Crystal structures of heterodimeric Fc domains
Disclosed are the atomic coordinates of compositions comprising Fc heterodimer proteins in crystalline form derived from high resolution x-ray diffraction. Further disclosed are systems and methods for using all or a portion of these atomic coordinates to identify and design improved Fc heterodimer proteins. Further disclosed are compositions comprising a mixture of (i) a solubilized Fc heterodimer protein and (ii) a mother liquor solution. The mother liquor solution comprises between 2% and 10% (v/v) ethylene glycol, between 10% and 25% (w/v) polyethylene glycol having an average molecular weight of between 2000 Daltons and 10000 Daltons, and between 0.05 M and 0.40 M ammonium iodide. Further disclosed are systems and methods of identifying a mutation which promotes heterodimeric Fc chain pair formation in which structure based modeling is performed to identify a candidate mutation to an Fc chain using all or a portion of the disclosed three-dimensional atomic coordinates.
1. A composition comprising an Fc heterodimer protein in crystalline form, wherein:
said Fc heterodimer protein comprises the amino acid sequences set forth in (i) SEQ ID NOS:2 and 3 or (ii) SEQ ID NOS:4 and 5;
said crystal is in space group P2 1 2 1 2 1 ; and
said crystal has unit cell dimensions a=49±2 Å, b=75±2 Å, c=149±2 Å, α=β=γ=90°.
2. The composition of claim 1 , wherein said Fc heterodimer protein comprises the amino acid sequences set forth in SEQ ID NOS:2 and 3 and has a three dimensional structure characterized by the atomic coordinates of (i) chains A and B of FIG. 27 or (ii) chains a and b of FIG. 27 .
3. The composition of claim 1 , wherein said Fc heterodimer protein comprises the amino acid sequences set forth in SEQ ID NOS:4 and 5 and has a three dimensional structure characterized by the atomic coordinates of (i) chains A and B of FIG. 26 or (ii) chains a and b of FIG. 26 .
4. The composition of claim 1 , wherein said Fc heterodimer protein comprises the amino acid sequences set forth in SEQ ID NOS: 2 and 3 forming a CH3 domain interface, and wherein the Fc heterodimer protein provides complementary hydrophobic and electrostatic surfaces, created by residues 366, 392, 394 of SEQ ID NO: 2 and residues 351, 405, 407 of SEQ ID NO: 3, at the CH3 domain interface with opposite surface complementarity to corresponding wild type Fc interface surfaces.
5. The composition of claim 1 , wherein said Fc heterodimer protein comprises the amino acid sequences set forth in SEQ ID NOS: 4 and 5 forming a CH3 domain interface, and wherein the Fc heterodimer protein provides complementary hydrophobic and electrostatic surfaces, created by residues 366, 392, 394 of SEQ ID NO: 4 and residues 351, 405, 407 of SEQ ID NO: 5, at the CH3 domain interface with distinct surface complementarity relative to the corresponding wild type Fc interface surfaces.
6. The composition of claim 1 , wherein said Fc heterodimer protein comprises a D399-K409 salt bridge.
7. The composition of claim 4 , wherein said CH3 domain interface is formed in two orientations and said crystalline form of said Fc heterodimer protein comprises a 50:50 mixture of the two orientations.
8. A method of obtaining the composition of claim 1 , comprising the steps of:
a) producing and purifying said Fc heterodimer protein; and
b) subjecting the purified Fc heterodimer protein of step a) to conditions which promote crystallization, thereby obtaining the Fc heterodimer protein in crystalline form.
9. The method of claim 8 , wherein the conditions which promote crystallization comprise mixing the purified Fc heterodimer protein with a mother liquor solution, wherein the mother liquor solution comprises between 2% and 10% (v/v) ethylene glycol, between 10% and 25% (w/v) polyethylene glycol having an average molecular weight of between 2000 Daltons and 10000 Daltons, and between 0.05 M and 0.40 M ammonium iodide.
10. The method of claim 9 , wherein the mother liquor solution comprises 5% (v/v) ethylene glycol, 18% (w/v) polyethylene glycol having an average molecular weight of 3350 Daltons, and 0.15 M ammonium iodide.
11. The method of claim 9 , wherein the purified Fc heterodimer protein is mixed with a first aliquot of the mother liquor solution and suspended over a second aliquot of the mother liquor in a hanging drop method.
12. The method of claim 11 , wherein the purified Fc heterodimer protein is mixed with a first aliquot of the mother liquor solution in a 2:1 ratio.
13. The method of claim 11 , wherein the purified Fc heterodimer protein is incubated at a temperature of between 15° C. and 25° C. after the mixing.
14. A crystallizable composition comprising a mixture of (i) a solubilized Fc heterodimer protein comprising the amino acid sequence set forth in (a) SEQ ID NOS: 2 and 3 or (b) SEQ ID NOS: 4 and 5 and (ii) a mother liquor solution, wherein the mother liquor solution comprises between 2% and 10% (v/v) ethylene glycol, between 10% and 25% (w/v) polyethylene glycol having an average molecular weight of between 2000 Daltons and 10000 Daltons, and between 0.05 M and 0.40 M ammonium iodide.
15. The crystallizable composition of claim 14 , wherein the mother liquor solution comprises 5% (v/v) ethylene glycol, 18% (w/v) polyethylene glycol having an average molecular weight of 3350 Daltons, and 0.15 M ammonium iodide.