; this embodiment is preferred for pH 6.5 dependent polypeptide binders. In another embodiment, B4 is selected from the group consisting of S, T, R, K, and H, which is preferred for pH 8 dependent polypeptide binding. In another embodiment, B3 is selected from the group consisting of MSLK (SEQ ID NO: 44), MTLK (SEQ ID NO: 45) and MKLR (SEQ ID NO: 46); most preferably B3 is MSLK (SEQ ID NO: 44). Each of these embodiments represents either specific peptide domains in preferred embodiments described herein, or represents consensus sequences of such preferred embodiments.
In various further embodiments, Z3 is selected from the group consisting of:







(SEQ ID NO: 47)









EMEQQAFFYMKLR;



 







(SEQ ID NO: 48)









EMEQQALFYMKLR;



 







(SEQ ID NO: 49)









TFEQQSFFYMSLK;



 







(SEQ ID NO: 51)









(B5)(B6)EQQ(S/A)(F/L)FYM(B7)L(K/R),






where B5, B6, and B7 are independently any amino acid;








(SEQ ID NO: 52)







(G/R/S/M/P/W/V/T/R)(M/L/I/A/E/F)EQQ(S/A)(F/


L)FYM(B5)L(K/R);


 







(SEQ ID NO: 53)







(V/H/K/W)(M/W/I/L/H)EQQ(S/A)(F/L)FYM(B5)L(K/R);


 







(SEQ ID NO: 54)







EMEQQALFYMKLK;


 







(SEQ ID NO: 55)







VWEQQSFFYMVLK;


 







(SEQ ID NO: 56)







HWEQQSFFYMLLK;


 







(SEQ ID NO: 57)







HMEQQSFFYMMLK;


 







(SEQ ID NO: 58)







KIEQQSFFYMMLK;


 







(SEQ ID NO: 59)







WLEQQSFFYMALK;


 







(SEQ ID NO: 60)







WLEQQSFFYMQLK;


 







(SEQ ID NO: 61)







WLEQQAFFYMELK;


 







(SEQ ID NO: 62)







WLEQQSFFYMKLK;


 







(SEQ ID NO: 63)







FLEQQSFFYMRLK;


 







(SEQ ID NO: 64)







WHEQQSFFYMMLK;


 







(SEQ ID NO: 65)







WHEQQSFFYMRLK;


 







(SEQ ID NO: 66)







EMEQQALFYMKLK;


 







(SEQ ID NO: 67)







GMEQQSFFYMILK;


 







(SEQ ID NO: 68)







RLEQQSFFYMTLK;


 







(SEQ ID NO: 69)







SLEQQSFFYMNLK;


 







(SEQ ID NO: 70)







MIEQQSFFYMRLK;


 







(SEQ ID NO: 71)







PIEQQSFFYMHLK;


 







(SEQ ID NO: 72)







WLEQQSFFYMHLK;


 







(SEQ ID NO: 73)







VLEQQSFFYMDLK;


 







(SEQ ID NO: 74)







WAEQQSFFYMGLK;


 







(SEQ ID NO: 75)







TEEQQSFFYMTLK;


 







(SEQ ID NO: 76)







TFEQQSFFYMSLK;


 







(SEQ ID NO: 77)







RLEQQSFFYMSLK;


 







(SEQ ID NO: 78)







EREQQSFFYMGLK;


 







(SEQ ID NO: 79)







EREQQSFFYMGLK;


 







(SEQ ID NO: 80)







HMKQQSFFYMSLR;


 







(SEQ ID NO: 81)







HWVQQSFFYMGLK;


 







(SEQ ID NO: 82)







DWVQQSMFYMELK;


 







(SEQ ID NO: 83)







DWVQQSLFYMNLK;


and


 







(SEQ ID NO: 84)







EWVQQSLFYMGLK.






In the polypeptides of the invention according to general formula 1, Z2 is a peptide of between 17 and 50 amino acid residues. Z2 can be any suitable length between 17-50 amino acids (17-45, 17-40, 17-25, 17-30, 17-25, 17-20, etc.) to permit appropriate spacing between helices Z1 and Z3 for binding to IgG Fc regions. There are no specific amino acid sequence requirements in the Z2 domain, and additional peptide domains can be added within Z2 as desired for a given intended purpose. In one embodiment, Z2 is a peptide of between 17 and 32 amino acids. In one embodiment, Z2 comprises or consists of the amino acid sequence G(F/V)(E/D)(V/G)(Y/C)L(L/F)R(D/E/N)AVKG(I/V/F)KP (SEQ ID NO: 85); this embodiment is based on heat map mutational studies described in the examples that follow. In another embodiment, Z2 comprises or consists of the amino acid sequence GFEVYLLRDAVKG(I/V/F)KP (SEQ ID NO: 86). In a preferred embodiment, Z2 comprises or consists of GFEVYLLRDAVKGIKP (SEQ ID NO: 87). Each of these embodiments represents either specific peptide domains in preferred embodiments described herein, or represents consensus sequences of such preferred embodiments.
In various embodiments, the polypeptides of the invention comprise or consist of a peptide selected from the group consisting of:







(SEQ ID NO: 88)







EY(C/A)SATAEDALKHGFEVYLLRDAVKGIKPEMEQQALFYMKLR;


 







(SEQ ID NO: 89)







EY(C/A)SRTARDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMKLK;


 







(SEQ ID NO: 90)







EY(C/A)SRTAVDALKHGFEVYLLRDAVKGIKPVWEQQSFFYMVLK;


 







(SEQ ID NO: 91)







EY(C/A)SRTAADALKHGFEVYLLRDAVKGIKPWLEQQSFFYMALK;


 







(SEQ ID NO: 92)







EY(C/A)SRTAVDALKHGFEVYLLRDAVKGIKPWLEQQAFFYMELK;


 







(SEQ ID NO: 93)







EY(C/A)SRTAMDALKHGFEVYLLRDAVKGIKPFLEQQSFFYMRLK;


 







(SEQ ID NO: 94)







EY(C/A)SHTAMDALKHGFEVYLLRDAVKGIKPHWEQQSFFYMLLK;


 







(SEQ ID NO: 95)







EY(C/A)SHTAVDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMRLK;


 







(SEQ ID NO: 96)







EY(C/A)SHTAVDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMRLK;


 







(SEQ ID NO: 97)







EY(C/A)SWTAVDALKHGFEVYLLRDAVKGIKPHMEQQSFFYMMLK;


 







(SEQ ID NO: 98)







EY(C/A)AFTAVDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMQLK;


 







(SEQ ID NO: 99)







EY(C/A)SVTALDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMRLK;


 







(SEQ ID NO: 100)







EY(C/A)SLTAVDALKHGFEVYLLRDAVKGIKPKIEQQSFFYMMLK;


 







(SEQ ID NO: 101)







EY(C/A)SLTAVDALKHGFEVYLLRDAVKGIKPWHEQQSFFYMLLK;


 







(SEQ ID NO: 102)







EY(C/A)SLTAVDALKHGFEVYLLRDAVKGIKPWHEQQSFFYMLLK;


 







(SEQ ID NO: 103)







EY(C/A)SATAEDALKHGFEVYLLRDAVKGIKPEMEQQALFYMKLR;


 







(SEQ ID NO: 104)







EY(C/A)SRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK;


 







(SEQ ID NO: 105)







EY(C/A)SRTAVDALKHGFEVYLLRDAVKGIKPVLEQQSFFYMDLK;


 







(SEQ ID NO: 106)







EY(C/A)SRTAMDALKHGFEVYLLRDAVKGIKPRLEQQSFFYMTLK;


 







(SEQ ID NO: 107)







EY(C/A)SRTAVDALKHGFEVYLLRDAVKGIKPRLEQQSFFYMSLK;


 







(SEQ ID NO: 108)







EY(C/A)SRTAMDALKHGFEVYLLRDAVKGIKPTEEQQSFFYMTLK;


 







(SEQ ID NO: 109)







EY(C/A)SRTAMDALKHGFEVYLLRDAVKGIKPTEEQQSFFYMTLK;


 







(SEQ ID NO: 110)







EY(C/A)SKTATDALKHGFEVYLLRDAVKGIKPSLEQQSFFYMRLK;


 







(SEQ ID NO: 111)







EY(C/A)STTAIDALKHGFEVYLLRDAVKGIKPGMEQQSFFYMILK;


 







(SEQ ID NO: 112)







EY(C/A)SLTAVDALKHGFEVYLLRDAVKGIKPMIEQQSFFYMRLK;


 







(SEQ ID NO: 113)







EY(C/A)SFTAADALKHGFEVYLLRDAVKGIKPWAEQQSFFYMGLK;


 







(SEQ ID NO: 114)







EY(C/A)SWTAMDALKHGFEVYLLRDAVKGIKPPIEQQSFFYMHLK;


 







(SEQ ID NO: 115)







EY(C/A)SMTAMDALKHGFEVYLLRDAVKGIKPSLEQQSFFYMNLK;


 







(SEQ ID NO: 116)







EY(C/A)AMTAVDALKHGFEVYLLRDAVKGIKPWLEQQSFFYMHLK;


 







(SEQ ID NO: 117)







EYCVSRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK;


and


 







(SEQ ID NO: 118)







EYAVSRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK.






Each of these embodiments represents either specific polypeptides in preferred embodiments described herein, or represents consensus sequences of such preferred embodiments. In a preferred embodiment, Z2 comprises or consists of







(SEQ ID NO: 119)







EY(C/A)VSRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK;


 







(SEQ ID NO: 117)







EYCVSRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK;


or


 







(SEQ ID NO: 118)







EYAVSRTAVDALKHGFEVYLLRDAVKGIKPTFEQQSFFYMSLK.






In another embodiment, the polypeptides comprise an amino acid sequence of general formula 5, Z4-Z1-Z2-Z3 (SEQ ID NO: 8), wherein Z4 is a second peptide fused to Z1-Z2-Z3 (SEQ ID NO: 1). In this embodiment, the polypeptides of the invention are incorporated into a larger protein scaffold. Such a scaffold can be of any type that does not interfere with the polypeptide's ability to bind to IgG Fc regions. As noted above, the polypeptides of the invention serve as a module that can bind to the IgG Fc region, and thus can be combined with other polypeptide modules to carry out such binding and to add other functionality to as desired for a given purpose.
It will be understood that Z4 can be of any length; this embodiment permits any added functionality to be added to the polypeptides of the invention as desired for a given purpose. In one embodiment, Z4 is at least between 100-200 amino acids in length. As described in the examples herein, the inventors used the pyrazinamidase from the hyperthermophilic organism Pyrococcus horikoshii as a starting point for computational design of IgG Fc binders. As will be apparent to those of skill in the art, any other suitable starting protein could have been used to design the IgG Fc binding functionalities of the polypeptides of the invention. In one exemplary embodiment, Z4 is a second polypeptide comprising or consisting of the amino acid sequence:







(SEQ ID NO: 120)







PXXXALIVIDMQNDFV(S/—)(X/—)(X/—)PGGPLXVPGG


 


EXIIXXINXLLXAAR(F/—)XXG(X/—)(X/—)IPVVXTRDWH(X/


 


—)(Q/—)PENHISFXXDXGP(K/—)(Z/—)(P/—)(X/—)(X/


 


—)(T/—)(X/—)(X/—)(X/—)(X/—)(X/—)(X/—)(X/—)(X/


 


—)(G/—)(D/—)(D/—)(S/—)(T/—)(Q/—)(E/—)(G/—)(X/


 


—)(L/—)WPPHXVQGXXGAELXPXL(G/—)(I/—)(F/)(Y/—)(A/)


 


(P/—)QEGD(X/—)(X/—)(X/—)XVIXKXFXTDXXXYSAFXG


 


TD(X/—)(X/—)(X/—)(X/—)(T/—)(G/—)LXXXLRERGVD


 


TVIVXGVAT;






wherein “X” means any amino acid and “-” means that the position may be absent.
This embodiment is based on a consensus sequence of proteins with structural similarity to Pyrococcus horikoshii pyrazinamidase. Several proteins with similar enzymatic functionality as the activity of the Pyrococcus horikoshii pyrazinamidase, have almost identical backbone structure. The sequence similarity diverges easily so that even though only 22% identity might exist, two proteins of this family have almost an identical backbone structure. Thus, a scaffold protein based on the Pyrococcus horikoshii pyrazinamidase can be easily replaced by one of its structural homologues.
In another embodiment, Z4 may comprise or consist of an amino acid sequence with at least 90% identity (i.e.: at least 90%, 92%, 95%, 96%, 97%, 98%, 99%, or 100% identical) to an amino acid sequence selected from the group consisting of:







>1IM5: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 121)







(M/)PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGAL


IVATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKA


TEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVAT;


 


>3R2J: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 122)







(M/—)(A/—)(H/—)(H/—)(H/—)(H/—)


(H/—)(H—)VGTGSNDDDDKSPDPPTLCVTVSSTTDVLIIADM


QVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSF


VTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVE


DNGVSTGLAGLLHSIGARRV FVCGVAY;


 


>3EEF: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 123)







MKPALVVVDMVNEFIHGRLATPEAMKTVGPARKVIETFRRSGLPVVYVN


DSHYPDDPEIRIWGRHSMKGDDGSEVIDEIRPSAGDYVLEKHAYSGFYG


TNLDMILRANGIDTVVLIGLDA;


 


>2WTA: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 124)







(M/—)(G/—)(S/—)(S/—)H/—)(H/—)


(H/—)(H/—)(H/—)(H—)SSGENLYFQGHMKMNKQP


QNSALVVVDVQNGFTPGGNLAVADADTIIPTINQLAGCFENVVLTQDWH


PDNHISFAANHPGKQPFETIELDYGSQVLWPKHCIQGTHDAEFHPDLNI


PTAQLIIRKGFHAHIDSYSAFMEADHTTMTGLTG YLKERGIDTVYV


VGIAT;


 


>3V8E: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 125)







MKTLIVVDMQNDFISPLGSLTVPKGEELINPISDLMQDADRDWHRIVVT


RDWHPSRHISFAKNHKDKEPYSTYTYHSPRPGDDSTQEGILWPVHCVKN


TWGSQLVDQIMDQVVTKHIKIVDKGFLTDREYYSAFHDIWNFHKTDMNK


YLEKHHTDEVYIV GVAL;


 


>3O94: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 126)







(M/—)(G/—)(S/—)(S/—)H/—)(H/—)


(H/—)(H/—)(H/—)(H—)SSGLVPRGSHMTKALISI


DYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEE


NDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHY


SAFSGTDLDIRLRERRVSTVILTGVLT;


 


>3LQY: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 127)







GMTTENTTALLLIDFQNDYFSTYNGAKNPLVGTEAAAEQGAKLLAKFRQ


QGLPVVHVRHEFPTDEAPFFLPGSDGAKIHPSVAAQEGEAVVLKHQINS


FRDTDLKKVLDDAGIKKLVIVGAMT;


 


>2B34: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 128)







MAARKLIARINPTNSALFVCDLQEKFASNIKYFPEIITTSRRLIDAARI


LSIPTIVTEQYPKGLGHTVPTLKEGLAENTPIFDKTKFSMCIPPTEDTL


KKVQNVILVGIEA;


 


>3OQP: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 129)







GMTTPRRALIVIDVQNEYVTGDLPIEYPDVQSSLANIARAMDAARAAGV


PVVIVQNFAPAGSPLFARGSNGAELHPVVSERARDHYVEKSLPSAFTGT


DLAGWLAARQIDTLTVTGYMT);


 


>2A67: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 130)







AMKNRALLLIDFQKGIESPTQQLYRLPAVLDKVNQRIAVYRQHHAPIIF


VQHEETELPFGSDSWQLFEKLDTQPTDFFIR KTHANAFYQTNLNDLLT


EQAVQTLEIAGVQT;


 


>4H17: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 131)







GMSVPTTMFRLTGRDYPPAKLSHASLIIIDAQKEYLSGPLKLSGMDEAV


ANIARLLDAARKSGRPIIHVRHLGTVGGRFDPQGPAGQFIPGLEPLEGE


IVIEKRMPNAFKNTKLHETLQELGHLDLIVCGFMS;


 


>3PL1: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 132)







MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKD


FHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGA


YTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIAT;


 


>3MCW: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 133)







GMPAPLRFSSDKPLLLLIDMQQAVDDPSWGPRNHPQAEQACAGLLQAWR


ARGLPLIHIRHDSVEPNSTYRPGQPGHAFKPEVEPRPGETVIAKQTNSA


FIGTGLEALLRANGWLELVVAGVST;


 


>1YZV: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 134)







(M/—)(A/—)(S/—)(S/—)H/—)(H/—)


(H/—)(H/—)(H/—)(H—)MSRLLKHYGSCKTAFFCC


DIQEKFMGRIANSANCVFVANRFAGLHTALGTAHSVYIVTEQYPKGLGA


TSADI RLPPDAHVFSKKRFAMLVPQVMPLVDLPEVEQVVLWGFET;


 


>3IRV: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 135)







MSLAEVNPMSKPLVRWPINPLRTAVIVVDMQKVFCEPTGALYVKSTADI


VQPIQKLLQAARAAQVMVIYLRHIVRGDGSDTGRMRDLYPNVDQILARH


DPDVEVIEALAPQSDDVIVDKLFYSGFHNTDLDTVLRARDVDTIIVCGT


VT;


 


>3HB7: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 136)







YFQGMAKHAILVIDMLNDFVGEKAPLRCPGGETIIPDLQKIFEWVRGRE


GDDIHLVHIQEAHRKNDADFRVRPLHAVKGTWGSDFIPELYPQEDEYIV


QKRRHSGFAHTDLDLYLKEEGIDTVVLTGVWT;


 


>3KL2: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 137)







MSLTTSKTRKSGVAMTEKLELDPARTAIVLIEYQNEFTSDGGVLHGAVA


DVMQHTGMLANTVAVVDAARQAGVPIMHAPITFAEGYGELTRHPYGILK


GVVDGKAFVKGTWGAAIVDELAPVNGDIVIEGKRGLDTFASTNLDFILR


SKGVDTIVLGGFL TNC;


 


>2FQ1: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 138)







GHMAIPKLQAYALPESHDIPQNKVDWAFEPQRAALLIHDMQDYFVSFWG


ENCPMMEQVIANIAALRDYCKQHNIPVYYTAQPKEQSDEDRALLNDMWG


PGLTRSPEQQKVVDRLTPDADDTVLVKWRYSAFHRSPLEQMLKESGRNQ


LIITGVYA;


and


 


>3TG2: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 139)







MAIPKIASYPLPVSLPTNKVDWRIDASRAVLLIHNMQEYFVHYFDSQAE


PIPSLIKHIQQLKAHAKQAGIPVVYTAQPANQDPAERALLSDFWGPGLS


EETAIIAPLAPESGDVQLTKWRYSAFKKSPLLDWLRETGRDQLIITGV


YA.






Each of these embodiments represents the N-terminal portion of a specific protein with structural similarity to Pyrococcus horikoshii pyrazinamidase; thus, each corresponds to the region of the Pyrococcus horikoshii pyrazinamidase that is not needed for the IgG Fc binding function of the polypeptides of the invention, but may help to provide structural features that provide improved binding.
In one specific embodiment, Z4 comprises or consists of







>1IM5: A|PDBID|CHAIN|SEQUENCE







(SEQ ID NO: 140)







PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVA


 


TRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISK


 


ATEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVAT.






In another embodiment, the polypeptides of the invention comprise or consist of a polypeptide with an amino acid sequence with at least 90% identity (i.e.: at least 90%, 92%, 95%, 96%, 97%, 98%, 99%, or 100% identical) to an amino acid sequence selected from the group consisting of:







Original computationally designed sequence:







(SEQ ID NO: 141)







PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT


RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPD


KEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEV


YLLRDAVKGIKPEMEQQAFFYMKLRGIKIVQF;


 


Sequence of best binder from round 2: FcB6.cons1:







(SEQ ID NO: 142)







PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT


RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPD


KEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDAKKHGFEV


LLRDAVKGIKPEMEQQALFYMKLRGIKIVQF;


 


Sequence of FcB6.1







(SEQ ID NO: 143)







PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT


RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPD


KEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEV


YLLRDAVKGIKPTFEQQSFFYMSLKGIKIVQF;


 


Cysteine knock-out version of the enzyme FcB6.1







(SEQ ID NO: 144)







PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVAT


RDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPD


KEAYSGFEGTDLAKILRGNGVKRVYICGVATEYAVSRTAVDALKHGFEV


YLLRDAVKGIKPTFEQQSFFYMSLKGIKIVQF;






Full-Length Variants Selected for Binding at pH 6.5:







focusedLib-S4-10


(SEQ ID NO: 145)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSVTALDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMRLKGIKIVQF;


 


focusedLib-S4-11


(SEQ ID NO: 146)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGSPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAADALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMALKGIKIVQF;


 


focusedLib-S4-12


(SEQ ID NO: 147)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


RDAVKGIKPVWEQQSFFYMVLKGIKIVQF;


 


focusedLib-S4-13


(SEQ ID NO: 148)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSLTAVDALKHGFEVYLL


RDAVKGIKPWHEQQSFFYMLLKGIKIVQF;


 


focusedLib-S4-15


(SEQ ID NO: 149)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSHTAMDALKHGFEVYLL


RDAVKGIKPHWEQQSFFYMLLKGIKIVQF;


 


focusedLib-S4-16


(SEQ ID NO: 150)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIIPKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSLTAVDALKHGFEVYLL


RDAVKGIKPKIEQQSFFYMMLKGIKIVQF;


 


focusedLib-S4-2


(SEQ ID NO: 151)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAMDALKHGFEVYLL


RDAVKGIKPFLEQQSFFYMRLKGIKIVQF;


 


focusedLib-S4-3


(SEQ ID NO: 152)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSHTAVDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMRLKGIKIVQF;


 


focusedLib-S4-4


(SEQ ID NO: 153)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSWTAVDALKHGFEVYLL


RDAVKGIKPHMEQQSFFYMMLKGIKIVQF;


 


focusedLib-S4-5


(SEQ ID NO: 154)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


RDAVKGIKPWLEQQAFFYMELKGIKIVQF;


 


focusedLib-S4-6


(SEQ ID NO: 155)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTARDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMKLKGIKIVQF;


 


focusedLib-S4-7


(SEQ ID NO: 156)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVAFTAVDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMQLKGIKIVQF;


 


focusedLib-S4-8


(SEQ ID NO: 157)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSLTAVDALKHGFEVYLL


RDAVKGIKPWHEQQSFFYMLLKGIKIVQF;


 


focusedLib-S4-9


(SEQ ID NO: 158)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSHTAVDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMRLKGIKIVQF;






Full-Length Variants Selected for Binding at pH 8







focusedLib-S4-35


(SEQ ID NO: 159)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSWTAMDALKHGFEVYLL


RDAVKGIKPPIEQQSFFYMHLKGIKIVQF;


 


focusedLib-S4-36


(SEQ ID NO: 160)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSFTAADALKHGFEVYLL


RDAVKGIKPWAEQQSFFYMGLKGIKIVQF;


 


focusedLib-S4-37


(SEQ ID NO: 161)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


RDAVKGIKPVLEQQSFFYMDLKGIKIVQF;


 


focusedLib-S4-38


(SEQ ID NO: 162)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAMDALKHGFEVYLL


RDAVKGIKPRLEQQSFFYMTLKGIKIVQF;


 


focusedLib-S4-39


(SEQ ID NO: 163)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSTTAIDALKHGFEVYLL


RDAVKGIKPGMEQQSFFYMILKGIKIVQF;


 


focusedLib-S4-40


(SEQ ID NO: 164)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSLTAVDALKHGFEVYLL


RDAVKGIKPMIEQQSFFYMRLKGIKIVQF;


 


focusedLib-S4-42


(SEQ ID NO: 165)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSKTATDALKHGFEVYLL


RDAVKGIKPSLEQQSFFYMRLKGIKIVQF;


 


focusedLib-S4-43


(SEQ ID NO: 166)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


RDAVKGIKPRLEQQSFFYMSLKGIKIVQF;


 


focusedLib-S4-44


(SEQ ID NO: 167)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSMTAMDALKHGFEVYLL


RDAVKGIKPSLEQQSFFYMNLKGIKIVQF;


 


focusedLib-S4-45


(SEQ ID NO: 168)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAMDALKHGFEVYLL


RDAVKGIKPTEEQQSFFYMTLKGIKIVQF;


 


focusedLib-S4-46


(SEQ ID NO: 169)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVAMTAVDALKHGFEVYLL


RDAVKGIKPWLEQQSFFYMHLKGIKIVQF;


 


focusedLib-S4-47


(SEQ ID NO: 170)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


RDAVKGIKPTFEQQSFFYMSLKGIKIVQF;


 


focusedLib-S4-48


(SEQ ID NO: 171)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAMDALKHGFEVYLL


RDAVKGIKPTEEQQSFFYMTLKGIKIVQF.;


 


(SEQ ID NO: 172)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKP EREQQSFFYMGLKGIKIVQF;


 


(SEQ ID NO: 173)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKP EREQQSFFYMGLKGIKIVQF;


 


(SEQ ID NO: 174)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPHMKQQSFFYMSLR GIKIVQF;


 


(SEQ ID NO: 175)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPHWVQQSFFYMGLK GIKIVQF;


 


(SEQ ID NO: 176)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPDWVQQSMFYMELK GIKIVQF;


 


(SEQ ID NO: 177)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPDWVQQSLFYMNLK GIKIVQF;


and


 


(SEQ ID NO: 178)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPEWVQQSLFYMGLK GIKIVQF;


 


FcB6


(SEQ ID NO: 179)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYLL


RDAVKGIKPEMEQQAFFYMKLRGIKIVQ;


 


FcB6.VV


(SEQ ID NO: 180)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSVTAVDALKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF;


 


FcB6.TV


(SEQ ID NO: 181)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVVTR


EWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSTTAVDALKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF;


and


 


FcB6.Cons2


(SEQ ID NO: 182)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDARKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF.






As used throughout the present application, the term “polypeptide” is used in its broadest sense to refer to a sequence of subunit amino acids. The polypeptides of the invention may comprise L-amino acids, D-amino acids (which are resistant to L-amino acid-specific proteases in vivo), or a combination of D- and L-amino acids. The polypeptides described herein may be chemically synthesized or recombinantly expressed.
In a further embodiment, the polypeptides of any embodiment of the invention may further comprise a tag, such as a detectable moiety or therapeutic agent. The tag(s) can be linked to the polypeptide through covalent bonding, including, but not limited to, disulfide bonding, hydrogen bonding, electrostatic bonding, recombinant fusion and conformational bonding. Alternatively, the tag(s) can be linked to the polypeptide by means of one or more linking compounds. Techniques for conjugating tags to polypeptides are well known to the skilled artisan. Polypeptides comprising a detectable tag can be used, for example, in detection and/or analytical and/or diagnostic assays. Any suitable detection tag can be used, including but not limited to enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive materials, positron emitting metals, and nonradioactive paramagnetic metal ions. The specific tag used will depend on the specific detection/analysis/diagnosis techniques and/or methods used such as flow cytometric detection, scanning laser cytometric detection, fluorescent immunoassays, enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), bioassays (e.g., neutralization assays), Western blotting applications, etc. The polypeptides of the invention can be fused to marker sequences to facilitate purification. Examples include, but are not limited to, the hexa-histidine tag, the myc tag or the flag tag.
In one embodiment, one or more polypeptides of any embodiment or combination of embodiments of the invention can be bound to a solid support. Such solid supports might be porous or nonporous, planar or nonplanar and include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene supports. The polypeptides can also, for example, usefully be conjugated to filtration media, such as NHS-, CNBr-, epoxy- or iodoacetyl-activated Sepharose or agarose for purposes of affinity chromatography. They can also usefully be attached to paramagnetic microspheres, typically by biotin-streptavidin interaction, or to microtiter plates. This embodiment provides a general device for instant tethering of any antibody or Fc fusion protein to a solid surface of choice.
In another aspect, the present invention provides pharmaceutical compositions, comprising one or more polypeptides of the invention and a pharmaceutically acceptable carrier. In this embodiment, the polypeptides of the invention may be used as a drug delivery device. The polypeptides of the invention can be conjugated to a specific cargo such as a therapeutic antibody targeting a specific surface receptor, or a therapeutic moiety bound to a targeting antibody (i.e.: where the antibody is provided to target a cell receptor to which the therapeutic moiety is bound). In one non-limiting embodiment, upon endocytosis and pH drop, the polypeptide could release the antibody and can be taken up by the cell whereas the antibody can remain bound to the receptor and will eventually be recycled and surface applied again. Conjugation methods for attaching to antigens and polypeptide are well known in the art and include, but are not limited to, the use of cross-linking agents.
The pharmaceutical compositions of the invention can be used, for example, in the methods of the invention described below. The pharmaceutical composition may comprise in addition to the polypeptide of the invention (a) a lyoprotectant; (b) a surfactant; (c) a bulking agent; (d) a tonicity adjusting agent; (e) a stabilizer; (f) a preservative and/or (g) a buffer.
In some embodiments, the buffer in the pharmaceutical composition is a Tris buffer, a histidine buffer, a phosphate buffer, a citrate buffer or an acetate buffer. The pharmaceutical composition may also include a lyoprotectant, e.g. sucrose, sorbitol or trehalose. In certain embodiments, the pharmaceutical composition includes a preservative e.g. benzalkonium chloride, benzethonium, chlorohexidine, phenol, m-cresol, benzyl alcohol, methylparaben, propylparaben, chlorobutanol, o-cresol, p-cresol, chlorocresol, phenylmercuric nitrate, thimerosal, benzoic acid, and various mixtures thereof. In other embodiments, the pharmaceutical composition includes a bulking agent, like glycine. In yet other embodiments, the pharmaceutical composition includes a surfactant e.g., polysorbate-20, polysorbate-40, polysorbate-60, polysorbate-65, polysorbate-80 polysorbate-85, poloxamer-188, sorbitan monolaurate, sorbitan monopalmitate, sorbitan monostearate, sorbitan monooleate, sorbitan trilaurate, sorbitan tristearate, sorbitan trioleaste, or a combination thereof. The pharmaceutical composition may also include a tonicity adjusting agent, e.g., a compound that renders the formulation substantially isotonic or isoosmotic with human blood. Exemplary tonicity adjusting agents include sucrose, sorbitol, glycine, methionine, mannitol, dextrose, inositol, sodium chloride, arginine and arginine hydrochloride. In other embodiments, the pharmaceutical composition additionally includes a stabilizer, e.g., a molecule which, when combined with a protein of interest substantially prevents or reduces chemical and/or physical instability of the protein of interest in lyophilized or liquid form. Exemplary stabilizers include sucrose, sorbitol, glycine, inositol, sodium chloride, methionine, arginine, and arginine hydrochloride.
In a further aspect, the present invention provides isolated nucleic acids encoding a polypeptide of the present invention. The isolated nucleic acid sequence may comprise RNA or DNA. As used herein, “isolated nucleic acids” are those that have been removed from their normal surrounding nucleic acid sequences in the genome or in cDNA sequences. Such isolated nucleic acid sequences may comprise additional sequences useful for promoting expression and/or purification of the encoded protein, including but not limited to polyA sequences, modified Kozak sequences, and sequences encoding epitope tags, export signals, and secretory signals, nuclear localization signals, and plasma membrane localization signals. It will be apparent to those of skill in the art, based on the teachings herein, what nucleic acid sequences will encode the polypeptides of the invention.
In another aspect, the present invention provides recombinant expression vectors comprising the isolated nucleic acid of any aspect of the invention operatively linked to a suitable control sequence. “Recombinant expression vector” includes vectors that operatively link a nucleic acid coding region or gene to any control sequences capable of effecting expression of the gene product. “Control sequences” operably linked to the nucleic acid sequences of the invention are nucleic acid sequences capable of effecting the expression of the nucleic acid molecules. The control sequences need not be contiguous with the nucleic acid sequences, so long as they function to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the nucleic acid sequences and the promoter sequence can still be considered “operably linked” to the coding sequence. Other such control sequences include, but are not limited to, polyadenylation signals, termination signals, and ribosome binding sites. Such expression vectors can be of any type known in the art, including but not limited plasmid and viral-based expression vectors. The control sequence used to drive expression of the disclosed nucleic acid sequences in a mammalian system may be constitutive (driven by any of a variety of promoters, including but not limited to, CMV, SV40, RSV, actin, EF) or inducible (driven by any of a number of inducible promoters including, but not limited to, tetracycline, ecdysone, steroid-responsive). The construction of expression vectors for use in transfecting prokaryotic cells is also well known in the art, and thus can be accomplished via standard techniques. (See, for example, Sambrook, Fritsch, and Maniatis, in: Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989; Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.). The expression vector must be replicable in the host organisms either as an episome or by integration into host chromosomal DNA. In a preferred embodiment, the expression vector comprises a plasmid. However, the invention is intended to include other expression vectors that serve equivalent functions, such as viral vectors.
In a still further aspect, the present invention provides host cells that have been transfected with the recombinant expression vectors disclosed herein, wherein the host cells can be either prokaryotic (such as bacteria) or eukaryotic. The cells can be transiently or stably transfected. Such transfection of expression vectors into prokaryotic and eukaryotic cells can be accomplished via any technique known in the art, including but not limited to standard bacterial transformations, calcium phosphate co-precipitation, electroporation, or liposome mediated-, DEAE dextran mediated-, polycationic mediated-, or viral mediated transfection. (See, for example, Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press; Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.). A method of producing a polypeptide according to the invention is an additional part of the invention. The method comprises the steps of (a) culturing a host according to this aspect of the invention under conditions conducive to the expression of the polypeptide, and (b) optionally, recovering the expressed polypeptide. The expressed polypeptide can be recovered, for example, by heating bacterial cells expressing them to approximately up to 80° C. Therefore, little to no other physical or chemical step is necessary to release the polypeptides from the cells. Centrifugation eliminates cell debris and aggregates.
In another aspect, the invention provide methods for purifying antibodies or Fc fusion proteins, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to any embodiment of the present invention under suitable conditions for binding of antibodies or Fc fusion protein in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) dissociating the antibody or Fc fusion protein from the antibody-polypeptide or Fc fusion-polypeptide complexes, to isolate the antibody.
The methods of the invention permit improved methods for antibody purification, that do not require the use of Protein A and elution protocols that require lowering the pH to 3, which can lead to aggregation and denaturation of the antibody and of Fc-fusion proteins. For example, the inventors have developed polypeptides that bind strongly to IgG Fc regions at pH 8.0 and much more weakly at pH 5.5. Thus, the binding conditions can comprise, for example contacting the sample comprising antibodies or Fc fusion proteins with the one or more polypeptides at a pH 8, and the conditions for dissociating the antibody from the antibody-polypeptide complexes can comprise dissociating at a pH of about 5.5.
Other suitable conditions to promote binding of antibodies in the sample to one or more polypeptide of the invention can be determined by those of skill in the art, based on the teachings herein. The polypeptides of the invention for use in this aspect may comprise a conjugate as disclosed above, to provide a tag useful for any detection technique suitable for a given assay. Any such tag used will depend on the specific detection/analysis/diagnosis techniques and/or methods used, as discussed above. The methods may be carried in solution, or the polypeptide(s) of the invention may be bound or attached to a solid surface, as discussed above. Based on the teachings herein, it is within the level of skill in the art to determine specific conditions for the various types of diagnostic assays disclosed in this aspect of the invention.
The methods can be used to isolate any antibody (IgG) or Fc fusion proteins of interest, including, but not limited to human IgG1, IgG2 and IgG4, mouse IgG1 and IgG2. As used herein, “antibodies include antibodies fused to any protein or peptide of interest. Any suitable sample that contains antibodies or Fc fusion proteins may be used.
The methods can be used to isolate any antibody or Fc fusion proteins, including but not limited to large scale production/isolation of therapeutic/diagnostic monoclonal antibodies. Similarly, the methods may be used in any type of assay in which isolation of antibodies is desirable, including but not limited to affinity purification of antibodies in large or small scale, Western blot analysis, enzyme linked immunosorbent assays (ELISA), immunohistochemistry (IHC) and other immunoassay protocols, such as immunoprecipitations, where the polypeptides of the invention may be immobilized to a solid surface (such as beads).
In another aspect the present invention comprises methods for detection of an antibody in a sample, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to any embodiment of the present invention under suitable conditions for binding of antibodies or Fc fusion protein in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) detecting the antibody-polypeptide complexes.
This aspect of the invention can be used in any assay where detection of an antibody in a sample is desirable, whether antibody detection is the primary goal of the assay, or where the antibody to be detected is a marker for a protein of interest in the sample. Any suitable sample that may contain the antibody to be detected can be used, including but not limited to clinical samples (blood, plasma, serum, urine, semen, tissue samples, tissue sections, ascites fluid etc.), environmental samples, experimental samples (i.e.: research laboratory use), etc.
The inventors have developed polypeptides that bind strongly to IgG Fc regions at pH 8.0 and much more weakly at pH 5.5, as well as they developed IgG Fc binders that bind less pH sensitive. Thus, for the pH sensitive binder, binding conditions can comprise, for example contacting the sample comprising antibodies or Fc fusion proteins with one or more polypeptides at a pH 8, and the conditions for dissociating the antibody from the antibody-polypeptide complexes can comprise dissociating at a pH of about 5.5. Other suitable conditions to promote binding of antibodies in the sample to one or more polypeptide of the invention can be determined by those of skill in the art, based on the teachings herein. In one embodiment, wash steps are included to facilitate removal of unbound antibody prior to detection.
The polypeptides of the invention for use in this aspect may comprise a conjugate as disclosed above, to provide a tag useful for any detection technique suitable for a given assay. Any such tag used will depend on the specific detection/analysis/diagnosis techniques and/or methods used, as discussed above. The methods may be carried in solution, or the polypeptide(s) of the invention may be bound or attached to a solid surface, as discussed above. In one embodiment, one or more polypeptides of any embodiment or combination of embodiments of the invention can be bound to a solid support. Such solid supports might be porous or nonporous, planar or nonplanar and include, but are not limited to, glass, latex, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene supports. The polypeptides can also, for example, usefully be conjugated to filtration media, such as NHS-, CNBr-, epoxy- or iodoacetyl-activated Sepharose or agarose for purposes of affinity chromatography. They can also usefully be attached to paramagnetic microspheres, typically by biotin-streptavidin interaction, or to microtiter plates or beads made of material listed above. This embodiment provides a general device for instant tethering of any antibody or Fc fusion protein to a solid surface of choice.
Based on the teachings herein, it is within the level of skill in the art to determine specific conditions for the various types of diagnostic/detection assays disclosed in this aspect of the invention. Detection of immunocomplex formation can be accomplished by standard detection techniques, such as but not limited to standard techniques used to detect fluorescent dyes, enzymes, biotin, colloidal gold or radioactive iodine conjugated to the one or more polypeptides.
In another aspect, the present invention provides methods for drug delivery comprising administering to a subject in need thereof a therapeutically effective amount of a pharmaceutical composition comprising one or more polypeptides of the invention conjugated to a therapeutic antibody to treat a disorder that the subject suffers from. As discussed above, the polypeptides of the invention can act as drug carriers. For example, the polypeptides of the invention can be conjugated to a specific cargo such as a therapeutic antibody targeting a specific surface receptor, or a therapeutic moiety bound to a targeting antibody (i.e.: where the antibody is provided to target a cell receptor to which the therapeutic moiety is bound). In one non-limiting embodiment, upon endocytosis and pH drop, the polypeptide could release the antibody and can be taken up by the cell whereas the antibody can remain bound to the receptor and will eventually be recycled and surface applied again.
As used herein, a “therapeutically effective amount” refers to an amount of the therapeutic antibody or moiety that is effective for treating the disorder in the subject. The pharmaceutical composition, such as those disclosed above, and can be administered via any suitable route, including orally, parentally, by inhalation spray, rectally, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles. The term parenteral as used herein includes, subcutaneous, intravenous, intra-arterial, intramuscular, intrasternal, intratendinous, intraspinal, intracranial, intrathoracic, infusion techniques or intraperitoneally. Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). A suitable dosage range and treatment regimen can be determined by an attending physician.
EXAMPLES
Recombinant monoclonal antibodies and Fc-fusion proteins have become an important class of biological pharmaceuticals and research reagents. Their manufacture typically involves mammalian cells as the expression host and affinity chromatography as a key purification step. While upstream processes such as cell-line development and engineering have significantly enhanced antibody yields, the downstream purification steps remain expensive and reduce productivity. The vast majority of antibody purification pipelines employ a Protein A-based purification step, which contributes to the majority of the raw-material costs1, 2. Protein A is used in the manufacture of monoclonal antibodies, one of the fastest growing classes of drugs. The annual revenue of therapeutic antibodies is approximately $44 billion (2011) with expected growth. The vast majority of them are purified through a Protein A column, which contributes to about 35% of the raw cost of the antibodies. Antibody elution from a Protein A column is typically achieved by lowering the pH to 3. However, at such low pH, aggregation and denaturation of the antibody and of Fc-fusion proteins can easily occur.
pH-dependent binding occurs if protonation of an ionizable residue, such as histidine, shifts the binding equilibrium. Previous efforts to engineer highly pH-dependent protein switches have focused on either the rational introduction of ionizable groups at the interface, often compromising affinity at permissive pH or relied on histidine scanning mutagenesis3.
Computational de novo interface design potentially provides a new way to address this challenge, by focusing design of binding to sites on the target protein that contain ionizable groups. Our recently reported hot-spot-based design strategy starts by computing an idealized core interaction site (hotspot) and then scans a large set of scaffold proteins for surfaces that can present the hotspot and form stabilizing interactions with the target site4. Here, we describe the adaption of this methodology to develop a highly pH sensitive binding protein.
We set out to design an Fc binding protein that buries the consensus binding site on Fc and aimed to bury one of the solvent-exposed histidine residues on Fc, assuming that interactions targeting this site would show large pH sensitivity close to physiological relevant levels. The materials and methods used are described below.
We applied hotspot-guided protein interface design4, 5, using residue interactions from Protein A as binding hotspots6, and aimed to generate additional interactions with and around His433 or His310 to achieve pH-dependent binding. We start by generating ensembles of disembodied interaction hotspot residues Gln11, Phe14, and Leu18 from minimized Protein A6 (FIG. 1A-C), and searched for protein structures that could harbor a combination of these sidechains while focusing on protein scaffolds of solved structure with high expression and solubility.
17 designed proteins were expressed on the surface of yeast and binding was assessed by flow cytometry following incubation with 700 nM biotinylated human IgG1 (Rituximab) that had been fluorescently labeled and oligomerized through binding to streptavidin-phycoerythrin (SAPE). 10 designs had detectable binding signals. We decided to focus on the binder codenamed FcB6 which showed the strongest signal, and which was designed to hydrogen bond to both Asn434 and His433, and was thereby an excellent candidate to optimize for pH-dependent binding.
Herein we disclose novel protein variants that bind to the constant region of IgG antibodies (Fc) and methods for designing them. These variants can be used for the purification of a variety of antibodies and their fusions, and thereby could replace or supplant the role of Protein A. The new Fc binding proteins have been designed de novo. About 850 protein scaffolds were computationally screened and designed for binding to the constant region of an IgG. Several rounds of directed evolution were performed to improve the binding behavior, to optimize affinity and pH dependence.
The originally computationally designed sequence, starting with a Pyrococcus horikoshii pyrazinamidase, is as follows:







FcB6


(SEQ ID NO: 179)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHI SFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDK


EAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSATAEDALKHGFEVYL


LRDAVKGIKPEMEQQAFFYMKLRGIKIVQ






Subsequent sequence alignment that resulted from various diversification and selections refer back to this sequence. After a first round of optimization (“error prone PCR based mutagenesis), binding affinity improvement was observed as shown in FIG. 2. The top 2 enhanced sequences that came out of the error prone PCR based mutagenesis round are shown below:







FcB6.VV


(SEQ ID NO: 180)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSVTAVDALKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF;


and


 


FcB6.TV


(SEQ ID NO: 181)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVVTR


EWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSTTAVDALKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF.






The consensus sequence for the error prone PCR based mutagenesis study indicated that positions A135 and E138 were clearly not ideal for the binding to IgG (see alignment, FIG. 2). Hence, we sampled all position for these two positions as well as position 141 and screened this new library, referred to as “consensus” library, by yeast surface display for better binding (“consensus mutagenesis screen”). We discovered that when alanine 135 was allowed to change into all possible amino acids, it preferred to become an arginine. We confirmed again that changing glutamate 138 to valine greatly improves binding affinity. Additionally, L141 could be either a lysine or arginine, with lysine resulting in a better binding.
Top Binders from the Consensus Library:
A135R, E138V and L141K or L141R
Complete Sequences:







FcB6.Cons1


(SEQ ID NO: 142)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDAKKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF;


and


 


FcB6.Cons2


(SEQ ID NO: 182)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDARKHGFEVYLL


RDAVKGIKPEMEQQALFYMKLRGIKIVQF.






We next sought to improve binding affinity while optimizing pH dependent binding (pH focused screen”). For optimization of pH dependence, positions within FcB6 that are close to histidine 433 of the binding partner IgG were allowed to vary, this included also maximal variations of the suboptimal positions A135 and E138. The objective was to identify variants that would have different affinities for Fc at different pH levels. The purpose of this will be that the bound antibody or Fc fusion protein could then be easily eluted with small variation of the pH value. Hence the objective of the selection of this library was to identify binders that would bind tight at one pH level, but a lot weaker at others. Sequence alignments for well binding clones at indicated pH levels using a PBS buffer are shown below: Sequences resulting from the yeast surface display selection at pH 6.5 are shown in FIG. 3A and at pH 8 are shown in FIG. 3B.
We then determined the Kd of exemplary isolated clones for IgG at different pHs. Measurements were taken via titrations of biotinylated Rituxan (Rituximab) using yeast surface display as discussed in the materials and methods sections. These studies showed that, on average, variants that were isolated at pH 8 did not have optimized binding at pH 6.5, whereas isolates from the lower pH selections (at pH 6.5) tend to bind similarly at either pH. When comparing sequences between the two selection trajectories at the two different pH levels, we quickly could identify clones with different sequence profiles. From the pH 8 screen, we isolated various clones that had several fold poorer binding affinity at pH 6.5 compared to pH 8. Hence, we achieved our objective to identify variants that would have different affinity for the Fc domain at different pH levels. One exemplary clone (FcB6.1) had reasonable affinity (around 2 nM using this assay) and 6-7 fold worse affinity at pH 6.5, and was further characterized.
Our designed protein (FcB6) and its variants are modeled to bind to the consensus region between the CH2 and CH3 domain of the Fc region of IgGs (FIG. 1) and to parts of the CH2 domain that contains histidine 433 and asparagine 434. The computational designed protein uses various residues on a helical structure to bind to the cleft between those two domains, to which other native proteins, such as Protein A, neonatal receptor (FcRn) or the rheumatoid factor bind to. Within this helix sequence (Z3), it uses a glutamine residue to hydrogen bond to the backbone atoms of residue leu251, ile253 and asn434 of the IgG, which are located within the cleft between CH2 and CH3. FcB6 is designed to place a phenylalanine (F167) behind a loop containing the surface exposed Ile253 on the Fc domain. This phenylalanine provides not only van der Waals contact to nearby residues, it also electrostatically favorably interacts with a local helix dipole below the isoleucine-253-containing loop on the IgG. Additionally, FcB6 uses a tyrosine to wedge against the loop that contains histidine 433 at its midpoint. These core residues, next to leu171 (which is slightly less conserved), are highly conserved within FcB6 throughout several selections schemes.
Next to binding to the consensus site, the computational design FcB6, as modeled, provides many new binding contacts to CH2 through a second alpha helix (Z1) that covers the area around histidine 433, which allows for the optimization of pH dependent binding. A very crucial contact is Ser134 of the design, which introduces a buried hydrogen bond to the histidine 433 of Fc. The mutation E138V (as identified through selections) allows to shield-off the solvent from one side, strengthening thereby this hydrogen bond, because exchanges with water molecules become less likely. It also does not have a charge which could interfere with the surface charge on the IgG. The V-shaped valine residue at position 138 fits perfectly next to the above-described tyrosine 168 to encompass the histidine. Other residues are capable of shielding the histidine from the solvent, as selections also indicate, however the valine residue has the best fit and is thereby preferred. Selections also demonstrated that A138, which is located almost above histidine 433, but spatially next to the valine 138 (former E138) when facing the interface with Fc—is preferentially an arginine. The long side chain of the arginine introduces a large area for van der Waals contacts with the histidine, and the positive charge interacts highly beneficially with the negative surface charge of the epitope on Fc. However, as soon as the histidine 433 residues becomes protonated, which happens when lowering the pH level (< ̃6.5), it also becomes positively charged, thereby introducing a repulsion between arginine 135 of the design and the now also positively charged histidine. Additionally, the hydrogen bond with serine 134 and the histidine is not possible anymore due to the protonation, which further weakens overall the interaction between IgG and the design, thus making it highly pH sensitive.
Alternatively, mutations at 135 that cover the histidine, but do not have a charge, result in improvements of the binding affinity due to a larger contact area and they can still render the interaction slightly pH sensitive, as the buried hydrogen bond with serine 134 will be still dependent on the protonation state of the histidine 433. Hence interaction that cover and contact the histidine will still produce reasonable binding to the IgG, but with less pH sensitivity.
We also performed deep sequencing analysis of mutagenized and selected clones after mild selection conditions to figure out tolerated residues at different positions. These studies showed that Z2 (as defined above) can be modified as follows:







(SEQ ID NO: 85)


G(F/V)(E/D)(V/G)(Y/C)L(L/F)R(D/E/N)AVKG(I/V/F)KP






The most interesting polypeptides obtained from the pH focused screen are shown below. The binding constant for FcB6.1 was measured to be 33 nM at pH 8 and >1 μM at pH 5.5.







Sequence of FcB6.1


(SEQ ID NO: 143)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


 


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


 


AYSGFEGTDLAKILRGNGVKRVYICGVATEYCVSRTAVDALKHGFEVYLL


 


RDAVKGIKPTFEQQSFFYMSLKGIKIVQF






And a cysteine knock-out version of the polypeptide:







(SEQ ID NO: 144)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


 


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


 


AYSGFEGTDLAKILRGNGVKRVYICGVATEYAVSRTAVDALKHGFEVYLL


 


RDAVKGIKPTFEQQSFFYMSLKGIKIVQF.






Both Protein A and FcB6 present a helix for binding between the CH2 and CH3 domain, and the core interface residues Q164, F167, Y168, M161 and L171 present the same contacts with Fc (FIG. 1D). However, no other amino acid is identical, and FcB6 differs substantially in binding mode from Protein A as most of its additional contacts are with the CH3 domain of Fc and not with CH2. The wild-type protein on which FcB6 is based on the structure of pyrazinamidase of Pyrococcus horikoshii7, and is completely inert to Fc suggesting that the designed surface mediates binding. Further competition with Protein A completely inhibited binding of FcB6 to the IgG1 Rituxan, indicating that it was indeed binding to the same consensus epitope.
To confirm the designed binding mode and identify possible avenues for improving the computationally designed sequence, we used PCR mutagenesis in concert with one round of fluorescent-activated cell sorting (FACS) and next-generation sequencing, resulting in a fine-resolution map of the sequence-function landscape8, 9. We evaluated changes within the C-terminal 52 residues, which contains the binding epitope of FcB6, using Illumina Miseq paired-end sequencing. We simplified the sequence analysis by assuming that all mutations are additive in their contribution to binding, and identified enriched and depleted mutations (data not shown). The core residues, S134, Q164, F167 and Y168, at the designed interface with Fc are highly conserved. The sequence fitness landscape suggests L171 could be switched to Trp; modeling of this substitution shows that it increases the packing density, adding more surface area for binding as well as forming an additional hydrogen bond to Fc Asn315. However, deep sequencing of sort 2 shows depletion of L171W under more stringent selection conditions. Further, two amino acid residues that originated from the wildtype scaffold (K142, K158) were conserved, likely due to contributions to the overall electrostatic complementarity of the complex. The two positions that allow the most substitutions are E135 and A138. Substitutions of these identities were also identified as consensus after 3 rounds of sorting and conventional sequencing (data not shown).
To optimize both binding and pH-dependent behavior, we constructed a library, guided by the deep sequencing data and Rosetta energy calculations, and carried out rounds of selection for increased binding affinity under two different pH conditions (pH 6.5 and 8). In the library, L166 was substituted with a phenylalanine, S124 and A165 were allowed to be either alanine or serine, and E135, A138, K170, E160 and M161 were allowed to be any of the 20 amino acids. Six clones from the 4th round of sorting were screened for binding at pH 6.5 and pH 8, and the variant with the largest difference (6-7 fold greater signal at pH 8 than pH 6.5 on the yeast surface) was subjected to more detailed analysis and will be referred to as FcB6.1. FcB6.1 contains the substitution E138V and an additional positive charge, A135R. Structural modeling of the designed variant shows a nearly perfect fit around Fc His433: R135 covers and packs against this residue, and also interacts favorably with the close-by highly negatively charged surface on Fc. Modeling rationalized this choice of substitutions by suggesting that protonation of Fc His433 would considerably reduce binding affinity by eliminating a buried hydrogen bond to Ser134, increasing the cost of desolvation for the histidine, and resulting in charge repulsion between the positive charge of Arg135 of FcB6.1 and the protonated (positively charged) His433. The FcB6.1 variant contains several additional mutations including M161F, which increases the buried hydrophobic surface area at the interface, and reduces the identical residues with Protein A to 3 residues only, and E160T, which reduces the negative charge projected towards CH3.
Protein production yields and stability are key determinants for the usefulness of affinity reagents. FcB6.1 is an attractive candidate in this regard as it is derived from a protein scaffold of a hyperthermophilic organism. FcB6.1 expresses well in E. coli, yielding around  ̃60-70 mg/L in shake flasks without any optimization, and is very stable. CD spectral analysis indicates melting only starts at temperatures higher than 80° C. FcB6.1 can be readily obtained in nearly pure form by subjecting bacteria to 80° C. for 20 min followed by centrifugation. FcB6.1 is stable to urea up to 3 M and guanidine HCl up to 1.5 M guanidine. Also, repeated heating cycles up to 80° C. did not denature the protein. Thus, FcB6.1 has considerable potential utility in chip- or bead-based assays and diagnostics: a simple heating procedure or denaturant wash would allow recovery of the antibody capture agent.
To examine the specificity of FcB6.1, we measured binding to biotinylated human IgG from different subclasses and commonly used IgGs from other species. Binding of the IgGs to the minimized Protein A variant10 (miniA) was measured for comparison. As expected FcB6.1 binds tightly to human IgG2, IgG4 and IgG1, slightly better than the miniA, and comparably to mouse IgG1 and IgG2a. FcB6.1 only binds weakly to IgG3 (which Protein A does not bind), and unlike Protein A, weakly to rat IgG2a.
Surface plasmon resonance measurements of the purified protein indicated a dissociation constant of around 33 nM to immobilized Rituxan at pH 8.2 and severely reduced affinity (>1 μM) at pH 5.5; very favorable characteristics for pH dependent chromatography. To test whether FcB6.1 could serve for affinity purification of IgG molecules, we added a C-terminal cysteine residue accompanied by a short glycine serine linker to couple the protein site-specifically to a resin (SulfoLink, Thermo Scientific). To simulate a possible purification scenario, we spiked an IgG mix (20 μg, InnovativeTM Research) into the supernatant of 293 Freestyle cell culture and incubated it with FcB6.1cys coated resin while rotating (see Methods). Almost complete elution was achieved by dropping the pH to 5.5 to ensure complete protonation of His433 and increasing the salt concentration to 500 mM (instead of commonly used 150 mM). Compared to Protein A, the FcB6.1cys resin allows much milder conditions for elution, which can be crucial for antibodies that tend to aggregate and particularly to Fc-fusion constructs; indeed higher molecular weight aggregates were observed after elution from a Protein A resin under same conditions.
Partition of FcB6 and Variants
Combinatorial Libraries to Evaluate Changes to One of the Interface Helices: Residues 157-172
To test small changes around the core interface helix that is similar to Protein A (4 residues in the original design, 3 in the FcB6.1 variants), we tested a combinatorial library for binding and found the consensus shown in FIG. 4 after 3 rounds of sorting:
Evaluation of pH Dependent Binding Through Point Mutations
To narrow down the residues that are responsible for the high pH sensitivity, we introduced “reverting” mutations to the optimized clone FcB6.1; this means we introduced single mutations back to the original design before optimization. Mutations demonstrated that the A135R and E138V were crucial mutations for pH dependence as well as binding.







FcB6.1


(SEQ ID NO: 144)


PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATR


 


DWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKE


 


AYSGFEGTDLAKILRGNGVKRVYICGVATEYAVSRTAVDALKHGFEVYLL


 


RDAVKGIKPTFEQQSFFYMSLKGIKIVQF






Summary:

Two Alpha Helix Peptide Stretches Define the Functional Sites

The interface of FcB6 consists of two alpha helices that bind to the region between CH2 and CH3 domain of an IgG. They can be at any length as long as they are within a certain distance that allows them to interact with each other. The most C-terminal helix (Z1 in general formula 1) buries the crucial histidine 433 of the IgG it binds to. In FcB6.1 (or Fc24.47), this helix contains the sequence







(E130-H143)


(SEQ ID NO: 17)


EYCVSRTAVDALKH


 


Ra1-Ra2-Ra3-Ra4-Ra5-Ra6-Ra7-Ra8-Ra9-Ra10-Ra11-


 


Ra12-Ra13-Ra14






Note: Ra3Cys (C132) used to be the active site residue, it is mutated into Ala for any application, such as affinity chromatography.
The specific residues that are preferred for the pH dependent contact are Ra5 Ser (S134) and Ra6 Arg (R135). Ra9 Val can be replaced but is preferred at this position.
The second helix (Z3 in general formula 1) buries the crucial histidine 433 of the IgG it binds to. This helix contains the information about pH dependent binding. The sequence of this helix in FcB6.1 is







(positions T160-K172)


(SEQ ID NO: 49)


TFEQQSFFYMSLK


 


Rb1-Rb2-Rb3-Rb4-Rb5-Rb6-Rb7-Rb8-Rb9-Rb10-Rb11-


 


Rb12-Rb13






in which Rb2-F, Rb5-Q, Rb8-F and Rb9-Y build the core of the binding interaction
Changes are allowed in helix 2, but it is preferred that residues Rb5, Rb8 and Rb9 are Q, F, and Y, respectively.
In summary, we have demonstrated that computational protein design can be readily employed to design affinity reagents with very favorable characteristics for biotechnology. Here, we targeted the consensus-binding site within the Fc hinge region of an IgG antibody, based on the natural Fc interaction with Protein A, but also introduced specificity for the protonation state of His433. The ability to engineer pH sensitivity will be of benefit for various fields, such as drug delivery, biosensors and as addressed here affinity chromatography.
Methods
Computational Methods
The hotspot residues Gln11, Phe14 and Leu18 of the minimized Protein A structure (116×) were excised and the disembodied hydrophobic residues were subjected to small docking perturbations against the Fc surface to generate “hotspot libraries” (FIG. 1B-C, Fig. S1), whereas for the glutamine residue, additional inverse rotameric conformations were computed (FIG. 1C). The same procedure was repeated for tryptophan residues instead of the phenylalanine and asparagine instead of glutamine resulting in a total of 3 independent residue libraries. To prepare the starting configurations of all 865 preselected structures of our scaffold set4, each one of these structures was docked against Fc using patchdock11, with the constraint to bury Ile253, Met252, Met428 or Tyr436 using the “knob” features, out of which we sampled the top 100 conformations for 2 different protocols. Two protocols for RosettaScripts12 were generated, Fc-2stubs.xml and Fc-3stubs.xml (Suppl.), with the first protocol only considering 2 hotspot libraries, the glutamine based stubs and phenylalanine stub set. The second protocol included all three hotspot libraries, the third being derivatives of Leu18 (Fig. S1). To prune the list of resulting designs, next to computed binding energy, shape complementarity13 (>0.63) was applied calculated using the CCP4 package v. 6.0.214. Beneficial mutations identified via yeast binding selections were computed using FoldIt15. Poisson Boltzman electrostatic surface models were computed using APBS16.
Antibody Biotinylation
All antibodies were biotinylated using SoluLink's biotinylation kit as instructed by the manufacturer.
Initial Design Evaluation and Yeast Surface Titrations
Yeast surface display and titrations were done similar as previously described17. Yeast cells (EBY100) containing plasmid encoding the designs, were grown overnight at 30° C. in SDCAA medium. For induction, they were sub-cultured into SGCAA to achieve an O.D. of 1, and grown at 22° C. for 16-20 h. Cells were washed once with PBS containing 0.5% BSA (PBS-BSA), before adding 700 nM biotinylated IgG (Rituximab) into a total volume of 50 μl of the same buffer. Labeling was performed at 4° C. on a rotating platform for 4 h before adding 175 nM streptavidin-PE (Invitrogen) and 4-8 μg/ml FITC labeled anti-Cmyc antibody (ICL labs) for an additional 1 h. Cells were washed once with ice cold PBS-BSA immediately before measuring their fluorescence via an Accuri C6 flow cytometer, data was analyzed using the FlowJo 7.6.1 and 8.8.7 software.
Library Constructions
Error prone mutagenesis was achieved through a Mutazyme II DNA polymerase kit (Agilent-Stratagene). 100 ng of the FcB6 gene in pETCON were subjected to 30 cycles of amplification. Mutagenized PCR fragments were co-transformed18 with linearized pETCON vector4 into EBY100 resulted in 1.5×10e8 variants. 10 individual clones were conventionally sequenced, indicating an average error rate of around 3 nucleotide substitutions per gene. The focused library was constructed through PCR using ultramer oligonucleotides with degenerate codons for the described positions, with upGS and downCmyc primers (Table S2). Resulting two fragments were co-transformed with linearized plasmid. After transformation into yeast, this library contained around 5×10e7 variants.
Library Selections
The epPCR library of the original design was incubated while rotating for 4 h at 4° C. with 750 nM biotinylated Rituxan and an additional hour with 187.5 nM streptavidin-PE and 2 μg/ml anti-myc Fitc-labeled antibody. 6.17×10e7 cells were examined and 106,000 cells were selected using fluorescence-activated cell sorting on a BD Influx sorter. For the second, focused library, 4 sorts were performed using 100 nM, 100 nM, 20 nM and 5 nM of biotinylated Rituxan under non-avid conditions17.
Library Preparation and Next-Generation Sequencing
Plasmids were extracted similarly as previously described9. Briefly, around 5×10e7 cells were treated with zymolase 50 U in 400 μl Solution buffer 1 (Zymo Research yeast plasmid miniprep II) and incubated at 37° C. for 4 h and vortexed every hour. Cells were freeze-thawed once and treated as instructed in Zymo kit manual with the exception that lysate was applied to higher-yield columns (QIAgen, plasmid miniprep kit), followed by plasmid elution with 30 μl EB (QIAgen). Possible contaminating genomic DNA was eliminated through digestion with ExoI (NEB) and Lambda exonuclease (NEB) as described9. After a QIAgen PCR clean-up step, Illumina adapters and population specific-barcodes were added through PCR (Suppl.). PCR product was purified through gel extraction (QIAgen). A total of 330 μl of a 7 pM solution was combined with 270 μl of a 6 pM PhiX v3 control (Illumina) and sequenced with a 300 bp cycle kit V1 using a Miseq (Illumina) with appropriate sequencing primers (Table S1), resulting in a forward and reverse read of the 153 bp long C-terminus. After quality filtering 942,049 sequences of the naïve population were compared to 375,962 of the selected pool.
Sequencing Analysis
Sequencing reads were split based on their 8 bp barcode into naïve and sorted population. Pools were treated identically in sequence analysis and quality filtration. Custom scripts were used to align all paired-end reads with both reads above an average Phred quality score above 10. Reads without gaps were merged into a single sequence and differences between sequences resolved using the higher quality score for the read. Sequences were counted and compared through custom python scripts similar to previously reported8, 9.
Cloning, Expression and Purification
FcB6.1 variants were codon optimized using DNAworks using standard E. coli codons. Variants were cloned into pET29b using the NdeI and XhoI sites. Point mutations were generated through overlap PCR, and terminal cysteine addition was achieved through extended primers (Table S1). Mutation C132A was introduced through overlap PCR (Table S1). Protein variants were expressed in LB or TB media at 37° C. for 4 or 16 h through induction with 1 mM IPTG. For purification, cells were resuspended in 50 mM Tris 150 mM NaCl buffer, heated to 80° C. for 20 min and debris eliminated through centrifugation. Protein was then applied to a standard Ni-column.
Binding Analysis
The affinity of the design variants FcB6.1-C132A was determined using a Biacore T100 that was provided by the Analytical Biopharmacy Core facility. A streptaviding-coated chip (Biacore, Uppsala, Sweden) was coated with 300 RU of biotinylated Rituxan. FcB6.1-C132A was titrated in either TBS-BP (25 nM Tris at pH 8.2 with 0.1% BSA and 0.005% (v/v) P20) or PBS-BP (25 mM PBS at pH 5.5 with 0.1% BSA and (v/v) 0.005% P20. The protein was applied at a flow rate of 100 μl/min with 60 sec for association and 90 sec for dissociation. For regeneration of the unbound antibody, two cycles of 20 sec at 20 μl/min of a 100 mM glycine solution at pH 3 were allowed.
Resin Coupling
A buffer exchanged was performed into 25 mM Tris pH 8.2. 25 mM TCEP was used for at least 1 h at room temperature, to reduce possibly disulfide-bonded dimers. About 3 mg of protein per 1 ml SulfoLink resin material (Thermo Scientific) was incubated following procedures from the instruction manual. Resin was washed with 10 column volumes of 25 mM Tris at pH 8.2 with 500 mM NaCl, followed by 10 column volumes 25 mM Tris pH 8.2 followed by incubation with 50 mM cysteine as instructed by the manufacture's manual. After final wash with Tris-NaCl followed by washing with TBS column was ready to use.
IgG Purification
20 μg of a human IgG mix (Innovative Research, Inc.) was spiked into 1 ml of 293 Freestyle suspension cell supernatant. Suspension cells were harvested after 2 weeks of expressing an unrelated protein, when the cell density reached 2-3×10e6 cells/ml. To adjust the pH of the supernatant, 1/100 of 1 M Tris pH 8.2 were added and the supernatant-IgG mix was incubated while rotating for 30 min at 4° C. 500 μl resin was allowed to settle and washed with 10 column volumes TBS at pH 8.2. Antibodies were eluted with 25 mM phosphate buffer with 500 mM NaCl at 5.5, or with 100 mM glycine buffer at pH 3. For comparison to Protein A, a agarose resin (Pierce) was purchased and purification was done in the same manner. The version of FcB6.1 that was tethered to agarose was bound through a C-terminal cysteine that was genetically added through a linker: GGGSCLEHHHHHH(SEQ ID NO: 183).
CD Spectrum
CD data were collected on an Aviv 420 spectrometer. Far-UV CD wavelength scans (260-200 nm) at 25 μM protein concentration, with either different urea or guanidine hydrochloride (gua) concentrations, and temperature ranges (25-95° C.) were collected in a 1 mm path length cuvette. Temperature induced protein denaturation was followed by the change in ellipticity at 220 nm in a 1 mm path length cuvette.
REFERENCES


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## Claims

1. A polypeptide comprising the amino acid sequence of general formula 1 Z1-Z2-Z3 (SEQ ID NO: 1), wherein
Z1 is EY(A/C)VSxTADxxxH (SEQ ID NO: 184);
Z2 is GxxxxLxRxAVKGxKP (SEQ ID NO: 185); and
Z3 is a xxxQQxxFYMxxx (SEQ ID NO: 186),
wherein x is any amino acid.

2. The polypeptide of claim 1, wherein Z1 is selected from the group consisting of







(SEQ ID NO: 15)









EYCVSRTAVDAKKH;


 







(SEQ ID NO: 16)









EYAVSRTAVDALKH;


 







(SEQ ID NO: 17)









EYCVSRTAVDALKH;


 







(SEQ ID NO: 18)









EY(A/C)VSRTA(E/V/L/M/A/I/T)DALKH;


 







(SEQ ID NO: 19)









EY(A/C)VSRTA(E/V/L/R/M/A)DALKH;


 







(SEQ ID NO: 20)









EY(A/C)VSRTA(E/V/M/A/I/T)DALKH;


 







(SEQ ID NO: 21)









EY(A/C)VSRTAVDALKH;


 







(SEQ ID NO: 22)









EY(A/C)VSRTA(V/M)DALKH;


 







(SEQ ID NO: 23)









EY(A/C)VSRTAMDALKH;


 







(SEQ ID NO: 24)









EY(A/C)VSRTAADALKH;


 







(SEQ ID NO: 25)









EY(A/C)VSRTAMDALKH;


 







(SEQ ID NO: 26)









EY(A/C)VSRTALDALKH;


 







(SEQ ID NO: 27)









EY(A/C)VSRTAIDALKH;


 







(SEQ ID NO: 28)









EY(A/C)VSRTATDALKH;


 







(SEQ ID NO: 29)









EY(A/C)VSRTAVDALKH


 







(SEQ ID NO: 30)









EYAVSRTAMDALKH;


 







(SEQ ID NO: 31)









EYAVSRTAADALKH;


 







(SEQ ID NO: 32)









EYAVSRTAMDALKH;


 







(SEQ ID NO: 33)









EYAVSRTALDALKH;


 







(SEQ ID NO: 34)









EYAVSRTAIDALKH;


 







(SEQ ID NO: 35)









EYAVSRTATDALKH;


 







(SEQ ID NO: 36)









EYCVSRTAMDALKH;


 







(SEQ ID NO: 37)









EYCVSRTAADALKH;


 







(SEQ ID NO: 38)









EYCVSRTAMDALKH;


 







(SEQ ID NO: 39)









EYCVSRTALDALKH;


 







(SEQ ID NO: 40)









EYCVSRTAIDALKH;



and


 







(SEQ ID NO: 41)









EYCVSRTATDALKH.

3. The polypeptide of claim 1, wherein Z3 is selected from the group consisting of:







(SEQ ID NO: 47)









EMEQQAFFYMKLR;


 







(SEQ ID NO: 48)









EMEQQALFYMKLR;


 







(SEQ ID NO: 49)









TFEQQSFFYMSLK;


 







(SEQ ID NO: 51)









(B5)(B6)EQQ(S/A)(F/L)FYM(B5)L(K/R),






where B5 and B6 are independently any amino acid;







(SEQ ID NO: 52)


(G/R/S/M/P/W/V/T/R)(M/L/I/A/E/F)EQQ(S/A)


(F/L)FYM(B5)L(K/R);


 


(SEQ ID NO: 53)


(V/H/K/W)(M/W/I/L/H)EQQ(S/A)(F/L)FYM(B5)L(K/R);


 


(SEQ ID NO: 54)


EMEQQALFYMKLK;


 


(SEQ ID NO: 55)


VWEQQSFFYMVLK;


 


(SEQ ID NO: 56)


HWEQQSFFYMLLK;


 


(SEQ ID NO: 57)


HMEQQSFFYMMLK;


 


(SEQ ID NO: 58)


KIEQQSFFYMMLK;


 


(SEQ ID NO: 59)


WLEQQSFFYMALK;


 


(SEQ ID NO: 60)


WLEQQSFFYMQLK;


 


(SEQ ID NO: 61)


WLEQQAFFYMELK;


 


(SEQ ID NO: 62)


WLEQQSFFYMKLK;


 


(SEQ ID NO: 63)


FLEQQSFFYMRLK;


 


(SEQ ID NO: 64)


WHEQQSFFYMMLK;


 


(SEQ ID NO: 65)


WHEQQSFFYMRLK;


 


(SEQ ID NO: 66)


EMEQQALFYMKLK;


 


(SEQ ID NO: 67)


GMEQQSFFYMILK;


 


(SEQ ID NO: 68)


RLEQQSFFYMTLK;


 


(SEQ ID NO: 69)


SLEQQSFFYMNLK;


 


(SEQ ID NO: 70)


MIEQQSFFYMRLK;


 


(SEQ ID NO: 71)


PIEQQSFFYMHLK;


 


(SEQ ID NO: 72)


WLEQQSFFYMHLK;


 


(SEQ ID NO: 73)


VLEQQSFFYMDLK;


 


(SEQ ID NO: 74)


WAEQQSFFYMGLK;


 


(SEQ ID NO: 75)


TEEQQSFFYMTLK;


 


(SEQ ID NO: 76)


TFEQQSFFYMSLK;


and


 


(SEQ ID NO: 77)


RLEQQSFFYMSLK.

4. The polypeptide of claim 1, wherein Z2 has the amino acid sequence







(SEQ ID NO: 85)


G(F/V)(E/D)(V/G)(Y/C)L(L/F)R(D/E/N)AVKG(I/V/F)KP.

5. The polypeptide of claim 1, wherein the polypeptide comprises one of the following amino acid sequences selected from the group consisting of SEQ ID NOs: 117-119.

6. The polypeptide of claim 1, wherein the polypeptide comprises the amino acid sequence of general formula 5, Z4-Z1-Z2-Z3 (SEQ ID NO: 8), wherein Z4 is a peptide of at least between 100-200 amino acids in length.

7. The polypeptide of claim 6, wherein Z4 comprises the amino acid sequence of SEQ ID NO: 120.

8. The polypeptide of claim 1, wherein the polypeptide comprises one of the following amino acid sequences selected from the group consisting of SEQ ID NOs: 141-169 and 172-182.

9. A pharmaceutical composition comprising the polypeptide of claim 1 and a pharmaceutically acceptable carrier.

10. A composition, comprising the polypeptide of claim 1=bound to a solid support.

11. The polypeptide of claim 1, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:143.

12. The polypeptide of claim 2, wherein Z3 is selected from the group consisting of SEQ ID NOs: 47-49 and 51-77.

13. The polypeptide of claim 2, wherein Z2 has the amino acid sequence of SEQ ID NO:85.

14. The polypeptide of claim 12 wherein Z2 has the amino acid sequence of SEQ ID NO:85.

15. The polypeptide of claim 3 wherein Z2 has the amino acid sequence of SEQ ID NO:85.

16. A method for purifying antibodies or Fc fusion proteins, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to claim 1 under suitable conditions for binding of antibodies in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) dissociating the antibody from the antibody-polypeptide complexes, to isolate the antibody.

17. A method for detection of an antibody or Fc fusion protein in a sample, comprising
(a) contacting a sample comprising antibodies or Fc fusion proteins with one or more polypeptides according to claim 1 under suitable conditions for binding of antibodies or Fc fusion protein in the sample to the one or more polypeptides to form antibody-polypeptide complexes; and
(b) detecting the antibody-polypeptide complexes.