WO2002022796A1 - Calcium free subtilisin mutants - Google Patents

Abstract

Novel calcium free subtilisin mutants are taught, in particular subtilisins which have been mutated to eliminate amino acids 75-83 and which retain enzymatic activity and stability. Recombinant methods for producing same and recombinant DNA encoding for such subtilisin mutants are also provided.

Description

CALCIUM FREE SUBTILISIN MUTANTS

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

The U.S. Government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of Grant No. GM42560 awarded by National Institute of Health.

GENERAL OBJECTS OF THE INVENTION

A general object of the invention is to provide subtilisin mutants which have been mutated such that they do not bind calcium. Another object of the invention is to provide DNA sequences which upon expression provide for subtilisin mutants which do not bind calcium.

Another object of the invention is to provide subtilisin mutants which comprise specific combinations of mutations which provide for enhanced thermal stability. Another object of the invention is to provide a method for the synthesis of a subtilisin mutant which does not bind calcium-by the expression of a subtilisin DNA which comprises one or more substitution' , deletion or addition mutations in a suitable recombinant host cell.

A more specific object of the invention is to provide class I subtilase mutants, in particular BPN' mutants which have been mutated such that they do not bind calcium.

Another specific object of the invention is to provide DNA sequences which upon expression result in class I subtilase mutants, and in particular BPN' mutants which do not bind calcium. Another specific object of the invention is to provide a method for making subtilisin I-Sl or I-S2 mutants, and in particular BPN' mutants which do not bind calcium by expression of a class I subtilase mutant DNA sequence, and more specifically a BPN' DNA coding sequence which comprises one or more substitution, addition or deletion mutations in a suitable recombinant host cell.

Yet another specific object of the invention is to provide mutant subtilisin I-Sl or I-S2, and more specifically BPN' mutants which do not bind calcium and which further comprise particular combinations of mutations which provide for enhanced thermal stability, or which restore cooperativity to the folding reaction.

The subtilisin mutants of the present invention are to be utilized in applications where subtilisins find current usage. Given that these mutants do not bind calcium they should be particularly well suited for use in industrial environments which comprise chelating agents, e.g. detergent compositions, which substantially reduces the activity of wild-type calcium binding subtilisins.

BACKGROUND OF THE INVENTION

(1) Field of the Invention The present invention relates to subtilisin proteins which have been modified to eliminate calcium binding. More particularly, the present invention relates to novel subtilisin I-Sl and I-S2 subtilisin mutants, specifically BPN' mutants wherein the calcium A-binding loop has been deleted, specifically wherein amino acids 75-83 have been deleted, and which may additionally comprise one or more other mutations, e.g., subtilisin modifications, which provide for enhanced thermal stability and/or mutations which restore cooperativity to the folding reaction. (2) Description of the Related Art

Subtilisin is an unusual example of a monomeric protein with a substantial kinetic barrier to folding and unfolding. A well known example thereof, subtilisin BPN' is a 275 amino acid serine protease secreted by Bacillus amyloliquefaciens. This enzyme is of considerable industrial importance and has been the subject of numerous protein engineering studies (Siezen et al., Protein Engineering 4:719- 737 (1991); Bryan. Pharmaceutical Biotechnology 3(B): 147181 (1992); Wells et al.. Trends Biochem. Sci. 13:291-297 (1988)). The amino acid sequence for subtilisin BPN' is known in the art and may be found in Vasantha et al. , _ Bacteriol. 159:811-819 (1984). The amino acid sequence as found therein is hereby incorporated by reference [SEQUENCE ID NO:l]. Throughout the application, when Applicants refer to the amino acid sequence of subtilisin BPN' or its mutants, they are referring to the amino acid sequence as listed therein. Subtilisin is a serine protease produced by Gram positive bacteria or by fungi. The amino acid sequences of numerous subtilisins are known. (Siezen et al. , Protein Engineering 4:719-737 (1991)). These include five subtilisins from Bacillus strains, for example, subtilisin BPN' , subtilisin Carlsberg, subtilisin DY, subtilisin amylosacchariticus, and mesenticopeptidase. (Vasantha et al., "Gene for alkaline protease and neutral protease from Bacillus amyloliquefaciens contain a large open-reading frame between the regions coding for signal sequence and mature protein," J. Bacteriol. 159:811-819 (1984); Jacobs et al., "Cloning sequencing and expression of subtilisin Carlsberg from Bacillus licheniformis, Nucleic Acids Res. 13:8913-8926 (1985); Nedkov et al., "Determination of the complete amino acid sequence of subtilisin DY and its comparison with the primary structures of the subtilisin BPN', Carlsberg and amylosacchariticus, Biol. Chem. Hoope-Seyler 366:421-430 (1985); Kurihara et al., "Subtilisin amylosacchariticus, " J. Biol. Chem. 247:5619-5631 (1972); and Svendsen et al., "Complete amino acid sequence of alkaline mesentericopeptidase," FEBS Lett. 196:228-232 (1986)).

The amino acid sequences of subtilisins from two fungal proteases are known: proteinase K from Tritirachium albam (Jany et al., "Proteinase K from Tritirachium albam Limber, " Biol. Chem. Hoppe-Seyler 366:485-492 (1985)) and thermomycolase from the thermophilic fungus, Malbranchea pulchella (Gaucher et al. , "Endopeptidases: Thermomycolin, " Methods Enzymol. 45:415-433 (1976)). These enzymes have been shown to be related to subtilisin BPN' , not only through their primary sequences and enzymological properties, but also by comparison of x-ray crystallographic data. (McPhalen et al. , "Crystal and molecular structure of the inhibitor eglin from leeches in complex with subtilisin Carlsberg, " FEBS Lett.. 188:55-58 (1985) and Pahler et al., "Three-dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin, "EMBO 3:1311-1314 (1984)). Subtilisin BPN' is an example of a particular subtilisin gene secreted by

Bacillus amyloliquefaciens. This gene has been cloned, sequenced and expressed at high levels from its natural promoter sequences in Bacillus subtilis. The subtilisin BPN' structure has been highly refined (R= 0. 14) to 1.3 A resolution and has revealed structural details for two ion binding sites (Finzel et al., J. Cell. Biochem. Suppl. 10A:272 (1986); Pantoliano et al. , Biochemistry 27:8311-8317 (1988); McPhalen et al., Biochemistry 27: 6582-6598 (1988)). One of these (site A) binds Ca²⁺ with high affinity and is located near the N-terminus, while the other (site B) binds calcium and other cations much more weakly and is located about 32 A away (Figure 1). Structural evidence for two calcium binding sites was also reported by Bode et al. , Eur. J. Biochem. 166:673-692 (1987) for the homologous enzyme, subtilisin Carlsberg.

Further in this regard, the primary calcium binding site in all of the subtilisins in groups I-SI and I-S2 (Siezen et al., 1991, Table 7) are formed from almost identical nine residue loops in the identical position of helix C. X-ray structures of the I-Sl subtilisins BPN' and Carlsberg, as well as the I-S2 subtilisin Savinase, have been determined to high resolution. A comparison of these structures demonstrates that all three have almost identical calcium A-sites. The x-ray structure of the class I subtilase, thermitase from

Thermoactinomyces vulgaris, is also known. Though the overall homology of BPN' to thermitase is much lower than the homology of BPN' to I-Sl and I-S2 subtilisins, thermitase has been shown to have an analogous calcium A-site. In the case of thermitase, the loop is a . ten residue-interruption at the identical site in helix C.

Calcium binding sites are common features of extracellular microbial proteases probably because of their large contribution to both thermodynamic and kinetic stability (Matthews et al., J. Biol. Chem. 249:8030-8044 (1974); Voordouw et al., Biochemistry 15:3716-3724 (1976); Betzel et al., Protein Engineering 3:161-172 (1990); Gros et al., J. Biol. Chem. 266:2953-2961

(1991)). The thermodynamic and kinetic stability of subtilisin is believed to be necessitated by the rigors of the extracellular environment into which subtilisin is secreted, which by virtue of its own presence is protease-filled. Accordingly, high activation barriers to unfolding may be essential to lock the native conformation and prevent transient unfolding and.-proteolysis.

Unfortunately, the major industrial uses of subtilisins are in environments containing high concentrations of metal chelators, which strip calcium from subtilisin and compromise its stability. It would, therefore, be of great practical significance to create a highly stable subtilisin which is independent of calcium. The present inventors have previously used several strategies to increase the stability of subtilisin to thermal denaturation by assuming simple thermodynamic models to approximate the unfolding transition (Pantoliano et al., Biochemistry 26:2077-2082 (1987); Pantoliano et al., Biochemistry 27:8311-8317 (1988); Pantoliano et al. , Biochemistry 28:7205-7213 (1989); Rollence et al. , CRC Crit. Rev. Biotechnol. 8:217-224 (1988). However, improved subtilisin mutants which are stable in industrial environments, e.g., which comprise metal chelators, and which do not bind calcium, are currently not available.

OBJECTS AND SUMMARY OF THE INVENTION

Accordingly, it is an object of the invention to provide mutated or modified subtilisin enzymes, e.g., class I subtilases, which have been modified to elmiinate calcium binding. As used in this invention, the term "mutated or modified subtilisin" is meant to include any serine protease enzyme which has been modified to eliminate calcium binding. This includes, in particular, subtilisin

BPN' and serine proteases which are homologous to subtilisin BPN', in particular class I subtilases. However, as used herein, and under the definition of mutated or modified subtilisin enzyme, the mutations of this invention may be introduced into any serine protease which has at least 50%, and preferably 80% amino acid sequence identity with the sequences referenced above for subtilisin BPN' , subtilisin Carlsberg, subtilisin DY, subtilisin amylosacchariticus, mesenticopeptidase, thermitase, or Savinase and, therefore, may be considered homologous.

The mutated subtilisin enzymes of this invention are more stable in the presence of metal chelators and may also comprise enhanced thermal stability in comparison to native or wild-type subtilisin. Thermal stability is a good indicator of the overall robustness of a protein. Proteins of high thermal stability often are stable in the presence of chaotropic agents, detergents, and under other conditions, which normally tend to inactivate proteins. Thermally stable proteins are, therefore, expected to be useful for many industrial and therapeutic applications in which resistance to high temperature, harsh solvent conditions or extended shelf- life is required. It has been further discovered that combining individual stabilizing mutations in subtilisin frequently results in approximately additive increases in the free energy of stabilization. Thermodynamic stability has also been shown to be related to resistance to irreversible inactivation at high temperature and high pH. The single-site changes of this invention individually do not exceed a 1.5 Kcal/mol contribution to the free energy of folding. However, these small incremental increases in the free energy of stabilization result in dramatic increases in overall stability when mutations are combined, since the total free energy of folding for most proteins is in the range of 5-15 Kcals/mol (Creighton, Proteins: Structure and Molecular Properties. W.H. Freeman and Company, New York (1984)).

X-ray crystallographic analysis of several combination mutants reveals that conformational changes associated with each mutation tend to be highly localized with minimal distortion of the backbone structure. Thus, very large increases in stability can be achieved with no radical changes in the tertiary protein structure and only minor independent alterations in the amino acid sequence. As previously suggested (Holmes et al, J. Mol. Biol. 160:623 (1982)), contributions to the free energy of stabilization can be gained in different ways, including improved hydrogen bonding and hydrophobic interactions in the folded form and decreased chain entropy of the unfolded enzyme. This is significant since thermostable enzymes generally have more extended half-lives at broader temperature ranaes, thereby improving bio-reactor and shelf-life performance.

As noted supra, the invention provides subtilisin mutants which comprise one or more deletion, substitution or addition mutations which provide for the elimination of calcium binding. Preferably, this will be effected by deletion, substitution or insertion of amino acids into the calcium A-site, which in the case of class I subtilases comprises 9 amino acid residues in helix C. In the case of subtilisin BPN' , the subtilisin mutants will preferably comprise one or more addition, deletion or substitution mutations of the amino acids at positions 75-83, and most preferably will comprise the deletion of amino acids 75-83, of SEQUENCE ID NO: 1. The deletion of amino acids 75-83 has been discovered to effectively eliminate calcium binding to the resultant subtilisin mutant while still providing for subtilisin BPN' proteins having enzymatic activity. Such subtilisin mutants lacking amino acids 75-83 of SEQUENCE ID NO:

1 may further include one or more additional amino acid mutations in the sequence, e.g., mutations which provide for reduced proteolysis. It is another object of the invention to produce subtilisin mutants lacking calcium binding activity which have been further mutated to restore cooperativity to the folding reaction and thereby enhance proteolytic stability. It is another object of the invention to provide thermostable subtilisin mutants which further do not bind calcium and comprise specific combinations of mutations which provide for substantially enhanced thermal stability.

In particular, the subtilisin mutants of the present invention will include subtilisins from Bacillus strains, such as subtilisin BPN' , subtilisin Carlsberg, subtilisin DY, subtilisin amylosacchariticus and subtilisin mesenticopeptidase, which comprise one or more deletion, substitution or addition mutations.

The present invention further provides for subtilisin mutants lacking amino acids 75-83 of SEQUENCE ID NO: 1, which have new protein-protein interactions engineered in the regions around the deletion leading to large improvements in stability. More specifically, mutations at ten specific sites in subtilisin BPN' and its homologues are provided, seven of which individually, and in combination, have been found to increase the stability of the subtilisin protein. Improved calcium-free subtilisins are thus provided by the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1. X-ray Crystal structure of S15 subtilisin

A. ct-carbon plot shows the positions of mutations as noted. The numbering of wild type subtilisin is kept. Dotted spheres show the position of calcium at the weak ion binding site (B-site) and the former position of the high affinity, binding site (A-site). The A-site loop (dashed line) is absent in this mutant. N- and C- termini are indicated. The N-terminus is disordered (dotted line).

B. Close-up view of the A-site deletion., The loop from S12 subtilisin is shown as a dotted line with the continuous helix of S15. Superimposed is the

3* sigma difference electron density (FO12-FO15. , phases from S15) showing the deleted A-site loop.

Figure 2. X-ray crystal structure of the calcium A-site region of S12 subtilisin. Calcium is shown as a dotted sphere with one-half the van der Waals radius. Dashed lines are coordination bonds, while dotted lines represent hydrogen bonds under 3.2 A.

Figure 3. Differential Scanning Caloriinetry. The calorimetric scans of apo-S12 (T_m = 63.5°C) and S15 (T_m = 63.0°C) are shown. Measurements were performed with a Hart 7707 DSC (differential scanning calorimetry) heat conduction scanning microcalorimeter as described (Pantoliano et al. ,

Biochemistry 28:7205-7213 (1989)). Sample conditions were 50 mM of glycine, a pH of 9.63, a scan rate of 0.5°C/min. Excess heat capacity is measured in units of μJ/° . The calorimeter ampoules contained 1.78 mg of protein.

Figure 4. Titration calorimetry of subtilisin Sll. The heat of calcium binding for successive additions of calcium are plotted vs. the ratio of [Ca]/[P]. The data are best fit by a calculated binding curve assuming a binding constant of 7 x 10⁶ and ΔH equal to 11.3 kcal/mol using equation (1) from the text. For comparison, calculated curves assuming K_a = 1 x 10⁶ and 1 x 10^s are also shown. In this titration, [PI = lOOμM and the temperature was 25 °C.

Figure 5. Kinetics of calcium dissociation from subtilisin Sll as a function of temperature. lμM subtilisin Sll was added to lOμM Quin2 at time = 0.

Calcium dissociates from subtilisin and binds to Quin2 until a new equilibrium is achieved. The rate of calcium dissociation is followed by the increase in fluorescence of Quin2 when it binds to calcium.

A. The log of the percent of the protein bound to calcium is plotted vs. time. The kinetics of dissociation at four temperatures are shown. The dissociation follows first order kinetics for the first 25 % of the reaction. As this is well before equilibrium is approached, reassociation of calcium can be neglected.

B. Temperature dependence of the rate of calcium dissociation from S15 subtilisin in the presence of excess Quin2, pH 7.4 and over a temperature range of 25-45 °C. The natural log of the equilibrium constant for the transition state (calculated from the Eyring equation) is plotted vs. the reciprocal of the absolute temperature. The line is fit according to equation (3) in the text with T₀ = 298 K. Figure 6. Analysis of subtilisin refolding monitored by circular dichroism

(CD).

A. CD spectra are shown for S15 as follows: (1) S15 in 25 mM H₃PO₄ at pH 1.85; (2) S15 denatured at pH 1.85 and then neutralized to pH 7.5 by the addition of NAOH; (3) S 15 denatured at pH 1. 85 and neutralized to pH 7.5, 30 minutes after the addition of KCI to 0.6 M; and (4) Native S15 subtilisin. Protein concentrations of all samples was 1 μM.

B . Kinetics of refolding of S 15. Samples were denatured at pH 1.85 and then the pH was adjusted to 7.5. At time 0, KCI was added to the denatured protein. Recovery of native structure was followed at 222 run at KCI concentrations of 0.3 M and 0.6 M. The 0.6 M sample after 30 minutes of refolding was then used to record the corresponding spectrum in part A.

Figure 7. Kinetics of refolding of S 15 as a function of ionic strength. A. The log of the percent unfolded protein is plotted vs. time. The kinetics of refolding are shown at four ionic strengths. The amount of refolding was determined by circular dichroism (CD) from: the increase in negative ellipticity at 222 nm. 100% folding is determined from the signal at 222 nm for native S 15 at the same concentration and 0% folding is determined from the signal for acid-denatured S15. The refolding approximately follows first order kinetics for the first 90% of the reaction. Refolding was carried out at 25°C.

B. The log of first order rate constants for refolding obtained by CD or fluorescence measurements at 25 °C were plotted as a function of log of ionic strength. Ionic strength was varied from 1=0.25 to 1= 1.5. The rate of refolding increases linearly with log I. A ten-fold increase in I results in an approximately 90-fold increase in the refolding rate.

Figure 8. Temperature dependence of the refolding rate of S15 subtilisin in 0.6 M KCI, 23 nM KPO₄ pH 7.3. The natural log of the equilibrium constant for the transition state (calculated from the Eyring equation) is plotted vs. the reciprocal of the absolute temperature. The line is fit according to equation 3 in the text with T₀=298 K.

Figure 9. X-ray crystal structure of the weak ion binding region of ,S15 subtilisin. Coordination bonds are shown as dashed lines. Note the preponderance of charged amino acids. DESCRIPTION OF THE PREFERRED EMBODIMENTS

As discussed supra, calcium binding contributes substantially to the thermodynamic and kinetic-stability of extracellular microbial proteases. Moreover, with respect to subtilisin, hiah activation barriers to unfolding may be essential to retain the native conformation and to prevent transient unfolding and proteolysis given the protease-filled environment where subtilisin is secreted and as a result of auto-degradation. The unfolding reaction of subtilisin can be divided into two parts as follows:

N(Ca₂) «=» N(Ca) N <=> U where N(Ca₂) is the native form of subtilisin with calcium bound to both sites; N(Ca) is the native form of subtilisin with calcium bound to the high affinity calcium-binding site A (Finzel et al., J. Cell. Biochem. Suppl. 10A:272 (1986); Pantoliano et al., Biochemistry 27:8311-8317 (1988); McPhalen et al., Biochemistry 27:6582-6598 (1988)); N is the folded protein without calcium bound; and U is the unfolded protein. The total free energy of unfolding is therefore equal to Δgi + Δg₂ + Δg₃. From the binding constant, one can calculate the contribution of calcium to the free energy of subtilisin folding from the following equation: ΔG_binding = -RT ln (l + K_a[Ca]).

Thus, the contribution of site A to the stability of subtilisin in lOmM calcium is 6.6 kcal/mol at 25 "C. The contribution of calcium binding to site B in lOmM calcium and 50mM sodium is only 0.2 kcal/mol. This analysis is at odds with earlier studies which concluded that calcium binding to site B is responsible for the large decrease in the inactivation rate of subtilisin in the presence of millimolar concentrations of calcium (Braxton & Wells, Biochem. 37:7796-7801 (1992); Pantoliano et al, Biochem. 27: 8311-8317 (1988)) . Subtilisin is a relatively stable protein whose stability is in large part mediated by the high affinity calcium site (Voordouw et al. , Biochemistry 15:3716-3724 (1976); Pantoliano et al., Biochemistry 27:8311-8317 (1988)). The melting temperature of subtilisin at pH 8.0 in the presence of μmolar concentrations of calcium is approximately 75 °C and approximately 56 °C in the presence of excess EDTA (Takehashi et al. , Biochemistry 20:6185-6190 (1981); Bryan et al., Proc. Natl. Acad. Sci. USA.

83:3743-3745 (1986b)). Previous calorimetric studies of the calcium-free (apoenzyme, i.e., protein portion of enzyme) form of subtilisin indicated that it is of marginal stability at 25'C with a AG of unfolding of < 5 kcal/mol (Pantoliano et al. , Biochemistry 28:7205-7213 (1989)). Because calcium is such an integral part of the subtilisin structure, the apoenzyme is thought to be a folding intermediate of subtilisin.

In order to independently examine the two phases of the folding process, the present inventors constructed a series of mutant subtilisins. First, all proteolytic activity was eliminated in order to prevent auto-degradation from occurring during the unfolding and refolding reactions. This may be accomplished, for example, by converting the active-site serine 221 to cysteine.¹ This mutation has little effect on the thermal denaturation temperature of subtilisin, but reduces peptidase activity of subtilisin by a factor of approximately 3 x 104 (Abrahmsen et al., Biochemistry 30:4151-4159 (1991)). This mutant, therefore, allows the folding of subtilisin to be studied without the complications of proteolysis. In the present specification, a shorthand for denoting amino acid substitutions employs the single letter amino acid code of the amino acid to be substituted, followed by the number designating where in the amino acid sequence

The S221A mutant was originally constructed for this purpose. The mature form of this mutant was heterogeneous on its N-terminus, however, presumably due to some incorrect processing of the pro- enzyme. the substitution will be made, and followed by the single letter code of the amino acid to be inserted therein. For example, S221C denotes the substitution of serine 221 to cy steine. The subtilisin mutant with this single amino acid substitution is denoted subtilisin S221C. The resulting S221C subtilisin mutant is designated SI. The subtilisin may be further mutated in order to make the relatively unstable apoenzyme easier to produce and purify. Versions of SI with three or four additional mutations, for example, M50F, Q206I, Y217K and N218S, may also be employed in the method of the present invention. Such further mutations cumulatively increase the free energy of unfolding by 3.0 kcal/mol and increase the thermal denaturation temperature of the apoenzyme by 11.5 'C (Pantoliano et al., Biochemistry 28:7205-7213 (1989)). The mutant containing the M50F, Q206I, Y217K, N218S and S221C mutations is designated Sll and the mutant containing the M50F, Y217K, N218S and S221C is designated S12.²

In order to produce a subtilisin BPN' protein lacking calcium binding activity, the present inventors elected to delete the binding loop in the calcium

Asite to engineer a novel calcium-free subtilisin protein. This loop comprises an interruption in the subtilisin BPN' α-helix involving amino acids 63-85 of SEQUENCE ID NO:l (McPhalen and James 1988). Residues 75-83 of the subtilisin BPN' protein form a loop which interrupts the last turn of the 14-residue alpha helix involving amino acids 63-85 [SEQUENCE ID NO : 1] .³ Four of the

The specific activities of Sll, S12 and S15 against the synthetic substrate, SAAPFna, are the same. (S.A. = 0.0024 U/mg at 25'C, pH 8.0). These measurements were performed on protein freshly purified on a mercury affinity column.

This set of nine residues was chosen for deletion, as opposed to 74-82 (those actually belonging to the loop) out of preference for Ala 74 rather than Gly 83 in the resulting continuous helix. Alanine has a higher statistical likelihood for occurrence in α-helix, due to glycine's broader

(continued...) carbonyl oxygen licands to the calcium are provided by a loop composed of amino acids 75-83 [SEQUENCE ID NO: 1]. The geometry of the ligands is that of a pentagonal bipyramid whose axis runs through the carbonyls of amino acids 75 and 79. On one side of the loop is the bidentate carboxylate (D41), while on the other side is the N-terminus of the protein and the side chain of Q2. The seven coordination distances ran-e from 2.3 to 2.6 A, the shortest being to the aspartyl carboxylate. Three hydro^gen bonds link the N-terminal seament to loop residues 78-82 in parallel-beta arrangement. A high affinity calcium binding site is a common feature of subtilisins-which make larce contributions to their high stability. By binding at specific sites in the subtilisin tertiary structure, tertiary structure, calcium contributes its binding free energy to the stability of the native state. In the present invention, site-directed mutagenesis was used to delete amino acids 75-83 of SEQUENCE ID NO: 1, which creates an uninterrupted helix and abolishes the calcium binding potential at site A (Figure 1A and IB). The present inventors believed that a stabilization strategy based around calcium binding would allow survival in the extracellular environment. Since the major industrial uses of subtilisins are in environments containing high concentrations of metal chelators, it was of areat practical significance for the present inventors to produce a stable subtilisin which is independent of calcium and, therefore, unaffected by the presence of metal chelating agents. Thus, stabilizing mutations in subtilisin can be classified into three groups: 1) stabilizing only in calcium, 2) stabilizing only in chelants; 3) stabilizing in both conditions (Table 1). From this partitioning it is evident that the mechanism of thermal inactivation differs depending on whether the calcium sites are occupied. To understand why this is so, one must understand how the kinetics of inactivation

³(... continued) range of accessible backbone conformations. are related to the kinetics of unfolding and how the kinetics of unfolding are related to the kinetics of calcium loss.

While the present inventors chose to eliminate calcium binding by the removal of these amino acids (i.e. amino acids at positions 75-83), it should be possible to eliminate calcium binding by other mutations, e.g. , substitution of one or more of the amino acids at positions 75-83 with alternative amino acids and by insertion, substitution and/or deletion of amino acids proximate to positions 75-83. This may also be accomplished by site-specific mutagenesis.

Additionally, because this loop is a common feature of subtilisins, it is expected that equivalent mutations for other subtilisins, in particular class I subtilases, e.g., by site-specific mutagenesis, will likewise eliminate calcium binding and provide for enzymatically active mutants.

In particular, the present inventors synthesized by site-specific mutagenesis three subtilisin BPN' DNA's which have been mutated to eliminate amino acids 75-83 involved in calcium binding and which further comprise additional substitution mutations. These mutated subtilisin BPN' DNA's, upon expression of the DNA, provide for subtilisin proteins having enhanced thermal stability and/or which are resistant to proteolysis.

The specific subtilisin BPN' mutants synthesized by the present inventors are designated in this application as S15, S39, S46, S47, S68, S73, S79, S86, S88 and pS149. The specific point mutations set forth in the present application identify the particular amino acids in the subtilisin BPN' amino acid sequence, as set forth in SEQUENCE ID NO: 1, that are mutated in accordance with the present invention. For example, the S15 mutant comprises a deletion of amino acids 7583 and additionally comprises the following substitution mutations: S221C, N218S, M50F and Y217K. The S39 mutant similarly comprises a deletion of amino acids 75-83 and additionally comprises the following substitution mutations: S221C, P5A, N218S, M50F and Y217K. The S46 mutant comprises a deletion of amino acids 75-83 and additionally, comprises the following substitution mutations: M50F, Y217K and N218S. The S47 mutant similarly comprises a deletion of amino acids 75-83 and additionally comprises the following substitution mutations: P5A, N218S, M50F and Y217K. The S68 mutant comprises a deletion of amino acids 75-83 and additionally comprises the following substitution mutations: P5S, N218S, M50F and Y217K. The S73 mutant comprises a deletion of amino acids 75-83 as well as the following substitution mutations: Q2K, M50F, A73L, Q206V, Y217K and N218S. The S79 mutant comprises a deletion of amino acids 75-83 and additional comprises the following substitution mutations: Q2K, M50F, A73L, Q206C, Y217K and

N218S, . The S86 mutant comprises a deletion of amino acids 75-83 as well as the following substitution mutations: Q2K, S3C, M50F, A73L, Q206C, Y217K and N218S. The S88 mutant comprises a deletion of amino acids 75-83 as well as the following substitution mutations: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E. Finally, the pS149 mutant comprises a deletion of amino acids 75-83 as well as the mutations present in the S88 mutant and the following substitution mutations: S9A, I131L, E156S, G166S, G169A, S188P, N212G, K217L and T254A. The specific activities of the proteolytically active S46, S47, S68, S73, S79, S86, S88 and pS149 subtilisins have been found to be similar' or enhanced in relation to the wild-type enzyme.

Applicants also consider as part of their invention Δ75-83 subtilisin mutants which contain one or more of the following mutations: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, Q271E, S9A, 1131L, E156S, G166S, G169A, S188P, N212G, K217L and T254A. Furthermore, applicants consider as part of their invention Δ75-83 subtilisin mutants which contain one or more substitutions selected from the group consisting of S9A, I131L, E156S, G166S, G169A, S188P, N212G, K217L and T254A, and optionally together with at least one or more substitutions selected from the group consisting of Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E.

The various Δ75-83 subtilisins which were synthesized by the inventors are shown in Tables 1 and 2, below. The particular points of mutation in the amino acid sequence of subtilisin BPN' amino acid sequence, as set forth in SEQUENCE ID NO:l, are identified. The synthesis of these mutants is described in more detail infra.

The plus signs show that a subtilisin contains a particular mutation. X-ray crystal structure of wild type, S12 and S15 have been determined to 1.8 A. *S1, Sll, S12, S15 and S39 are low activity mutants constructed to aid in the evaluaion of structure and conformational stability.

*pS149 contains all of the mutations present in S88, in addition to the mutations depicted in the table.

In order to understand the contribution of calcium binding to the stability of subtilisin, the thermodynamics and kinetics of calcium binding to the high affinity calcium A-site were measured by microcalorimetry and fluorescence spectroscopy. Calcium binding is an enthalpically driven process with an association constant (K_a) equal to 7 x 10⁶ M^"1. The kinetic barrier to calcium removal from the A-site (23 kcal/mol) is substantially larger than the standard free energy of binding (9.3 kcal/mol). The kinetics of calcium dissociation from subtilisin (e.g, in excess EDTA) are accordingly very slow. For example, the half-life (t_1/2) of calcium dissociation from subtilisin, i.e. , the time for half of the calcium to dissociate from subtilisin, is 1.3 hours at 25'C.

X-ray crystallography shows that except for the region of the deleted calcium-binding loop, the structure of the subtilisin mutants and the wild type protein are very similar. The N-terminus of the wild-type protein lies beside the site A loop and furnishes one calcium coordination ligand, the side chain oxygen of Q2. In Δ5-83 subtilisin, the loop is -one, leaving residues 1-4 disordered. These first four residues are disordered in the X-ray structure since all its interactions were with the calcium loop. N-terminal sequencing confirms the first four amino acids are pesent, confirming that processing occurs at the normal site. The helix is shown to be uninterrupted and shows normal helical geometry over its entire length. X-ray crystallography further shows that the strucmres of subtilisin with and without the deletion superimpose with a root mean square (r. m. s.) difference between 261 α-carbon positions of 0. 17 A and are remarkably similar considering the size of the deletion. Diffuse difference density and higher temperature factors, however, indicate some disorder in the newly exposed residues adjacent to the deletion.

While the elimination of calcium binding is advantageous since it produces proteins that are more stable in the presence of metal chelators, it is disadvantageous in at least one respect. Specifically, the elimination of the calcium loop without any other compensating mutations results in the destabilization of the native state relative to the partially folded states and, therefore, a loss of cooperativity in folding! The present inventors thus sought to further genetically engineer the subtilisin S15 BPN' protein lacking amino acids 75-83 in order to restore cooperativity to the folding reaction. In most well designed proteins all parts of the molecule are interdependent, making the unfolding reaction highly cooperative. Cooperativity of the folding reaction allows proteins to achieve sufficient stabilities of the native state for proper function since the overall stability of the native conformation is roughly the sum of all local interactions.

Therefore, while the Δ75-83 subtilisin is an example of an engineered subtilisin which is active and stable in the absence of calcium, the present inventors sought to improve this protein by further mutation. The design of a particular highly stable calciwn-free subtilisin relies on an iterative engineering cycle. The present inventors found that the requisite first step in the cycle was to greatly diminish the proteolytic activity of subtilisin. This is necessary because calcium contributes greatly to the conformational stability of subtilisin and the early versions of calcium-free subtilisin are susceptible to proteolysis. After reducing the susceptibility to proteolysis, the next step in the cycle was to eliminate sequences essential for calcium binding, i.e., the A-site. Although the S15 Δ75-83 subtilisin is much less stable than the wild type subtilisin in the presence of calcium, this mutant is more stable than wild type subtilisin in the presence of the metal chelator EDTA.

Accordingly, the third step was to improve the stability of the calciumfree subtilisin protein. To improve the stability of calcium-free subtilisin, the present inventors next tried to create a home for the disordered N-tenninal residues. In order to create a highly stable calcium-free subtilisin, the N-terminal part of the protein which is destabilized by the deletion of the calcium A-loop may be modified. For example, the N-terminus which is disordered may be deleted or extended. This, however, is problematic because the requirements for processing the propeptide from the mature protein are not known. It is known, however, that the processing site is not determined by amino acid sequence since mutants Y1A (the C-terminus of the propeptide), A1C and Q2R do not alter the site of cleavage. It is also known that the native structure of the N-terminus in subtilisin does not determine the cleavage site because the A75-83 variants are processed correctly. Since it is not yet known how to alter the processing site, interactions with the existing N-terminus may be optimized. Examination of the structure of S15 subtilisin revealed numerous possibilities for improving stability of the mutant enzyme. The regions of the structure most affected by the deletion are the N -terminal amino acids 1-8, the 36-45 ω-loop, the 70-74 α-helix the 84-89 helix turn and the 202-219 β-ribbon. As previously stated, the first four residues in Δ75-83 subtilisin are disordered in the x-ray structure since all its interactions had been with the calcium loop. N- terminal sequencing shows, however, that the first four amino acids are present confirming that processing occurs at the normal site. Other than the N-terminus, there are three other residues whose side chain conformations are distinctly different from wild type. Y6 swings out of a surface niche into a more solvent- exposed position, as an indirect effect of the destabilization of the N-terminus. D41, a former calcium ligand, and Y214 undergo a coordinated rearrangement, forming a new hydrogen bond. The B-factors of all three residues increase significantly due to the deletion of amino acids 75-83. In addition, S87 and A88 do not change conformation but exhibit significantly increased B-factors. P86 terminates the a-hela from which the calcium loop was deleted. In view of the above, other mutations at one or more of the above mentioned sites, or at the amino acids proximate thereto, will provide for subtilisin BPN' mutants comprising greater enzymatic activity or increased stability. There are several logical strategies for remodeling this region of the protein to produce subtilisin BPN' mutants comprising greater enzymatic activity or increased stability. Since the N-terininal four amino acids are disordered in the x-ray structure, one possible approach would be to delete them from the protein. The requirements for processing the propeptide from the mature protein are not understood, however. Inserting or deleting amino acids from the N- terminal region is, therefore, problematic. For this reason insertions and deletions in the N-teπninal region were avoided in favor of amino acid substitutions. Many of the original amino acids in the above described regions of subtilisin which interacted with the amino acids 75-83 loop can be assumed to no longer be optimal. It was, therefore, possible to increase the stability of the molecule by substituting, deleting or adding at least one amino acid at positions whose environment was changed by the 75-83 deletion.

The first attempt was to mutate the proline at position 5 to alanine to create more flexibility at position 5. This increased flexibility allows the N-terminus to try to find a unique position along the new surface of the protein, created by deletion of the calcium loop. Once the N-terminus assumes a unique location its local interactions may then be optimized.

The P5A mutation was made to try to create more flexibility for the N- terminus and allow it to find a unique position along the new surface of the protein that was created by deletion of the calcium loop. In the native structure, the first five amino acids are in an extended conformation and form β-pair hydrogen bonds with the calcium loop as well as the Q2 side chain interaction with the calcium. The proline at position 5, which is conserved among seven bacterial subtilisins which have a homologous calcium A-site, may help stabilize the extended conformation. The P5A mutation in Δ75-83 subtilisin should thus result in an increase in the cooperativity of the unfolding reaction. The X-ray structure 'of this variant has been determined to 1.8 A. In toto, the present inventors selected amino acids at ten different positions whose environment had changed substantially for substitution. A mutagenesis and screening procedure was developed in order to screen all possible substitutions at a particular site. The technique for generating and screening subtilisin variants involves in vitro mutagenesis of the cloned subtilisin gene, expression of the mutated genes in B. subtilis, and screening for enhanced stability.

For example, site-directed mutagenesis was performed on the S46 subtilisin gene using oligonucleotides which were degenerate at one codon. The degenerate codon contained all combinations of the sequence NNB, where N is any of the four nucleotides and B is T, C or G. The 48 codons represented in this population encode for all twenty amino acids but exclude the ochre and umber termination codons. The mutagenized genes were used to transform B. subtilis. Examples of particular mutations are shown in Table U as follows:

Table II - Site-directed mutagenesis

O

To have a 98 % chance of finding tryptophan, glutamine, glutamate or methionine in the mutant population, one must screen about 200 mutant clones. Each of those codons is represented by only one of the 48 codons contained in the population of sequences NNB. Codons for all other amino acids are represented by at least two codons in the population and would require screening of about 1 00 mutant clones to have a 98 % chance of being represented in the mutant population.

To identify the optimum amino acid at a position, mutants were screened for retention of enzymatic activity at high temperature. 100 tLI of media was dispensed in each of the 96 wells of a microliter dish. Each well was inoculated with a Bacillus transformant and incubated at 37' with shaking. After 18 hours of growth, 20 μX of culture was diluted into 80 μX of 100 mM Tris-HCI, pH 8.0 in a second microliter dish. This dish was then incubated for one hour at 65'C. The dish was allowed to cool to room temperature following the high temperature incubation and 100 μX of 1 mM SAAPF-pNA was added to each well. The wells which cleaved the pNA (turned yellow) quickest were deemed to contain the most heat resistant subtilisin mutant. Once preliminary identification of a stable mutant was made from the second microliter dish, the Bacillus clone in the corresponding well in the first microliter dish was grown up for further analysis. The screening procedure identified stabilizing mutations at seven of the ten positions which were examined. As noted, these amino acid positions were selected at positions of the protein whose environment has changed substantially by virtue of the calcium domain deletion. No mutations were identified at positions 4, 74 and 214 which by themselves significantly increased the half-life of the mutant relative to the parent subtilisin. However, at position 214 the effect of only hydrophobic amino acids was screened. No mutations were found at positions 5, 41 and 43 which resulted in measurable but modest increases in stability. Moreover, several mutations were found at positions at 2, 3, 73, and 206 which significantly increased the half-life of the mutant relative to the parent subtilisin. These stabilizing mutations are shown in Table III as follows:

Table III - Stabilizing Mutations

Region of protein Site Increase

N-terminus: Q2K 2.0-fold

63-85 α-helix: A73L 2.6-fold

202-220 β-ribbon Q206V 4.5-fold

N-tenninus - β-ribbon S3C-Q206C (disulfide) 14-fold

Stabilizing amino acid modifications at positions 2(K), 73 (L) and 206(V) were then combined to create subtilisin S73. The properties of S73 subtilisin as well as S46, S79 and S86 are summarized in Table TV.

Table JN

Mutant Mutations¹ Specific activity² Half-life Increasi (60 C)3

S46 - lOOU/mg 2.3 min

S73 Q2K 160U/mg 25 min 11-fold

A73L Q206V

S79 Q2K Ν.D.⁴ 18 min 8-fold

A73L Q206C

S86 Q2K, 85U/mg 80 min 35-fold S3C⁵ A73L Q206C⁵

1) All of subtilisins S46, S73, S79 and S86 contain the mutations M50F, Y217K and Ν218S and Q271E.

2) Specific activity is measured against succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p- nitroanilide(SAAPF-pNA) in lOmM Tris-HCI, pH 8.0 at 25'C.

3) Half-life is measured at 60'C in lOmM Tris-HCI, pH 8.0 5OmM NaCl and lOmM EDTA.

4) Not determined.

5) Disulfide bond was formed between the cysteines at positions 3 and 206. The formation of a disulfide bond was confirmed by measuring the radius of gyration of the denatured protein by gel electrophoresis.

In many cases, the choice of amino acid at a particular position will be

influenced by the amino acids at neighboring positions. Therefore, in order to find the best combinations of stabilizing amino acids, it will be necessary in some

cases to vary the amino acids at two or more-positions simultaneously. In

particular, this was effected at positions 3 and 206 with amino acids whose side chains can potentially interact. It was determined that the best combination of

modifications was cysteine modifications at positions 3 and 206. This

modification was denoted as S86. Because of the close proximity and suitable

geometry between the cysteines at these two positions a disulfide cross-link forms

spontaneously between these two residues.

The stability of the S86 subtilisin was studied in relation to S73. It was

found that the half-life of S86 is 80 minutes at 60'C in lOmM Tris-HCI, pH 8-0,

50mM NaCl and lOmM EDTA, a 3.2-fold enhancement relative to S73

subtilisin. By contrast, a 3-206 disulfide cross-link would not be able to form in

native subtilisins which contain the calcium A-site because the 75-83 binding loop

separates the N-terminal amino acids from the 202-219 B ribbon.

Therefore, the enhancement in stability which occurs in the subject S86 mutant lacking the 75-83 binding loop will likely not be observed with native subtilisins similarly cysteine modified at these positions. It is expected that similar enhancement in stability will be inherent to other

subtilisins of the I-Sl and I-S2 group if their calcium loops were deleted (see

Siezen et al, Protein Enizineering, 4, pp. 719-737 at Figure 7). This is a

reasonable expectation based on the fact that the primary calcium site in these different, subtilisins are formed from almost identical 9 residue loops comprised in

the identical position of helix C . X-ray structures of the I-Sl subtilisins BPN and Carlsberg, as well as the I-

S2 subtilisin (savinase), have been determined to high resolution. Comparison of

these structures demonstrates that all three have almost identical calcium A-sites.

The x-ray structure of the class I subtilase, thermitase from

Thermoactinomyces vulgaris, is also known. Though the overall homology of

BPN' to thermitase is much lower than the homology of BPN' to I-Sl and I-S2 subtilisins, thermitase has been shown to have an analogous calcium A-site. In

the case of thermitase, the loop is a ten residue interruption at the identical site in

helix C.

Thus, it is expected that the stabilizing mutations exemplified herein will

impart similar beneficial effects on stability for the calcium loop-deleted versions

of other class I subtilases.

The stability of S73, S76 and S86 subtilisins relative to S46 subtilisin was compared by measuring their resistance to thermal inactivation at 60 "C in lOmM

Tris-HCI, pH 8.0, 50mM NaCl and lOmM EDTA. Aliquots were removed at

intervals and the activity remaining in each aliquot was determined. Under these

conditions, the half-life of S46 subtilisin is 2.3 minutes and the half-life of S73 is

25 minutes (Table TV).

In order to identify other mutants having increased stability any

mutagenesis technique known by those skilled in the art may be used. One

example of such a technique for generating and screening subtilisin variants involves three steps: 1) in vitro mutagenesis of the cloned subtilisin gene;

2) expression of mutated genes in B. subtilis, and 3) screening for enhanced

stability. The key element in the random mutagenesis approach is being able to

screen large numbers of variants.

Although random mutagenesis may be employed, the mutagenesis

procedure described above allows for mutations to be directed to localized regions of the protein (e.g., the N-terminal region). As noted supra, the S46, S47, S68,

S73, S79 and S86 mutants (which comprise the active-site S221) were found to be

enzymatically active. It is expected that other substitutions may be identified

which provide for equivalent or even greater stability and activity.

The activities of examples of the calcium-free subtilisin mutants of the

present invention against the substrate sAAPF-pNA in Tris-HCI, pH 8.0 and 25°C

are given in Table V as follows:

Table V

Subtilisin Specific activity Half-life (55 °C)

BPN' 80 U/mg 2 min

S12 0.0025 U/mg N.D.¹ S15 0.0025 U/mg N.D.¹ S39 0.0025 U/mg N.D.¹ S46 125 U/mg 22 min S47 90 U/mg 4.7 min S68 ~ 100 U/mg 25 min

Half-lives were not determined for inactive subtilisins.

As shown above, the subtilisin mutants S46, S47, S68, S73, S79 and S86

have enhanced catalytic activity in comparison with subtilisin BPN'. Changes in

catalytic efficiency due to the deletion were not expected because of the fact that

the active site of subtilisin is spatially distant from the calcium A-site.

The stability of these mutant subtilisins was compared to native subtilisin

BPN' by measuring their resistance to thermal inactivation. Since the stability of the calcium-free subtilisin mutants should be unaffected by metal chelating agents,

the experiment was carried out in EDTA. Thermal inactivation in EDTA is a two

step process as shown in the following mechanism:

N(Ca) + EDTA N + Ca:EDTA => U = I

The rate of calcium dissociation with the rate of unfolding as a function of

temperature for an inactive variant of subtilisin BPN' was compared in Bryan et al (Biochem. 31:4937-4945 (1992)) . Repartitioning of calcium from site A into a

strong chelator occurs at a rate 5 hour ^" at 45 ^°C. The kinetic barrier to calcium

removal is 23 kcal/mol. Calcium is a integral part of the subtilisin structure and

its association or dissociation requires significant but transient disruption in

surrounding protein-protein interactions. This disruption in structure would

explain the high activation energy and slow kinetics of calcium binding and

dissociation. For example, breaking main-chain hydrogen bonds between the N- terminal region and the 75-83 loop region would allow the relatively buried

calcium a passageway into or out of the protein. Global unfolding in lOmM

EDTA at 45^°C is much slower than calcium dissociation, however, occurring at a

rate of 0.04 hour ^" , with an activation energy of ~60 kcal/mol. Thus the

predominant mechanism of inactivation in EDTA is calcium dissociation followed

by unfolding and loss of activity.

Because calcium binding reaches equilibrium quickly relative to the rate of

unfolding, mutations which stabilize in EDTA must stabilize apo-subtilisin.

Increasing the binding constant for one of the calcium sites would not help unless

the increase in binding affinity were enormous. Consider a typical experiment in

which ImM EDTA is added to lOO g/ml subtilisin (3.6 μM) bound to a

stoichiometric amount of calcium. The calcium will partition between subtilisin

and EDTA according to the equation:

[SCa]/[S_total] = K_s._Ca [S]/(l + K_s._Ca [S] + K_E._Ca [E]) where [SCa]/[S_total] is the fraction of subtilisin bound to calcium, [S] ~ total

subtilisin and [E] — total EDTA. Since the binding constant of subtilisin for

calcium at site A (K_s._Ca) = 7 xlO M^~ and the binding constant of EDTA for

8 1 calcium (K_E._Ca) = 2 xlO M^" , then less than 0.02% subtilisin would be bound

to calcium at equilibrium. Examples of mutations which stabilize apo-subtilisin

are M50F and the disulfides C22- C87 and C206-C216 (Pantoliano et al, Biochem.

28:7205-12X3 (1989)) . The irony is that a mutation which preferentially

stabilizes apo-subtilisin relative to the bound form, will weaken calcium binding and catalyze inactivation under conditions of excess calcium and high temperature

(see the mechanism below). This phenomenon is displayed in the M50F mutant,

which is more stable than wild type in lOmM EDTA but less stable in lOmM

CaCl₂.

The experiment to determine stability of the calcium-free subtilisin mutants

was carried out in lOmM Tris-HCI, pH 8.0, 50mM NaCl and lOmM EDTA (the

association constant of EDTA for calcium is 2 x 10^s M^"1). The proteins were

dissolved in this buffer and heated to 55 °C. Aliquots were removed at intervals

and the activity remaining in each aliquot was determined. The kinetics of inactivation are plotted in Figure 10. Under these conditions, the half-life of the subtilisin mutants was much improved over that of subtilisin BPN'. These results

indicate that subtilisins which have been mutated to eliminate calcium binding at

site A have full catalytic activity and improved stability in EDTA relative to subtilisin BPN'. A reasonable level of stability in S46 was achieved even without

additional mutations to compensate for lost interactions resulting from deleting

amino acids 75-83.

The inactivation of subtilisin in excess calcium is diagramed in the

following mechanism:

K_a (site B) K_a (site A)

N(2Ca) N(Ca) + Ca - N + 2Ca

tk_j_ Ik₂ Ik₃

U U U I > >k₃

I

In excess calcium (e.g. ≥ImM) and moderate temperature, calcium binding and

dissociation is in rapid equilibrium because calcium binding is much faster than

unfolding. The rate of inactivation is determined by the fraction of each native

species times its unfolding rate. Using the above mechanism, one can show

that calcium dependent stabilization of subtilisin is dominated by site A rather

than site B. The rate of inactivation of BPN' at 65 ^°C as a function of calcium

concentration fits the data to the following mechanism:

33 M^"1 2.5xl0⁵ M^"1

N(Ca₂) - N(Ca) + Ca ~ N + 2Ca

10.0035 s^"1 10.0085 s^'1 18.7 s^"1 u u u

I > 25 s^"1

I The mechanism predicts that K_a's of site A and site B are 2.5 x 10 M and

33 M^" at 65^°. The rate of inactivation of subtilisin with only site A occupied

(NCa) is about 1000-times slower than apo-subtilisin (N) and the rate of

inactivation with both sites occupied (NCa₂) is about 2.5-times slower than with

only site A occupied.

The second prediction has been borne out by measuring the calcium

dependent stability of a mutant which has site B but lacks site A (Strausberg et al, Bio/Tech. 13:669-673 (1995)). The calcium-binding loop is formed from a nine

amino acid bubble in the last turn of a 14-residue α-helix involving amino acids

63-85 (McPhalen & James, Biochem. 27:6582-6598 (1988)). Deleting amino

acids 75-83 creates an uninterrupted helix and abolishes the calcium binding

potential at site A (Almog et al, Proteins 57:21-32 (1998); Bryan et al, Biochem.

37:4937-4945 (1992)) . The x-ray structure has shown that except for the region

of the deleted calcium-binding loop, the structure of the mutant and wild type

protein are remarkably similar considering the size of the deletion. The structures of subtilisin with and without the deletion superimpose with an rms difference

between 261 Cα positions of 0.17 A. The N-terminus of the wild-type protein lies

beside the site A loop, furnishing one calcium coordination ligand, the side chain oxygen of Q2. In Δ75-83 subtilisin, the loop is gone, but the helix is

uninterrupted and shows normal helical geometry over its entire length. The rate

of inactivation of Δ75-83 subtilisin is only 2.4-times slower in lOmM CaCl₂,

50mM NaCl than in lOmM EDTA, 50mM NaCl.

Another prediction of this last mechanism is that any mutations which

stabilize only in the presence of calcium will increase the binding constant for calcium to one or both of the calcium sites. This can be either through effects on

the binding sites themselves, as proposed for mutations A116E, G131D, P172D,

S63D, N76D and S78D (Pantoliano et al, Biochem. 28:1205-12X3 (1989);

Pantoliano et al, Biochem. 27:8311-8317 (1988); Rollence et al, CRC Crit. Rev.

Biotech. 8:2X1-224 (1988)), or through indirect effects on conformational stability as seen for mutations S9A, 131L, S53T, L126I, , E 156S, G166S, G169A,

S188P and T254A. The indirect effect on calcium binding arises because apo-

subtilisin displays a loss of cooperativity in the unfolding reaction (Bryan et al,

Biochem. 57:4937-4945 (1992)). Thus many mutations which stabilize in the

presence of calcium do not stabilize in the presence of EDTA, because they do not

influence the rate determining step in the unfolding of apo-subtilisin. In fact, most

mutations in natural subtilisins identified to date stabilize only in the presence of

calcium. These mutants increase calcium binding affinity because they

preferentially stabilize NCa relative to N. The premise that the effects of this

class of mutations indirectly increase calcium affinity by increasing general stability was tested using S88, a stabilize version of _75-83 subtilisin (Strausberg

et al. 1995) . The mutations S9A, I31L, E156S, G166S, G169A, N212G, S188P,

K217L and T254A were introduced into the S88 version of Δ75-83 subtilisin (see

Table VI).

Because the unfolding of the S88 subtilisin is cooperative in EDTA, these

mutations now stabilize subtilisin S88, independent of calcium concntration, to

approximately the same extent that they stabilize subtilisin BPN' in 50mM Tris-

HCI, pH 8.0, 50mM NaCl, lOmM CaCl₂. Thus, the present inventors have provided convincing evidence that

subtilisin mutants may be obtained which remain active and yet do not bind

calcium. It is expected therefore that these mutants may be utilized in industrial

environments that comprise chelating agents. While this has only been specifically

shown with subtilisin BPN', equivalent mutations should work with other serine proteases as well, most particularly other I-Sl or I-S2 subtilisins given that these subtilisins possess substantial sequence similarity, especially in the calcium

binding site.

Such strategies, for example, may involve comparing the sequence of

subtilisin BPN' to other serine proteases in order to identify the amino acids which

are suspected to be necessary for calcium binding and then making suitable

modifications, e.g., by site-specific mutagenesis. Since many subtilisins are

related to subtilisin BPN' not only through their primary sequences and enzymological properties, but also by X-ray crystallographic data, it is expected

that other active subtilisin mutants which lack calcium binding may be produced by site specific mutagenesis. For example, structural evidence exists that the homologous enzyme subtilisin Carlsberg also comprises two calcium binding sites.

Similarly, the X-ray structure of thermitase is known and this subtilisin has an

analogous calcium A binding-site to that of subtilisin BPN' . For thermitase, the

calcium binding loop is a ten residue interruption at the identical site in helix C.

Accordingly, these enzymes should also be amenable to the mutations described herein which eliminate the calcium binding site and produce a stable, active

enzyme. Moreover, as discussed supra. Siezen et al, has demonstrated that the

primary calcium binding site in all subtilisins in groups I-Sl and I-S2 are formed

from almost identical nine residue loops in the identical position of helix C. Thus,

in view of the almost identical structures of the calcium A-sites, the methods

described herein should be applicable to most if not all of the subtilisins in groups

I-Sl and I-S2 set forth in Siezen et al.

Alternatively, if the amino acids which comprise the calcium binding sites

are already known for a particular subtilisin, the corresponding DNA will be

mutated by site specific mutagenesis to delete one or more of such amino acids, or

to provide substitution, deletion or addition mutations which eliminate calcium

binding.

The subject mutant subtilisins will generally be produced by recombinant

methods, in particular by expression of a subtilisin DNA which has been mutated such that upon expression it results in a subtilisin protein which is enzymatically active and which does not bind calcium.

Preferably, the subtilisin DNA's will be expressed in microbial host cells,

in particular Bacillus subtilis, because this bacteria natorally produces subtilisin, is

an efficient secretor of proteins, and is able to produce the protein in an active

conformation. However, the invention is not restricted to the expression of the

subtilisin mutant in Bacillus, but rather embraces expression in any host cell which provides for expression of the desired subtilisin mutants. Suitable host cells

for expression are well known in the art and include, e.g., bacterial host cells such

as Escherichia coli, Bacillus, Salmonella, Pseudomonas; yeast cells such as

Saccharomyces cerevisiae, Pichia pastoris , Kluveromyces , Candida,

Schizosaccharomyces; and mammalian host cells such as CHO cells. Bacterial

host cells, however, are the preferred host cells for expression.

Expression of the subtilisin DNA will be provided using available vectors

and regulatory sequences. The actual selection will depend in large part upon the

particular host cells which are utilized for expression. For example, if the

subtilisin mutant DNA is expressed in Bacillus, a Bacillus promoter will generally

be utilized as well as a Bacillus derived vector. The present inventors in

particular used the pUBHO-based expression vector and the native promoter from

the subtilisin BPN' gene to control expression on Bacillus subtilis.

It is further noted that once the amino acid sequence of a particular subtilisin mutant which does not bind calcium has been elucidated, it may also be possible to make the subtilisin mutant by protein synthesis, e.g., by Merrifield

synthesis. However, expression of the subtilisin mutants in microbial host cells

will generally be preferred since this will allow for the microbial host cell to

produce the subtilisin protein in a proper conformation for enzymatic activity.

However, since the present inventors further teach herein a method for obtaining in vitro refolding of the subtilisin mutant, it should be possible to convert

improperly folded subtilisin mutants into an active conformation.

In order to further illustrate the present invention and the advantages

thereof, the following specific examples are given, it being understood that the

same is intended only as illustrative and in nowise limitative.

EXAMPLES

Example 1

Cloning and Expression The subtilisin gene from Bacillus

amyloliquefaciens (subtilisin BPN') has been cloned, sequenced, and expressed at

high levels from its natural promoter sequences in Bacillus subtilis (Wells et al. ,

Nucleic Acids Res. 11:7911-7925 (1983); Vasantha et al., J. Bacteriol.

159:811819 (1984)). All mutant genes were recloned into a pUBHO-based

expression plasmid and used to transform B. subtilis. The B. subtilis strain used

as the host contains a chromosomal deletion of its subtilisin gene and therefore

produces no background wild type (wt) activity (Fahnestock et al., Appl. Environ.

Microbial. 53:379-384 (1987)). Oligonucleotide mutagenesis was carried out as

previously described. (Zoller et al., Methods Enzymol. 100:468-500 (1983); Bryan et al., Proc. Natl. Acad. Sci. 83:3743-3745 (1986b)). S221C was expressed in a 1.51 New Brunswick fermentor at a level of approximately 100 mg

of the correctly processed mature form per liter. The addition of wild type

subtilisin to promote production of the mature form of S221C subtilisin was not

required in our bacillus host strain as was the case for prior strains (Abrahmsen et al., Biochemistry 30:4151-4159 (1991)).

Protein Purification & Characterization. Wild type subtilisin and the

variant enzymes were purified and verified for homogeneity essentially as

described in Bryan et al., Proc. Natl. Acad. Sci. 83:3743-3745 (1986b); Pantoliano et al., Biochemistry 26:2077-2082 (1987); and Biochemistry 27:8311-

8317 (1988). In some cases the C221 mutant subtilisins were re-purified on a

sulfhydryl specific mercury affinity column (Affi-gel 501, Biorad). Assays of

peptidase activity were performed by monitoring the hydrolysis of succinyl-

(L)Ala-(L)-Ala-(L)-Pro-(L)-Phe-p-nitroanilide, hereinafter sAAPFna, as described

by DelMar et al., Anal Biochem. 99:316-320 (1979). The protein concentration,

[P], was determined using P^{0 1%} = 1.17 at 280 mn (Pantoliano et al, Biochemistry

28:7205-7213 (1989)). For variants which contain the Y217K change, the P^{0 1%} at

280 nm was calculated to be 1.15 (or 0.96 X wt), based on the loss of one Tyr

residue (Pantoliano et al. , Biochemistry 28:7205-7213 (1989)).

N-terminal Analysis The first five amino acids of subtilisin S15 were

determined by sequential Edman degradation and HPLC analysis. This revealed that 100% of the material had the amino acid sequence expected from the DNA

sequence of the gene and that processing of the pro-peptide was at the same

position in the sequence for the mutant as for the wild type enzyme.

Example 2

Structure of the calcium A site of SI 2 subtilisin Calcium at site A is

coordinated by five carbonyl oxygen ligands and one aspartic acid. Four of the

carbonyl oxygen ligands to the calcium are provided by a loop composed of amino

acids 75-83 (Figure 2). The geometry of the ligands is that of a pentagonal bipyramid whose axis runs through the carbonyls of 75 and 79. On one side of

the loop is the bidentate carboxylate (D41), while on the other side is the N-

terminus of the protein and the side chain of Q2. The seven coordination

distances range from 2.3 to 2.6 A, the shortest being to the aspartyl carboxylate.

Three hydrogen bonds link the N-terminal segment to loop residues 78-82 in

parallel-beta arrangement.

Preparation of apo-subtilisin Sll and S12 subtilisin contain an equal molar

amount of tightly bound calcium after purification. X-ray crystallography has

shown this calcium to be bound to the A site (Finzel et al., J. Cell. Biochem.

Suppl. 10A:272 (1986); Pantoliano et al., Biochemistry 27:8311-8317 (1988);

McPhalen et al., Biochemistry 27:6582-6598 (198.8)).

Complete removal of calcium from subtilisin is very slow, requiring 24

hours of dialysis against EDTA at 25 °C to remove all calcium from the protein

and then 48 more hours of dialysis in high salt (Brown et al., Biochemistry

16:3883-3896 (1977)) at 4°C to remove all EDTA from the protein. To prepare

the calcium-free form of subtilisins Sll and S12, 20mg of lyophilized protein was

dissolved in 5ml of lOmM EDTA, lOmM tris(hydroxymethyl)amino-methane hydrochloric acid (hereinafter Tris-HCI) at pH 7.5 and dialyzed against the same

buffer for 24 hours at 25°C. In order to remove EDTA, which binds to subtilisin

at low ionic strength, the protein was then dialyzed twice against 2 liters of 0.9M NaCl, lOmM Tris-HCI at pH 7.5 at 4°C for a total of 24 hours and then three times against 2 liters of 2.5mM Tris-HCI at pH 7.5 at 4°C for a total of 24 hours.

Chelex 100 was added to all buffers not containing EDTA. When versions of

C221 subtilisin not containing stabilizing amino acid substitutions were used, up to

50% of the protein-precipitated during this procedure. It is essential to use pure

native apoenzyme in titration experiments so that spurious heat produced by

precipitation upon the addition of calcium does not interfere with the measurement of the heat of binding.

To ensure that preparations of apo-subtilisin were not contaminated with

calcium or EDTA, samples were checked by titration with calcium in the presence

of Quin2 prior to performing titration calorimetry.

Titration Calorimetry Measurements The calorimetric titrations were

performed with a Microcal Omega titration calorimeter as described in detail by

Wiseman et al. , Analytical Biochemistry 179:131-137 (1989). The titration

calorimeter consists of a matched reference cell containing the buffer and a solution cell (1.374 mL) containing the protein solution. Microliter aliquots of the ligand solution are added to the solution cell through a rotating stirrer syringe

operated with a plunger driven by a stepping motor. After a stable baseline was

achieved at a given temperature, the automated injections were initiated and the

accompanying heat change per injection was determined by a thermocouple sensor

between the cells. During each injection, a sharp exothermic peak appeared which

returned to the baseline prior to the next injection occurring 4 minutes later. The area of each peak represents the amount of heat accompanying binding of the

added ligand to the protein. The total heat (Q) was then fit by a nonlinear least

squares minimization method (Wiseman et al., Analytical Biochemistry 179:131-

137 (1989)) to the total ligand concentration, [Cal_total, according to the equation:

dQ/d[Ca]_total = ΔH[l/2+(l-(l +r)/2-Xr?2)/Xr-2Xr(l-r) + l +r²)^{1 2}] (1)

wherein 1/r = [P ^xK, and X_r = [Ca]_total/[P]_total.

The binding of calcium to the Sll and S12 subtilisins was measured by titration calorimetry as it allows both the binding constant and the enthalpy of

binding to be determined (Wiseman et al., Analytical Biochemistry 179:131-137

(1989); Schwarz et al. , J. Biol. Chem. 266:24344-24350 (1991)).

The Sll and S12 subtilisin mutants were used in titration experiments

because production of the wild type apoenzyme is impossible due to its proteolytic

activity and low stability. Titrations of Sll and S12 were performed at protein

concentrations [P] = 30μM and 100/xM. Titration of the Sll apoenzyme with

calcium at 25 °C is shown in Figure 4. The data points correspond to the negative heat of calcium binding associated with each titration of calcium. The titration

calorimeter is sensitive to changes in K_a under conditions at which the product of

K_j x [P] is between 1 and 1000 (Wiseman et al., Analytical Biochemistry 179:131-

137 (1989)). Since the K_a for subtilisin is about lxlO⁷ M^"1, these protein

concentrations result in values of K_a x [P] = 300 and 1000. At lower protein concentrations the amount of heat produced per titration is difficult to measure

accurately.

The results of fitting the titrations of Sll and S 12 to a calculated curve are

summarized in Table 2. The parameters in the table include binding parameters

for stoichiometric ratio (n), binding constant (K_a) and binding enthalpy (ΔH).

These parameters were determined from deconvolution using nonlinear least squares minimization (Wiseman et al., Analytical Biochemistry 179:131-137

(1989)). Measurements for each experimental condition were performed in duplicate at 25 °C. The protein concentrations ranged from 30 to 100 μM while

the concentration of the calcium solutions were about 20 times the protein

concentrations. Each binding constant and enthalpy were based on several

titration runs at different concentrations. Titration runs were performed until the

titration peaks were close to the baseline.

TABLE 2: Titration Calorimetry of the Calcium A Site in Subtilisin Mutants Sll and S12.

Mutant [P] Parameters calculated from fit n K. ΔH

Sll lOOμM 0.98 ± 0.01 7.8 ± 0.2 x 10° -11.3 ± 0.1

Sll 33μM 0.9 + 0.3 6.8 ± 1.5 x 10⁶ -10.9 ± 0.2

S12 lOOμM 0.99 ± 0.01 6.4 ± 0.2 x 10⁶ -11.8 ± 0.5

The average values obtained are similar for Sll and S12: ΔH = — 11

kcal/mol; K_a = 7 x 10⁶ M^"1 and a stoichiometry of binding of 1 calcium site per

molecule. The weak binding site B does not bind calcium at concentrations below the millimolar range, and therefore does not interfere with measurement of binding to the binding site A. The standard free energy of binding at 25°C is 9.3

kcal/mol. The binding of calcium is therefore primarily enthalpically driven with

only a small net loss in entropy (ΔS_binding = -6.7 cal/°mol).

Example 3

In vitro refolding of SI 5 subtilisin. For refolding studies subtilisin was

maintained as a stock solution in 2.5 mM Tris-HCI at pH 7.5 and 50mM KCI at a concentration of approximately 100μM. The protein was denatured by diluting the stock solution into 5M guanidine hydrochloride (Gu-HCl) at pH 7.5 or in most

cases into 25 mM H₃PO₄ or HC1 at pH 1.8 - 2.0. The final concentration of

protein was 0.1 to 5 μM. S15 was completely denatured in less than 30 seconds by these conditions. S12 required approximately 60 minutes to become fully

denatured. Acid-denatured protein was then neutralized to pH 7.5 by the addition

of Tris-base (if denatored in HC1) or 5M NaOH (if denatored in H₃PO₄).

Refolding was initiated by the addition of KCI, NaCl or CaCl₂ to the desired

concentration. For example, KCI was added from a stock solution of 4M to a

final concentration of 0.1 to 1.5M with rapid stirring. In most cases renaturation was carried out at 25 °C. The rate of remtoration was determined

spectrophotometrically by uv absorption from the increase in extinction at

λ = 286, from the increase in intrinsic tyrosine and tryptophan fluorescence

(excitation λ = 282, emission λ - 347), or by circular dichroism from the increase

in negative ellipticity at λ = 222 nm.

Example 4

X-ray Crystallography. Large single crystal growth and X-ray diffraction

data collection were performed essentially as previously reported (Bryan et al. ,

Proteins: Struct. Funct. Genet. 1 :326-334 (1986a); Pantoliano et al. ,

Biochemistry 27:8311-8317 (1988); Pantoliano et al., Biochemistry 28:7205-7213

(1989)) except that it was not necessary to inactivate the S221C variants with

diisopropyl fluorophosphate (DFP) in order to obtain suitable crystals. The

starting model for S12 was made from the hyperstable subtilisin mutant 8350 (Protein Data Bank entry ISOl.pdb). The S12 structure was refined and then

modified to provide the starting model for S15.

Data sets with about 20,000 reflections between 8.0 A and 1.8 A resolution

were used to refine both models using restrained least-squares techniques

(Hendrickson et al., "Computing in Crystallography" in Diamond et al., eds.,

Bangalore: Indian Institute of Science 13.01-13.23 (1980)). Initial difference

maps for S15, phased by a version of S12 with the entire site A region omitted, clearly showed continuous density representing the uninterrupted helix, permitting an initial S15 model to be constructed and refinement begun. Each mutant was

refined from R approximately 0.30 to R approximately 0.18 in about eighty

cycles, interspersed with calculations of electron density maps and manual

adjustments using the graphics modeling program FRODO (Jones, J. Appl.

Crystallogr. 11 :268-272 (1978)).

Except for the region of the deleted calcium-binding loop, the structures of

S12 and S15 are very similar, with a root mean square (r.m.s) deviation of 0.18 A

between 262 α-carbons. The N-terminus of S 12 (as in the wild-type) lies beside the site A loop, furnishing one calcium coordination ligand, the side chain oxygen

of Q2. In S15 the loop is gone, leaving residues 1-4 disordered. In S12 (as in

wild type) the site A loop occurs as an interruption in the last turn of a 14-residue

alpha helix; in S15 this helix is uninterrupted and shows normal helical geometry over its entire length. Diffuse difference density and higher temperatore factors

indicate some disorder in the newly exposed residues adjacent to the deletion.

Example 5

Differential Scanning Calorimetry The stability properties of S12 and S15

were studied using DSC (differential scanning calorimetry). The Δ75-83 mutant (S15) is very similar in melting temperature to the apoenzyme of S12. The DSC

profiles of apo-S12 and S15 are shown in Figure 3. The temperature of maximum

heat capacity is 63.0°C for S15 and 63.5°C for apo-S12 at pH 9.63. The DSC

experiments were carried out at high pH to avoid aggregation during the

denatoration process. The amount of excess heat absorbed by a protein sample as

the temperatore increased through a transition from the folded to unfolded state at constant pressure, which provided a direct measurement of the ΔH of unfolding

(Privalov et al., Methods Enzymol. 131:4-51 (1986)). ΔH_cal of unfolding for apo-

S12 and S15 is about 140 kcal/mol. Above pH 10.0, the unfolding transition for

S 15 fit a two-state model reasonably well, consistent with equilibrium

thermodynamics as expressed in the van't Hoff equation (din K / dT = ΔH_vH / (RT²)) with ΔH_vH (the van't Hoff enthalpy or apparent enthalpy)

approximately equal to ΔH_cal (the calorimetric or true enthalpy). At pH 9.63,

however, the melting profile for both proteins was asymmetric indicating that the

unfolding is not a pure two-state process. Example 6

Measuring kinetics of calcium dissociation. The dissociation of calcium

from subtilisin is a slow process. To measure this rate the fluorescent calcium

chelator Quin 2 was used. Quin 2 binds calcium with a K_a of 1.8 x 10⁸ at pH 7.5

(Linse et al. , Biochemistry 26:6723-6735 (1987)). The fluorescence of Quin 2 at

495nm increases by approximately 6-fold when bound to calcium (Bryant, Biochem. J. 226:613-616 (1985)). Subtilisin Sll or S12 as isolated contains one

calcium ion per molecule. When mixed with an excess of Quin 2, the kinetics of

calcium release from the protein can be followed from the increase in fluorescence

at 495nm. The reaction is assumed to follow the pathway N(Ca) ^■*->^• N + Ca +

Quin 2 ^•<- Quin(Ca). The dissociation of calcium from subtilisin is very slow

relative to calcium binding by Quin 2, such that the change in fluorescence of

Quin 2 is equal to the rate of calcium dissociation from subtilisin. As can be seen in Figure 5a, the initial release of calcium from Sll follows simple first order

kinetics.

Temperature dependence of calcium dissociation The first order rate

constant (k) for calcium dissociation was measured from 20° to 45°C. The plot of

In k vs. 1/T°K is roughly linear. The calcium dissociation data was curve fit

using transition state theory according to the Erying equation:

ΔG÷ = -RT In K+ = -RT In kh/k_BT (2)

wherein k_B is the Boltzman constant, h is Planck's constant and k is the first order rate constant for folding. A graph of In hk/k_BT vs. 1/T is shown in Figure

5b.

The data was then curve fit according to the equation (Chen et al.,

Biochemistry 28:691-699 (1989)):

In K+ = A + B(To/T) + C In (To/T) (3)

wherein A = [ΔCp+ + ΔS++(To)]/R; B = A - ΔG+(T₀)/RTo; C = ΔCp÷/R.

The data obtained yields the following results: ΔG-J- = 22.7 kcal/mol; ΔCp'-f *=

-0.2 kcal/°mol; ΔS'÷ = -10 cal/°mol; and ΔH'Ψ = 19.7 kcal/mol at a reference

temperatore of 25 °C. A possible slight curvature of the plot would be due to a

change in heat capacity associated with formation of the transition state (ΔCp'-f- =

0.2 kcal/°mol). ΔCp for protein folding has been shown to be closely correlated

with a change in exposure of hydrophobic groups to water (Privalov et al. , Adv.

Protein Chem. 39: 191-234 (1988); Livingstone et al., Biochemistry 30:4237-4244

(1991)). In terms of heat capacity, the transition state therefore appears similar to the native protein. The values for ΔS'- and ΔH'*f obtained from Figure 5b indicate that the transition state is enthalpically less favorable than the calcium

bound form with only a small change in entropy.

Other embodiments of the invention will be apparent to those skilled in the

art from consideration of the specification and practice of the invention disclosed

herein. It is intended that the specification and examples be considered as exemplary only, with the true scope and spirit of the invention being indicated by

the following claims.

All references cited herein are incorporated in their entirety, as if

individually incorporated by reference.

SEQUENCE LISTING

(1) GENERAL INFORMATION:

(i) APPLICANT: BRYAN, Philip N

ALEXANDER, Patrick STRAUSBERG, Susan L

(ii) TITLE OF INVENTION: CALCIUM FREE SUBTILISIN MUTANTS

(iii) NUMBER OF SEQUENCES: 1

(iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Bums, Doane, Swecker a Mathis

(B) STREET: P.O. Box 1404

(C) CITY: Alexandria

(D) STATE: Virginia

(E) COUNTRY: United States

(F) ZIP: 22313-1404

(v) COMPUTER READABLE FORM:

(A) MEDIUM TYPE: Floppy disk

(B) COMPUTER: IBM PC compatible

(C) OPERATING SYSTEM: PC-DOS/MS-DOS

(D) SOFTWARE: Patentln Release #1.0, Version #1.25

( i) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER:

( B ) FILING DATE :

(G) CLASSIFICATION:

(viii) ATTORNEY/AGENT INFORMATION:

(A) NAME: Meuth, Donna M

(B) REGISTRATION NUMBER: 36,607

(C) REFERENCE/DOCKET NUMBER: 028755-021

( ix) TELECOMMUNICATION INFORMATION :

(A) TELEPHONE: (703) 836-6620

(B) TELEFAX: (703) 336-2021

(2) INFORMATION FOR SEQ ID Nθ:l:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 1868 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

(ix) FEATURE:

(A) NAME/KEY: CDS

(B) LOCATION: 450..1599

(ix) FEATURE:

(A) NAME/KEY: mat_peptide

(B) LOCATION: 772..1599

(ix) FEATURE:

(A) NAME/KEY: misc_feature

(B) LOCATION: 450

(D) OTHER INFORMATION: /note= "Amino Acid Val at position 450 is fMet." (xi) SEQUENCE DESCRIPTION: SEQ ID N0:1:

TTTTTCCGCA ATTATATCAT TGACAATATC AACATCAATG ATATTCATTA TCATTATTTT SO

TATAAAATGG TTTCACAGCT TTTCTCGGTC AAGAAAGCCA AAGACTGATT TCGCTTACGT 120

TTCCATCAGT CTTCTGTATT CAACAAAAGA TGACATTTAT CCTGTTTTTG GAACAACCCC 180

CAAAAATGGA AACAAACCGT TCGACCCAGG AAACAAGCGA GTGATTGCTC CTGTGTACAT 240

TTACTCATGT CCATCCATCG GTTTTTTCCA TTAAAATTTA AATATTTCGA GTTCCTACGA 300

AACGAAAGAG AGATGATATA CCTAAATAGA AATAAAACAA TCTGAAAAAA ATTGGGTCTA 360

CTAAAATATT ATTCCATACT ATACAATTAA TACACAGAAT AATCTGTCTA TTGGTTATTC 420

TGCAAATGAA AAAAAGGAGA GGATAAAGA GTG AGA GGC AAA AAA GTA TGG ATC 473

Val Arg Gly Lys Lys Val Trp lie -107 -105 -100

AGT TTG CTG TTT GCT TTA GCG TTA ATC TTT ACG ATG GCG TTC GGC AGC 521 Sβr Leu Leu Phe Ala Leu Ala Leu lie Phe Thr Met Ala Phe Gly Ser -95 -90 -85

ACA TCC TCT GCC CAG GCG GCA GGG AAA TCA AAC GGG GAA AAG AAA TAT 569 Thr Ser Ser Ala Gin Ala Ala Gly Lys Ser Asn Gly Glu Lys Lys Tyr -80 -75 -70

ATT GTC GGG TTT AAA CAG ACA ATG AGC ACG ATG AGC GCC GCT AAG AAG 617 He Val Gly Phe Lya Gin Thr Met Ser Thr Met Ser Ala Ala Lys Lys -65 -60 -55

AAA GAT GTC ATT TCT GAA AAA GGC GGG AAA GTG CAA AAG CAA TTC AAA 655 Lys Asp Val He Ser Glu Lys Gly Gly Lys Val Gin Lys Gin Phe Lys -50 -45 -40

TAT GTA GAC GCA GCT TCA GCT ACA TTA AAC GAA AAA GCT GTA AAA GAA 713 Tyr Val Asp Ala Ala Ser Ala Thr Leu Asn Glu Lys Ala Val Lys Glu -35 -30 -25 -20

TTG AAA AAA GAC CCG AGC GTC GCT TAC GTT GAA GAA GAT CAC GTA GCA 761 Leu Lys Lys Asp Pro Ser Val Ala Tyr Val Glu Glu Asp His Val Ala -15 -10 -5

CAT GCG TAC GCG CAG TCC GTG CCT TAC GGC GTA TCA CAA ATT AAA GCC 809 His Ala Tyr Ala Gin Ser Val Pro Tyr Gly Val Ser Gin He Lys Ala 1 5 10

CCT GCT CTG CAC TCT CAA GGC TAC ACT GGA TCA AAT GTT AAA GTA GCG 857 Pro Ala Leu His Ser Gin Gly Tyr Thr Gly Ser Asn Val Lys Val Ala 15 20 25

GTT ATC GAC AGC GGT ATC GAT TCT TCT CAT CCT GAT TTA AAG GTA GCA 905 Val He Asp Ser Gly He Asp Ser Ser His Pro Asp Leu Lys Val Ala 30 35 40 45

GGC GGA GCC AGC ATG GTT CCT TCT GAA ACA AAT CCT TTC CAA GAC AAC 953 Gly Gly Ala Ser Met Val Pro Ser Glu Thr Asn Pro Phe Gin Asp Asn 50 55 60

AAC TCT CAC GGA ACT CAC GTT GCC GGC ACA GTT GCG GCT CTT AAT AAC 1001 Asn Ser His Gly Thr His Val Ala Gly Thr Val Ala Ala Leu Asn Asn 65 70 75

TCA ATC GGT GTA TTA GGC GTT GCG CCA AGC GCA TCA CTT TAC GCT GTA 1049 Ser He Gly Val Leu Gly Val Ala Pro Ser Ala- Ser Leu Tyr Ala Val 80 85 90 AAA GTT CTC GGT GCT GAC GGT TCC GGC CAA TAC AGC TGG ATC ATT AAC 1097 Lys Val Leu Gly Ala Asp Gly Ser Gly Gin Tyr Ser Trp He He Asn 95 100 105

GGA ATC GAG TGG GCG ATC GCA AAC AAT ATG GAC GTT ATT AAC ATG AGC 1145 Gly He Glu Trp Ala He Ala Asn Asn Met Asp Val He Asn Met Ser 110 115 120 125

CTC GGC GGA CCT TCT GGT TCT GCT GCT TTA AAA GCG GCA GTT GAT AAA 1193 Leu Gly Gly Pro Ser Gly Ser Ala Ala Leu Lys Ala Ala Val Asp Lys 130 135 140

GCC GTT GCA TCC GGC GTC GTA GTC GTT GCG GCA GCC GGT AAC GAA GGC 1241 Ala Val Ala Ser Gly Val Val Val Val Ala Ala Ala Gly Asn Glu Gly 145 150 155

ACT TCC GGC AGC TCA AGC ACA GTG GGC TAC CCT GGT AAA TAC CCT TCT 1289 Thr Ser Gly Ser Ser Ser Thr Val Gly Tyr Pro Gly Lys Tyr Pro Ser 160 165 170

GTC ATT GCA GTA GGC GCT GTT GAC AGC AGC AAC CAA AGA GCA TCT TTC 1337 Val He Ala Val Gly Ala Val Asp Ser Ser Asn Gin Arg Ala Ser Phe 175 130 135

TCA AGC GTA GGA CCT GAG CTT GAT GTC ATG GCA CCT GGC GTA TCT ATC 1385 Ser Ser Val Gly Pro Glu Leu Asp Val Met Ala Pro Gly Val Ser He 190 195 200 205

CAA AGC ACG CTT CCT GGA AAC AAA TAC GGG GCG TAC AAC GGT ACG TCA 1433 Gin Ser Thr Leu Pro Gly Asn Lys Tyr Gly Ala Tyr Asn Gly Thr Ser 210 215 220

ATG GCA TCT CCG CAC GTT GCC GGA GCG GCT GCT TTG ATT CTT TCT AAG 1481 Met Ala Ser Pro His Val Ala Gly Ala Ala Ala Leu He Leu Ser Lys 225 230 235

CAC CCG AAC TGG ACA AAC ACT CAA GTC CGC AGC AGT TTA GAA AAC ACC 1529 His Pro Asn Trp Thr Asn Thr Gin Val Arg Ser Ser Leu Glu Asn Thr 240 245 250

ACT ACA AAA CTT GGT GAT TCT TTC TAC TAT GGA AAA GGG CTG ATC AAC 1577 Thr Thr Lys Leu Gly Asp Ser Phe Tyr Tyr Gly Lys Gly Leu He Asn 255 260 265

GTA CAG GCG GCA GCT CAG TAA A ACATAAAAAA* CCGGCCTTGG CCCCGCCGGT 1629 Val Gin Ala Ala Ala Gin * 270 275

TTTTTATTAT TTTTCTTCCT CCGCATGTTC AATCCGCTCC ATAATCGACG GATGGCTCCC 1689

TCTGAAAATT TTAACGAGAA ACGGCGGGTT GACCCGGCTC AGTCCCGTAA CGGCCAAGTC 1749

CTGAAACGTC TCAATCGCCG CTTCCCGGTT TCCGGTCAGC TCAATGCCGT AACGGTCGGC 1809

GGCGTTTTCC TGATACCGGG AGACGGCATT CGTAATCGGA TCAGAAGCAA AACTGAGCA 1868

Claims

WHAT IS CLAIMED IS:

1. An enzymatically active subtilisin protein which has been mutated

to eliminate the ability of said subtilisin protein to bind calcium at a high affinity

calcium binding site, wherein the mutated subtilisin protein comprises a deletion

of amino acids 75-83 and at least one or more substitutions selected from the

group consisting of S9A, 13 IL, E156S, G166S, G169A, S188P, N212G, K217L,

L126I, M222Q and T254A, and optionally together with at least one or more

substitotions selected from the group consisting of Q2K, S3C, P5S, K43N, M50F,

A73L, Q206C, Y217K, N218S, and Q271E.

2. The subtilisin mutant of claim 1, wherein the following

substitotions are made: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, N218S,

Q271E, S9A, 13 IL, E156S, G166S, G169A, S188P, N212G, Y217L and T254A.

3. The subtilisin mutant of claim 1, wherein the subtilisin is from a

Bacillus strain.

4. The subtilisin mutant of claim 3, wherein the subtilisin mutant is a

subtilisin 13PN' mutant, a subtilisin Carlsberg mutant, a subtilisin DY mutant, a

subtilisin amylosacchariticus mutant or a subtilisin mesenticopeptidase mutant or a

subtilisin Savinase mutant.

5. The subtilisin mutant of claim 4, wherein the subtilisin mutant is a

subtilisin BPN' mutant.

6. An enzymatically active subtilisin protein which has been mutated

to eliminate the ability of said subtilisin protein to bind calcium at a high affinity

calcium binding site, wherein the mutated subtilisin protein comprises a deletion of amino acids 75-83 and the following substitotions mutations: Q2K, S3C, P5S,

K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E.

7. The subtilisin mutant of claim 6, wherein the subtilisin is from a

Bacillus strain.

8. The subtilisin mutant of claim 7, wherein the subtilisin mutant is a

subtilisin 13PN' mutant, a subtilisin Carlsberg mutant, a subtilisin DY mutant, a subtilisin amylosacchariticus mutant or a subtilisin mesenticopeptidase mutant or a

subtilisin Savinase mutant.

9. The subtilisin mutant of claim 8, wherein the subtilisin mutant is a

subtilisin BPN' mutant.

10. A recombinant method which provides for the expression of an

enzymatically active subtilisin protein which has been mutated to eliminate the

ability of said subtilisin protein to bind calcium at a high affinity calcium binding

site, wherein the mutated subtilisin protein comprises a deletion of amino acids

75-83 and at least one or more substitutions selected from the group consisting of

S9A, 13 IL, E156S, G166S, G169A, S188P, N212G, K217L, L126I, M222Q and T254A, and optionally together with at least one or more substitutions selected

from the group consisting of Q2K, S3C, P5S, K43N, M50F, A73L, Q206C,

Y217K, N218S, and Q271E, said method comprising:

(a) transforming a recombinant host cell with an expression vector

which contains an enzymatically active subtilisin DNA which upon expression

provides for the expression of a subtilisin which does not bind calcium protein;

(b) culturing said host cell under conditions which provide for the expression of the enzymatically active subtilisin mutant; and

(c) recovering the expressed enzymatically active subtilisin mutant from said microbial host.

11. The recombinant method of claim 10, wherein the subtilisin mutant

lacks the calcium A binding site.

12. The recombinant method of claim 10, wherein the subtilisin mutant

is a subtilisin BPN' mutant.

13. The recombinant method of claim 12, wherein the subtilisin BPN'

DNA comprises one or more additional mutations which provide for enhanced

thermal stability or which provide for restoration of cooperativity of folding of the subtilisin protein.

14. A recombinant method which provides for the expression of an

enzymatically active subtilisin protein which has been mutated to eliminate the

ability of said subtilisin protein to bind calcium at a high affinity calcium binding

site, wherein the mutated subtilisin protein comprises a deletion of amino acids

75-83 and the following substitotions mutations: Q2K, S3C, P5S, K43N, M50F,

A73L, Q206C, Y217K, N218S, and Q271E, said method comprising:

(a) transforming a recombinant host cell with an expression vector

which contains an enzymatically active subtilisin DNA which upon expression

provides for the expression of a subtilisin which does not bind calcium protein;

(b) cultoring said host cell under conditions which provide for the

expression of the enzymatically active subtilisin mutant; and

(c) recovering the expressed enzymatically active subtilisin mutant

from said microbial host.

15. The recombinant method of claim 14, wherein the subtilisin mutant

lacks the calcium A binding site.

16. The recombinant method of claim 14, wherein the subtilisin mutant is a subtilisin BPN' mutant.

17. The recombinant method of claim 16, wherein the subtilisin BPN'

DNA comprises one or more additional mutations which provide for enhanced thermal stability or which provide for restoration of cooperativity of folding of the subtilisin protein.

18. A recombinant DNA which encodes for a subtilisin protein which

has been mutated to eliminate the ability of said subtilisin protein to bind calcium

at a high affinity calcium binding site, wherein the mutated subtilisin protein

comprises a deletion of amino acids 75-83 and at least one or niore substitutions

selected from the group consisting of S9A, I31L, E156S, G166S, G169A, S188P,

N212G, K217L, L126I, M222Q and T254A, and optionally together with at least one or more substitotions selected from the group consisting of Q2K, S3C, P5S,

K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E, and which mutated

subtilisin protein retains enzymatic activity and stability.

19. The recombinant DNA of claim 18, wherein the subtilisin DNA is a

subtilisin BPN' coding sequence.

20. A recombinant DNA which encodes for a subtilisin protein which

has been mutated to eliminate the ability of said subtilisin protein to bind calcium

at a high affinity calcium binding site, wherein the mutated subtilisin protein

comprises a deletion of amino acids 75-83 and the following substitutions

mutations: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E, and which mutated subtilisin protein retains enzymatic activity and

stability.

21. The recombinant DNA of claim 20, wherein the subtilisin DNA is a

subtilisin BPN' coding sequence.