CA2155335C

Improved method for the refolding of proteins

Abstract

A novel, generally applicable method for producing correctly folded proteins from a mixture of misfolded proteins, e.g. bacterialinclusion-body aggregates. A major new aspect of the method is that over-all efficiency is achieved by subjecting proteins to a time-sequence of multiple denaturation-renaturation cycles, resulting in gradual accumulation of the correctly folded protein. The method hasproven efficient for a variety of recombinant proteins. Also provided are novel encrypted recognition sites for bovine coagulation factorXa. The encrypted recognition sites described may be activated in vitro by controlled oxidation or by reversible derivatization of cysteineresidues and thereby generate new cleavage sites for factor Xa. Two new recombinant serine protease exhibiting narrow substrate specificityfor factor Xa recognition sites are also provided. They may replace natural coagulation factor Xa for cleavage of chimeric proteins.

CA2155335C, drawing sheet 1
Sheet 1 of 70

Term

Term ended

Expired 4 February 2014, 12.6 years ago.

  1. Priority
  2. Filed
  3. Granted
  4. Expired
  5. Today

2 claims: 1 independent, 1 dependent

  1. 1
    155 CLAIMS 1. A method for generating a processed ensemble of polypeptide molecules, in which processed ensemble the conformational states represented contain a substantial fraction of polypeptide molecules in one particular folded conformation, from an initial ensemble of polypeptide molecules which have the same amino acid sequence as the processed ensemble of polypeptide molecules, in which initial ensemble the conformational states represented contain a substantial fraction of polypeptide molecules in unfolded or misfolded conformations, the method comprising subjecting the initial ensemble of polypeptide molecules to a series of at least five successive cycles each of which comprises a sequence of 1) at least one denaturing step comprising conditions exerting a denaturing and/or unfolding influence on the polypeptide molecules of the ensemble so as to denature a fraction of the polypeptides in the ensemble, followed by
  2. 2
    2) at least one renaturing step comprising conditions having a renaturing influence on the polypeptide molecules having conformations resulting from the preceding step so as to renature a fraction of the denatured and/or unfolded polypeptides in the ensemble, 156 the series of the at least five successive cycles being so adapted that the processed ensemble of polypeptide molecules has a higher fraction of polypeptide molecules in the particular folded conformation than a) the initial ensemble and b) a corresponding initial ensemble which has been subjected to one of the cycles only. 2. A method according to claim 1, wherein the substantial fraction of polypeptide molecules in one particular folded conformation in the processed ensemble constitutes at least 5% (w/w) of the initial ensemble of polypeptide molecules . 3. A method according to claim 1 or 2, wherein the polypeptide molecules of the processed ensemble comprise cysteine-containing molecules, and the processed ensemble comprises a substantial fraction of polypeptide molecules in one particular folded conformation which, in addition have identical disulphide bridging topology. 4. A method according to any one of claims 1 to 3, wherein the polypeptide molecules are molecules which have an amino acid sequence identical to that of an authentic polypeptide, or are molecules which comprise an amino acid sequence corresponding to that of an authentic polypeptide joined to one or two additional 157 polypeptide segments . 5. A method according to claim 4, wherein the amino acid sequence corresponding to that of an authentic polypeptide is joined to the additional polypeptide segment or segments via a cleavable junction or similar or dissimilar cleavable junctions. 6. A method according to any one of claims 1 to 5, wherein the series comprises at least 8 cycles and at most 2000 cycles. 7. A method according to claim 6, wherein the series comprises at least 10 cycles and at most 200 cycles. 8. A method according to any one of claims 1 to Ί, wherein the duration of each denaturing step is at least 1 millisecond and at most 1 hour, and the duration of each renaturing step is at least 1 second and at most 12 hours . 9. A method according to claim 8, where in the denaturing conditions of each individual denaturing step are kept constant for a period of time, and the renaturing conditions of each individual renaturing step are kept constant for a period of time, the periods of time during which conditions are kept constant being separated by transition periods during which the conditions are changed. 21 5 5 3 35 158 10. A method according to claim 9, in which the transition period between steps for which conditions are kept constant has a duration between 0.1 second and 12 hours . 11. A method according to claim 10, wherein the period of time for which the denaturing conditions of the denaturing step are kept constant has a duration of between 1 and 10 minutes, and the period of time for which the renaturing conditions of the renaturing step are kept constant has a duration of between 1 and 45 minutes . 12. A method according to any one of claims 1 to 11, wherein the polypeptide molecules comprise a polypeptide segment which is capable of directing preferential cleavage by a cleaving agent at a specific peptide bond. 13. A method according to claim 12, wherein the cleavage-directing polypeptide segment is one which is capable of directing preferential cleavage at a specific peptide bond by a chemical or enzymatic cleaving agent selected from the group consisting of cyanogen bromide, hydroxylamine, iodosobenzoic acid, N-bromo-succinimide, bovine coagulation factor X a , analogues and homologues thereof, and bovine enterokinase and analogues and homologues thereof . 14. A method according to claim 12 or 13, wherein the 159 polypeptide segment which directs preferential cleavage is a sequence which is selectively recognised by the bovine coagulation factor X a or an analogue or homologue thereof . 15. A method according to claim 14, wherein the polypeptide segment has an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO: 40, SEQ ID NO: 41 and SEQ ID NO: 42. 16. A method according to any one of claims 1 to 15, wherein the polypeptide molecules comprise a polypeptide segment which is in vitro-convertible into a derivatized polypeptide segment capable of directing preferential cleavage by a cleaving agent at a specific peptide bond. 17. A method according to claim 16, wherein the in vitro-convertible polypeptide segment is convertible into a derivatized polypeptide segment which is selectively recognised by the bovine coagulation factor X a or an analogue and/or homologue thereof. 18. A method according to claim 17, wherein the in vitro-convertible polypeptide segment has an amino acid sequence selected from the group consisting of SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45 and SEQ ID NO: 46. 19. A method according to claim 18, wherein the polypeptide molecules comprise a polypeptide segment 160 21 5 5 335 with either the amino acid sequence SEQ ID NO: 43 or SEQ ID NO: 44, which is converted into a derivatized polypeptide, which is selectively recognised by bovine coagulation factor X a or an analogue and/or homologue thereof, by reacting the cysteine residue with N-(2-mercaptoethyl)morpholyl-2-thiopyridyl disulphide or mercaptothioacetate-2- thiopyridyl disulphide, or with the amino acid sequence SEQ ID NO: 45 or SEQ ID NO: 46, which is converted into a derivatized polypeptide, which is selectively recognised by bovine coagulation factor X a , by oxidation of the thioether moiety in the methionine side group to a sulphoxide or sulphone derivative. 20. A method according to claim 15 wherein the polypeptide segment selected from the group consisting Of SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 41 and SEQ ID NO: 42 is linked N-terminally to the authentic polypeptide . 21. A method according to any one of claims 18 or 19, wherein the polypeptide segment selected from the group consisting of SEQ ID NO;43, SEQ ID NO: 44, SEQ ID NO: 45 and SEQ ID NO: 46 is linked N-terminally to the authentic polypeptide. 161 22. A method according to any one of claims 1 to 21, wherein the polypeptide molecules are in contact with a liquid phase during the denaturing and renaturing steps, the liquid phase being an aqueous phase or an organic phase . 23. A method according to claim 22, wherein the polypeptide molecules are confined to an environment which allows changing or exchanging the liquid phase without entraining the polypeptide molecules. 24. A method according to claim 23, wherein the polypeptides are confined to a dialysis device or a liquid two-phase system. 25. A method according to claim 23, wherein the polypeptide molecules are bound to a solid or semisolid carrier, said carrier being selected from a filter surface;a hollow fibre or a beaded chromatographic medium;a fibrous cellulose matrix;an HPLC or FPLC matrix;a substance having molecules of such a size that the molecules with the polypeptide molecules bound thereto, when dissolved or dispersed in a liquid phase, can be retained by means of a filter;a substance capable of forming micelles or participating in the formation of micelles allowing the liquid phase to be changed or exchanged without entraining the micelles;and a water-soluble polymer. 162 26. A method according to claim 25, wherein the chromatographic medium is an agarose or polyacrylamide gel. 27. A method according to claim 25 or 26, wherein the polypeptide molecules are non-covalently absorbed to the carrier through a moiety having affinity to a component of the carrier. 28. A method according to claim 27, wherein a biotin group or an analogue thereof is bound to an amino acid moiety of the polypeptide, and the carrier has avidin, streptavidin or an analogue thereof attached thereto. 29. A method according to claim 25, 26 or 27, wherein the polypeptide molecules have an amino acid sequence identical to SEQ ID NO: 47, and the carrier comprises a Nitrilotriacetic Acid derivative (NTA) charges with Ni ++ ions . 30. A method according to any one of claims 22 to 29, wherein the liquid phase used in at least one of the denaturing steps and/or in at least one of the renaturing steps contains at least one disulphidereshuffling system, and wherein the polypeptide comprises at least one disulphide bond formed between cysteine residues . 31. A method according to claim 30, wherein at least 21 5 5 3 35 163 one disulphide-reshuffling system is one which is capable of preferentially reducing and/or reshuffling incorrectly formed disulphide bridges in unfolded and/or misfolded polypeptide molecules under conditions with respect to concentration of the denaturing agent at which unfolded and/or misfolded proteins are denatured. 32. A method according to claim 31, wherein the presence of the disulphide reshuffling system in at least one step results in a ratio between the relative amount of reduced/reshuffled initially incorrectly formed disulphide bridges and the relative amount of reduced/reshuffled initially correctly formed disulphide bridges of at least 1.05. 33. A method according to any one of claims 30 to 32, wherein the disulphide-reshuffling system contains glutathione, 2-mercaptoethanol or thiocholine, each of which in admixture with its corresponding symmetrical disulphide. 34. A method according to any one of claims 30 to 33, wherein all cysteine residues in the polypeptide molecules have been converted to mixed disulphide products of either glutathion, thiocholine, mercaptoethanol or mercaptoacetic acid, during at least one of the denaturing/renaturing cycles. 35. A method according to claim 34, wherein the 21 5 5 3 35 164 conversion of the cysteine residues to mixed disulphide products is accomplished by reacting the fully denatured and fully reduced ensemble of polypeptide molecules with an excess of a reagent which is a high-energy mixed disulphide compound. 36. A method according to claim 35, wherein the highenergy mixed disulphide compound is aliphatic-aromatic. 37. A method according to claim 35 or 36, wherein the high-energy mixed disulphide compound is selected from the group consisting of glutathionyl-2-thiopyridyl disulphide, 2-thiocholyl-2-thiopyridyl disulphide, 2mercaptoethanol-2-thiocholyl disulphide and mercaptoacetate-2-thiopyridyl disulphide. 38. A method according to any one of claims 22 to 37, wherein the polarity of the liquid phase used in the renaturing of the polypeptide molecules has been modified by the addition of a salt, a polymer, trifluoroethanol or other hydrofluoro compound. 39. A method according to any one of claims 1 to 38, wherein the denaturing and renaturing of the polypeptide molecules is accomplished by direct changes in physical parameters to which the polypeptide molecules are exposed, or by changes in physical parameters which enhances or moderates the denaturing and renaturing conditions . 165 40. A method according to claim 39, wherein said physical parameters are selected from temperature and pressure . 41. A method according to any one of claims 22 to 38, wherein the chemical composition of the liquid phase with which the polypeptide molecules are in contact is changed between the denaturing and renaturing steps. 42. A method according to claim 41, wherein denaturing of the polypeptide molecules is accomplished by contacting the polypeptide molecules with a liquid phase in which at least one denaturing compound is dissolved, and wherein renaturing of the polypeptide molecules is accomplished by contacting the polypeptide molecules with a liquid phase which either contains at least one dissolved denaturing compound in such a concentration that the contact with the liquid phase will tend to renature rather than denature the ensemble of polypeptide molecules in their respective conformation states resulting from the preceding step, or contains no denaturing compound. 43. A method according to claim 42, wherein the denaturing of the polypeptide molecules is achieved or enhanced by decreasing or increasing pH of the liquid phase . 44. A method according to claim 41, wherein the 166 chemical changes in the liquid phase are accomplished by changing between a denaturing solution B comprising at least one denaturing compound and a renaturing solution A. 45. A method according to claim 44, wherein the concentration of said at least one denaturing compound in B is adjusted after each cycle. 46. A method according to claim 44, wherein the concentration of said at least one denaturing compound in B is decremented after each cycle. 47. A method according to claim 44, wherein the concentration of said at least one denaturing compound in B is kept constant in each cycle. 48. A method according to any one of claims 42 to 47, wherein at least one denaturing compound is selected from urea, guanidine-HC1, and di-C^alkylformamide such as dimethyl formamide and di-Chalky!sulphone . 49. A method according to any one of claims 1 to 48, in which the polypeptide molecules of the ensemble have a length of at least 25 amino acid residues and at most 5000 amino acid residues. 50. A method according to any of claims 1 to 49, wherein the polypeptides of the initial ensemble are 167 artificial polypeptides produced in prokaryotic cells by means of recombinant DNA-techniques . 51. A method according to claim 50, wherein the initial· sample of polypeptide molecules are unfolded or misfolded diabody molecules (artificial bispecific and bivalent antibody fragments) or monomer fragments of diabody molecules . 52. A method for producing correctly folded diabody molecules, wherein an initial ensemble of polypeptide molecules comprising unfolded and/or misfolded polypeptides having amino acid sequences identical to monomer fragments of diabody molecules is subjected to a series of at least two successive cycles each of which comprises a sequence of 1) at least one denaturing step comprising conditions exerting a denaturing and/or unfolding influence on the polypeptide molecules of the ensemble, so as to denature a fraction of the polypeptides in the ensemble, followed by 2) at least one renaturing step comprising conditions having a renaturing influence on the polypeptide molecules having conformations resulting from the preceding step so as to renature a fraction of the denatured and/or unfolded polypeptides in the ensemble, 168 the series of cycles being so adapted that a substantial fraction of the initial ensemble of polypeptide molecules is converted to a fraction of correctly folded diabody molecules. 53. A method according to claim 52, wherein the polypeptide molecules are in contact with a liquid phase containing at least one disulphide reshuffling system in at least one denaturing/renaturing cycle.