AU2013201097B2 - Proteoglycan degrading mutants for treatment of cns - Google Patents

Abstract

The present disclosure relates to the preparation and deletion mutants of chondroitinase proteins and their use in methods for promoting the diffusion of therapeutic composition into tissues and their use for neurological functional recovery after central nervous system ('CNS') injury or disease. See Fig 7. WO 2004/110360 PCT/US2004/015662 IdD 2b0 3b0 60 6 doo bOo 800 m 9 WT-ABCI - 1 1 . 1 - '11, - " 1 NA2O(.p oplpl--lw -11 (A45-N1 023) NA60 [7- (F85-N1023) NA60 CA80 (F85-A942)

Description

Regulation 3.2 AUSTRALIA Patents Act 1990 COMPLETE SPECIFICATION DIVISIONAL APPLICATION APPLICANT: ACORDA THERAPEUTICS, INC. Invention Title: PROTEOGLYCAN DEGRADING MUTANTS FOR TREATMENT OF CNS The following statement is a full description of this invention, including the best method of performing it known to me: WO 2004/110360 PCT/US2004/015662 PROTEOGLYCAN DEGRADING MUTANTS FOR TREATMENT OF CNS CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit and priority of U.S. Provisional Application Serial No. 60/471,240, Attorney Docket No. 127304.01300, filed May 16, 2003; U.S. Provisional Application Serial No. 60/471,239, Attorney Docket No. 127304.01200, filed May 16, 2003; U.S. Provisional Application Serial No. 60/471,300, Attorney Docket No. 127304.01400, filed May 16, 2003; U.S. Provisional Application Serial No. 60/474,372 Attorney Docket No.127304.01700, filed May 16, 2003; and U.S. Pat. Application entitled FUSION PROTEINS FOR TREATMENT OF CNS, filed cocurrently herewith on May 17, 2004, U.S. Patent Application Serial No. [not yet assigned] Attorney Docket No. 127304.01201 the contents of each of these references incorporated herein by reference in their entirety. BACKGROUND AND SUMMARY (0002] Chondroitinases are enzymes of bacterial origin that act on chondroitin sulfate, a component of the proteoglycans that are components of the extracellular matrix of a wide variety of tissues such as the central nervous system and for example they can mediate the attachment between the retina and the vitreous body of the human eye. Examples of chondroitinase enzymes are chondroitinase ABC I, SEQ ID NO: 37, which is produced by the bacterium Proteus vulgaris (P. vulgaris), and chondroitinase AC; SEQ ID NO: 5, which is produced by Flavobacterium heparinum. Chondroitinases ABC I SEQ ID NO: 37, and chondroitinase AC SEQ ID NO: 5, function by degrading polysaccharide side chains in protein-polysaccharide complexes, without degrading the protein core.

WO 2004/110360 PCT/US2004/015662 2 [0003] Yarnagata et al. (J. Biol. Chem. 243:1523-1535, 1968) describe the purification of the chondroitinases like ABC I SEQ ID NO: 37 from extracts of P. vulgaris. This enzyme selectively degrades the glycosaminoglycans chondroitin-4-sulfate, dermatan sulfate, and chondroitin-6-sulfate (also referred to respectively as chondroitin sulfates A, B, and C which are side chains of proteoglycans) at pH 8 at higher rates than it degrades chondroitin or hyaluronic acid. The products of the degradation are high molecular weight unsaturated oligosaccharides and an unsaturated disaccharide. However, chondroitinase ABC I, SEQ ID NO: 37, does not act on keratosulfate, heparin or heparitin sulfate. [0004] Uses of chondroitinases include rapid, specific and non-surgical disruption of the attachment of the vitreous body to the neural retina of the eye, thereby facilitating removal of the vitreous body. [0005] P. vulgaris chondroitinase, for example ABC I SEQ ID NO: 37 migrates with an apparent molecular mass of about 110 kDa when resolved by SDS-PAGE. The appearance of a doublet in SDS-PAGE resolution of chondroitinase ABC has been reported (Sato et al., Agric. Biol. Chem. 50:4,1057-1059, 1986). However, this doublet represents intact chondroitinase ABC and a 90 kDa degradation product. Commercial chondroitinase ABC protein preparations contain variable amounts of this 90 kDa degradation product and an additional 18 kDa degradation product also derived from chondroitinase ABC I, SEQ ID NO: 37. [0006] Chondroitinase ABC II, SEQ ID NO: 27, has also been isolated and purified from P. vulgaris, Chondroitinase ABC 11, SEQ ID NO: 27, is a polypeptide of 990 amino acids with an apparent molecular mass by SDS-PAGE of about 112 kDa. Its molecular mass as determined by electrospray and laser desorption mass spectrometry is about 111,772 daltons. Chondroitinase ABC II, SEQ ID NO: 27, has an isoelectric point of 8.4-8.45. Its enzymatic activity is distinct from, but complementary to, that of chondroitinase ABC I SEQ WO 2004/110360 PCT/US2004/015662 3 ID NO: 37. Chondroitinase ABC I, SEQ ID NO: 37, endolytically cleaves proteoglycans to produce end-product disaccharides, as well as at least two other products which are thought to be tetrasaccharides, Chondroitinase ABC II, SEQ ID NO: 27, digests at least one of these tetrasaccharide products from the chondroitinase ABC I (SEQ ID NO: 37) digestion of proteoglycan. [0007] After a injury in the adult mammalian central nervous system (CNS), the inability of axons to regenerate may lead to permanent paralysis. An injury-caused lesion will develop glial scarring, which contains extracellular matrix molecules including chondroitin sulfate proteoglycans (CSPGs). CSPGs inhibit nerve tissue growth in vitro, and nerve tissue regeneration fails at CSPGs rich regions in vivo. [0008] A number of molecules, and specified regions of them, have been implicated in the ability to support the sprouting of neurites from a neuronal cell, a process also referred to as neurite outgrowth. The term neurite refers to both axon and dendrite structures. This process of spouting neurites is essential in neural development and regeneration, especially after physical injury or disease has damaged neuronal cells. Neurites elongate profusely during development both in the central and peripheral nervous systems of all animal species. This phenomenon pertains to both axons and dendrites. However, neurite regrowth in the CNS decreases as the animal's age increases. 10009] Chondroitinase enzymes have shown efficacy in improving functional outcomes in several in vivo models of spinal cord injury. Recombinantly produced chondroitinases AC (SEQ ID NO: 5) and chondroitinase B (SEQ ID NO: 12) polypeptides have shown efficacy in vitro by overcoming the barrier of an inhibitory substrate border, such as aggrecan, resulting in neurite extension for rat cortical neurons. 100101 The inventors have discovered through a deletion analysis based on the available crystal structures, mutant polypeptides capable of degrading chondroitin sulfate WO 2004/110360 PCT/US2004/015662 4 proteoglycans (CSPGs). The cleavage activity of all these mutants have been screened in vitro by zymographic assay using aggrecan as a substrate. A truncated polypeptide of chondroitinase AC (nA50-cA275), (SEQ ID NO: 11), lacking 50 and 275 amino acids from the amino and carboxy termini respectively and having a molecular weight of 38 kDa compared to 75kDa of the full length protein, was found to be the minimal size that retained activity as tested by a zymographic assay. The deletion mutant of chondroitinase B (nA 120-c A120), (SEQ ID NO: 17), lacking 120 amino acids from each of the amino and carboxy termini and having a molecular weight of 26 kDa compared to 52kDa of the full length protein, was shown to retain activity as well in a zymographic assay. Reduction in the size and complexity of the molecule may facilitate diffusion to the site of action and potentially reduce immunogenicity for prolonged therapeutic use. These smaller chondroitinases could be potential therapeutics for spinal cord injury. [00111 The present disclosure relates to mutants of chondroitinase genes, polypeptides and proteins derived therefrom, and their use in methods for promoting neurological functional recovery after central nervous system ("CNS") injury or disease. The mutant genes, polypeptides and proteins derived from them preferably include deletion, substitution, or a combination of these from the structural units the mature gene or polypeptide; more preferably the mutant genes or polypeptides are deletion mutants of the mature gene or polypeptide. These mutant genes or polypeptides, preferably biologically active, may be used in various pharmaceutical compositions. [0012] Polypeptide mutants of chondroitinases, for example chondroitinase ABC Type I, SEQ ID NO: 1 or 37, Chondroitinase ABC Type II, SEQ ID NO: 27, Chondroitinase AC, SEQ ID NO: 5, and Chondroitinase B, SEQ ID NO: 12, are provided. Other mammalian enzymes mutants with chondroitinase-like activity may independently include such enzymes as hyaluronidase 1, SEQ ID NO: 30, hyaluronidase 2, SEQ ID NO: WO 2004/110360 PCT/US2004/015662 5 31, hyaluronidase 3, SEQ ID NO: 32, hyaluronidase 4, SEQ ID NO: 33, and optionally PH 20, SEQ ID NO: 34. These deletion or substitution mutant may be used alone or in combination with chondroitinases or their deletion or substitution mutants as therapeutic compositions and mixtures. Further provided is the use of these mutants, and preferably the chondroitinase deletion or substitution mutants to promote neurological functional recovery in mammals following injury to the CNS, including but not limited to contusion injury. 100131 One embodiment of the present invention are isolated nucleic acid molecules consisting of, and preferably comprising, a nucleotide sequence encoding the amino acid sequence of polypeptides that are deletion and or substitution mutants of proteoglycan degrading molecules. Independently, nucleic acid molecules of the present invention may encode for mutant proteoglycan degrading polypeptides of chondroitinase, for example chondroitinase ABC Type I, SEQ ID NO: 1 or 37, Chondroitinase ABC Type II, SEQ ID NO: 27, Chondroitinase AC, SEQ ID NO: 5, and Chondroitinase B, SEQ ID NO: 12, hyaluronidase 1, SEQ ID NO: 30, hyaluronidase 2, SEQ ID NO: 31, hyaluronidase 3, SEQ ID NO: 32, hyaluronidase 4, SEQ ID NO: 33, or optionally PH-20, SEQ ID NO: 34 and combinations of these. Preferably the nucleic acids encode for chondroitinase deletion and or substitution mutants, most preferably the nucleic acids encode for chondroitinase ABC type I or 11 polypeptides. The invention is also directed to nucleic acid molecules consisting of, and preferably comprising, a nucleotide sequence complementary to the above-described nucleic acid sequences. Also provided for are nucleic acid molecules at least 80%, preferably 85% or 90%, still more preferably 95%, 96%, 97%, 98%, or 99% identical to any of the above described nucleic acid molecules. Also provided for are nucleic acid molecules which hybridize under stringent conditions to any of the above-described nucleic acid molecules. The present invention also provides for recombinant vectors comprising these nucleic acid molecules, and host cells transformed with such vectors.

WO 2004/110360 PCT/US2004/015662 6 [0014] Also provided are isolated polypeptides consisting of, and preferably comprising, the amino acid sequence of deletion and or substitution mutants of proteoglycan degrading polypeptides. Independently, proteoglycan degrading polypeptides can include chondroitinases, for example ABC Type I, SEQ ID NO: 1 or 37, Chondroitinase ABC Type II, SEQ ID NO: 27, Chondroitinase AC, SEQ ID NO: 5, and Chondroitinase B, SEQ ID NO: 12, hyaluronidase 1, SEQ ID NO: 30, hyaluronidase 2, SEQ ID NO: 31, hyaluronidase 3, SEQ ID NO: 32, hyaluronidase 4, SEQ ID NO: 33, optionally PH-20, SEQ ID NO: 34. Preferably the polypeptides are deletion mutants of chondroitinases. Pharmaceutical compositions may be prepared from the mutant proteoglycan degrading molecules such as these chondroitinases and or hyaluronidases; the composition may include one or more of the deletion and substitution mutants from different proteoglycan degrading polypeptides. [0015] In one aspect of the invention, biologically active proteoglycan degrading polypeptide are provided having a deletion or substitution of at least one amino acid. The mutant proteoglycan degrading polypeptides include those having the minimal size yet retain a degree of activity as determined by the enzyme assays described in the specification. .Preferred deletion or substitution mutants of the proteoglycan degrading molecule are those which degrade chondroitin and have one or more amino acid deletions from the N-terminus, about 1 to at least aboutl20 amino acids and/or the C-terminus, about 1 to at least about 275 amino acids, more preferably the deletions are from a chondroitinase or a substituted chondroitinase, and even more preferably chondroitinase ABC I or 11 or a substituted chondriotinase ABC I or I. [00161 One aspect of this invention are deletion and or substitution mutants of proteoglycan degrading polypeptides, preferably deletion mutants of chondroitinase polypeptides, that promote neurite regeneration and or plasticity in the CNS and or promote or inhibit the diffusion of therapeutic molecules into tissues by degradation of proteoglycans.

WO 2004/110360 PCT/US2004/015662 7 [0017] The mutant proteoglycan degrading polypeptides, preferably deletion and or substitution mutants of chondroitinases, may promote neurite regeneration in the CNS and or promote or inhibit the diffusion of therapeutic molecules into tissues by degradation of proteoglycans and can be obtained through expression of suitably modified DNA sequences. Thus, the present invention also provides suitable expression vectors and host cells compatible with them, [00181 In yet other aspects, the invention comprises pharmaceutical compositions that include biologically active polypeptide of deletion and or substitution mutants of proteoglycan degrading molecules, and preferably deletion or substitution mutants of chondroitn degrading polypeptides as described above, in combination with a pharmaceutically acceptable carrier. [0019] The deletion mutants and or substitution mutants of the proteoglycan degrading polypeptides of the present invention may be used to promote the regeneration of neurites in nerve tissue. These mutants might also be useful in the treatment of other CNS disorders in which plasticity, regeneration, or both might be beneficial. For example CNS injuries and disorders may include but not limited to contusion injury, traumatic brain injury, stroke, multiple sclerosis, brachial plexus injury, amblioplia. Because of their proteoglycan degrading properties, they may be used to promote the delivery of theraprutic compositions and diagnostics to tissues and cells that are normally impermeable to them. Alternatively, they may be used to inhibit penetration of therapeutic compositions, diagnositics or cells to tissues that use part of the extracellular matrix to enter tissues. Because of their smaller size compared to the full length enzyme, the deletion and or substitution mutants are easier to make and easier to deliver to target cells and tissues. These and other even smaller deletion or substitution mutants of proteoglycan degrading molecules could be used as potential WO 2004/110360 PCT/US2004/015662 8 therapeutics with lesser immunogenicity and similar or higher tissue penetration ability for the treatment of CNS injury. [0020] The deletion mutants may offer significant advantages over the full length proteins in the therapeutic development process. The tissue penetration of the enzymes may be significantly effected by the protein size. The effect of protein size on tissue penetration is difficult to predict, but dependent on size and charge. The rate of penetration depends on tissue composition, charge interactions and hydration effects. Having active enzymes of widely ranging size may allow selection of an enzyme based on optimal tissue penetration properties, perhaps maximizing effective concentrations or limiting peripheral exposure to the enzyme. [00211 The immune response of a mammal to a bacterial protein may or may not limit the ability to use the protein or polypeptide as a therapeutic. The generation of antibodies to the protein can restrict repeated exposures, as well as potentially inactivate the protein therapeutic making it ineffective. The smaller mutant proteoglycan degrading enzymes, preferably mutant chondroitinase enzymes, may limit the antigenic sites, limit an immune response or at least simplify the process of engineering an enzyme with reduced immunogenicity. [00221 The release rate of proteins from matrices often used in sustained release formulations can be dependent upon size and cross-linking. The effective release rate of deletion mutants of proteoglycan degrading polypeptide from the matrix can be engineered through the manipulation of the size of the enzyme. Having a repertoire of chondroitinase enzymes of various size and charge will give an significant advantage for the development of a sustained release formulations.

WO 2004/110360 PCT/US2004/015662 9 A BRIEF DESCRIPTION OF THE FIGURES [00231 FIG. 1(A) shows Anti-His-tag Western Blot (top) and zymogram (bottom) demonstrating chondroitinase B deletion NA120 CAl20 mutant (SEQ ID NO: 17) expression activity; FIG. 1(B) shows Anti-His-tag Western Blot (top) and zymogram (bottom) demonstrating chondroitinase AC deletion NA50 CA275 mutant (SEQ ID NO: 11) expression activity; [0024] FIG. 2 shows illustrates the relative substrate degrading activity of various detetion mutant polypeptides of Chondroitinase AC (SEQ ID NO: 6-11) relative to the full length Chondroitinase AC SEQ ID NO: 5 ; [0025] FIG. 3(A)shows a schematic of deletion mutant polyp eptides of chondroitinase AC (SEQ ID NO: 6-11); FIG. 3(B) shows confirmation of chondroitinase AC deletion mutants by Western blotting; [0026] FIG. 4. shows confirmation of protein expression and catalytic activity of Chondroitinase AC deletion mutants (SEQ ID NO: 6-11)by (A) Western Blotting and (B) zymography; [00271 FIG. 5 shows a schematic of deletion mutant polypeptides (SEQ ID NO: 13 17) of chondroitinase B (SEQ ID NO: 12); [00281 FIG. 6 shows confirmation of protein expression and catalytic activity of Chondroitinase B and deletion mutants (SEQ ID NO: 12-17) by (A) Western Blotting and (B) zymography; [0029] FIG. 7 shows a schematic of Chondroitinase ABC I deletion mutant polypeptides (SEQ ID NO: 2-4) of Chondroitinase ABC I SEQ ID NO: 1; DETAILED DESCRIPTION {0030J Before the present compositions and methods are described, it is to be understood that this invention is not limited to the particular molecules, compositions, methodologies or protocols described, as these may vary. It is also to be understood that the terminology used in the description is for the purpose of describing the particular versions or embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. [00311 It must also be noted that as used herein and in the appended claims, the singular forms "a", "an", and "the" include plural references unless the context clearly dictates otherwise. Thus, for example, reference to a "cell" is a reference to one or more cells and equivalents thereof known to those skilled in the art, and so forth. Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are incorporated by reference. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. The reference to any prior art in this specification is not, and should not be taken as, an acknowledgement or any form of suggestion that the prior art forms part of the common general knowledge in Australia. [0032] "Optional" or "optionally" means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where the event occurs or material is present and instances where the event does not occur or where the material is not present. [0'33] One aspect of the present disclosure relates to a series of deletion and or substitution mutants of chonchoitinase genes that can be used to generate deletion mutant enzymes with substantially lower molecular weight, but modified, and preferably equivalent 10 WO 2004/110360 PCT/US2004/015662 11 or superior proteoglycan degrading catalytic activity compared to the wild type enzymes. The deletion and or substitution mutants can be generated by polymerase chain reaction. The resulting mutants are expressed and then enzymatic activity of the mutant polypeptide can be confirmed by using zymography. [00341 The mutants of the proteoglycan degrading molecules can be used to treat mammalian CNS injuries, typically caused by trauma or disease. In particular, a deletion mutant of a proteoglycan degrading polypeptide molecule like chondroitinase, for example ABC Type I, (SEQ ID NO: 1 or 37), Chondroitinase ABC Type 11, (SEQ ID NO: 27), Chondroitinase AC, (SEQ ID NO: 5), and Chondroitinase B, (SEQ ID NO: 12), or mammalian enzymes with chondroitinase-like activity such as hyaluronidase 1, (SEQ ID NO: 30), hyaluronidase 2, (SEQ ID NO: 31), hyaluronidase 3, (SEQ ID NO: 32), hyaluronidase 4, (SEQ ID NO: 33), and optionally PH-20, (SEQ ID NO: 34), or mixtures of any of these may be used to provide a therapeutic treatment for CNS injuries and disorders which may include but not limited to contusion injury, traumatic brain injury, stroke, multiple sclerosis, brachial plexus injury, amblioplia, spinal cord injuries. Spinal cord injuries includes disease and traumatic injuries, such as the crushing of neurons brought about by an auto accident, fall, contusion, or bullet wound, as well as other injuries. Practice of the present methods can confer clinical benefits to the treated mammal, providing clinically relevant improvements in at least one of the subject's motor coordination functions and sensory perception. Clinically relevant improvements can range from a detectable improvement to a complete restoration of an impaired or lost function of the CNS. [0035] Mutants of proteoglycan degrading molecules, for example the deletion mutants of Chondroitinase AC (SEQ ID NO: 5), may have their enzyme activity stabilized by the addition of excipients or by lyophilization. Stabilizers may include carbohydrates, amino acids, fatty acids, and surfactants and are known to those skilled in the art. Examples WO 2004/110360 PCT/US2004/015662 12 include carbohydrates such as sucrose, lactose, mannitol, and dextran, proteins such as albumin and protamine, amino acids such as arginine, glycine, and threonine, surfactants such as TWEEN@ and PLURONIC@, salts such as calcium chloride and sodium phosphate, and lipids such as fatty acids, phospholipids, and bile salts. The stabilizers may be added to the proteoglycan degrading polypeptide deletion mutants in a ratio of 1:10 to 4:1, carbohydrate to polypeptide, amino acids polypeptide, protein stabilizer to polypeptide, and salts to polypeptide 1:1000 to 1:20; surfactant to polypeptide; and 1:20 to 4:1, lipids to polypeptide. Other stabilizers include high concentrations of ammonium sulfate, sodium acetate or sodium sulfate, based on comparative studies with heparinase activity. The stabilizing agents, preferably the ammonium sulfate or other similar salt, are added to the enzyme in a ratio of 0.1 to 4.0 mg ammonium sulfate/rU enzyme. [0036] The proteoglycan degrading mutant polypeptides may be formulated as compositions and can be administered topically, locally or systemically to a subject or patient. Preferably the subject is a mammal and even more preferably a human in need of a proteoglycan degrading composition such as one of the chondroitinases. Topical or local administration is can be used for greater control of application. One or more proteoglycan degrading mutant polypeptides, singularly or in combination, can be mixed with an appropriate pharmaceutical carrier prior to administration. Examples of generally used pharmaceutical carriers and additives are conventional diluents, binders, lubricants, coloring agents, disintegrating agents, buffer agents, isotonizing agents, preservants, anesthetics and the like. Specifically pharmaceutical carriers that may be used are dextran, serum albumin, gelatin, creatinine, polyethylene glycol, non-ionic surfactants (e.g. polyoxyethylene sorbitan fatty acid esters, polyoxyethylene hardened castor oil, sucrose fatty acid esters, polyoxyethylene polyoxypropylene glycot) and similar compounds.

WO 2004/110360 PCT/US2004/015662 13 [0037] Compositions of the present invention having a proteoglycan degrading polypeptide or a nucleic acid for expressing it may also include theraptutic molecules, diagnostics, and agents for promoting neurite growth and regeneration. Examples of diagnostic molecules may include but are not limited to fluorescent probes, radioisotopes, dyes, or magnetic contrast agents. Compounds that facilitate plasticity, neurite growth, and regeneration can include but are not limited to molecules that over come neurite out growth inhibition, or promote nerve growth such as soluble NOGO antagonists like NgR 27 aii, neural cell adhesion molecules like L1, neurotrophic factors, growth factors, phosphodiesterase inhibitors, and inhibitors of MAG or MOG. Additionally, deletion mutants may be combined with other compounds that promote remyelination such as neuregulins (GGF2) and antibodies that promote remyelination. [0038] Plasticity of the nervous system refers to any type of functional reorganization. This reorganization occurs with development, learning and memory and brain repair. The structural changes that occur with plasticity may include synapse formation, synapse removal, neurite sprouting and may even include strengthening or weakening existing synapses. Regeneration is generally differentiated from plasticity by the long range growth of axons in disrupted tracts that is characteristic of regeneration. [00391 The biological activity of the proteoglycan degrading molecules of the present invention may be used to control the degradation rate of proteoglycans in a tissue, and for example be chosen to have a slower degradation activity for sensitive tissues and a higher degradation rate for degrading potions of tissue which are thicker. The activity may be contolled by one of more amino acid substitutions or deletions in the polypeptide or vectors used to express them; the activity may be controlled by the concentration or combination of proteoglycan degrading polypeptides in a composition. The proteoglycan degrading activity may be made to be greater or less than that of the full length polypeptide. For example, it can WO 2004/110360 PCT/US2004/015662 14 be made to be less than that of the full length Chondroitinase AC (SEQ ID NO: 5), and can be made to be less than half as active as the full length polypeptide as shown in FIG. 2. Also, as further illustrated in FIG. 2, the proteoglycan degrading activity can be made to be greater than the full length Chondroitinase AC (SEQ ID NO: 5), it can be made more active than the full length polypeptide by a factor of 1.5 or more; it can be more active than the full length polypeptide by a factor of 2.5 or more. [00401 Native or wild-type P. vulgaris bacterial strains typically can be used to produce chondroitinases ABC I, (SEQ ID NO: 1 or 37), and chondroitinase ABC II, (SEQ ID NO: 27), and mutants of these full length polypeptide under ordinary growth conditions. Wild-type strains of P. vulgaris can be induced to produce detectable levels of chondroitinase ABCI and its mutants by providing an inducing substrate, such as chondroitin sulfate, as the sole carbon source. [00411 Mutant nucleic acids can be used for expressing mutant proteoglycan degrading polypeptides. The expressed polypeptides or the mutant nucleic acids can be used to treat mammalian CNS injuries, typically caused by trauma or disease. In particular, a deletion mutant nucleic acid for expressing proteoglycan degrading polypeptide molecule like chondroitinase ABC Type I, may include but are not limited to cloned chondroitinase ABC I, (SEQ ID NO: 22 or 28), chondroitinase ABC II, (SEQ ID NO: 26), nucleic acids for expressing fusion proteins of deletion mutants TAT-chondroitinase ABC I NA60 (SEQ ID NO: 43) and mutants of these genes in . coili can be expressed using a heterologous expression system with an artificial inducer. Chondroitinase AC (SEQ ID NO: 22 or 28), and chondroitinase B (SEQ ID NO: 26), and their mutants may be cloned from F. heparinuin and expressed in E. coli. [00421 The full length proteoglycan degrading molecules like Chondroitinase AC (SEQ ID NO: 5), as well as the deletion and or substitution mutants of the proteoglycan WO 2004/110360 PCT/US2004/015662 15 degrading polypeptides may be cloned in a number of bacterial as well as mammalian expression vectors. Non-limiting of these vectors include pET15b, pET14b, pGEX 6P1, pDNA4HisMax, or pSECTag2b. The deletion mutants and substituted polypeptides of the present invention exhibit the ability to degrade proteoglycans such as chondroitin CS and DS, and have a smaller size and molecular weight than the mature enzyme polypeptides which is expected to facilitate their diffusion into cells, tissues and across membranes. Expression vectors can include the nucleic acid sequence that expresses a mutant proteoglycan degrading polypeptide operably linked to an expression control sequence. Operably linked can refer to a linkage between an expression control sequence and coding sequence, where the linkage permits the expression control sequence to control the expression of the coding sequence. [0043] The properties of the naturally occurring, substituted and or deletion mutants of the proteoglycan degrading molecules may be altered by introducing a variety of mutations in the protein. Such alterations are suitably introduced using the mutagenesis techniques, for example but not limited to PRC mutagenesis, and the mutated polypeptides molecules suitably synthesized using the expression vectors. [0044] Mutant proteoglycan degrading polypeptides of the present invention include deletions and or substitutions of amino acids from mature proteoglycan degrading polypeptides. Preferably the deletions or substitutions include any two consecutive or separated amino acids, N or C terminal amino acid deletions or substitutions, and internal amino acid deletions or substitutions in the polypeptide. The deletions and or substitutions can start with any amino acid in the molecule and it is possible to have two separated deletions in the molecule. The deletion or substitution results in mutant proteoglycan degrading polypeptide that are smaller than the mature enzyme and retain proteoglycan degrading ability. Mutant proteoglycan degrading polypeptides can be fused or linked to another polypeptide. Polypeptide is used to unambigously encompases amino acid sequences WO 2004/110360 PCT/US2004/015662 16 for mutants of any length which have proteoglycan degrading activity and improve plasticity including those minus the signal sequence that is initially part of polypeptide when it is translated and that is cleaved off by a host-translational modification. [0045] Mutant nucleic acids of the present invention include deletions and or substitutions of nucleotides from genes which express the mature proteoglycan degrading polypeptides. The deletion and substitution mutations at the DNA level are used to introduce amino acid substitutions and or deletions into the encoded protein. These nucleotide deletions and substitutions can be used to introduce deletions and or substitutions into important conforinational or active regions of the polypeptide, A nucleic acid fragment is a nucleic acid having fewer nucleotides than the nucleotide sequence encoding the entire amino acid sequence of a mature proteoglycan degrading polypeptide, yet which preferably encodes a mutant polypeptide which retains some biological activity of the full length protein, e.g., the expressed polypeptide fragment retains the ability to induce degradation of proteoglycans, promote diffusion of therapeutics into cells and tissue, or promote regeneration of neurites. Genes encoding either N or C terminal mutants of proteoglycan degrading polypeptide domains linked to other polypeptides can also be used in constructs for expression of fusion proteins linked to mutant proteoglycan degrading polypeptides. [0046] The deletion and or substitution mutant proteoglycan degrading polypeptides of the present invention may also include derivatives of these polypeptides which have been been chemically or enzymatically modified, but which retain their biological activity to degrade proteoglycans. The proteoglycan degrading activity of these mutants may be controlled depending upon the deletion and or substitution made to the polypeptide or the nucleic acid used to express the polypeptide. Variants, fragments, or analogs of the mature proteoglycan degrading polypeptides or nucleic acids and vectors used to express them include mutant p6lypeptides and nucleic acids having a sequence which differs from the WO 2004/110360 PCT/US2004/015662 17 mature polypeptide or nucleic acid sequence by one or more deletions, substitutions, or a combination of both such that the mutant proteoglycan degrading polypeptides retain their biological activity and can degrade proteoglycans, and preferably degrade chondroitin sulfate proteoglycans. [0047] Due to the degeneracy of the genetic code, one of ordinary skill in the art will recognize that a large number of the nucleic acid molecules having a sequence at at least 80%, preferably 85% or 90%, still more preferably 95%, 96%, 97%, 98%, or 99% identical to a nucleic acid sequence encoding for a mutant proteoglycan degrading molecule will encode a mutant polypeptide having proteoglycan degrading activity and preferably chondroitin degrading ability. It will be further recognized that, for such nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a mutant polypeptide having proteoglycan degrading activity. This is because amino acid substitutions that are either less likely or not likely to significantly effect polypeptide activity (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid) to degrade proteoglycans and preferably to degrade chondroitin. [0048] Variants included in the invention may contain individual substitutions, deletions or additions to the nucleic acid or polypeptide sequences. Such changes will alter, add or delete a single amino acid or a small percentage of amino acids in the encoded sequence. Variants are referred to as "conservatively modified variants" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. [0049] The discovery that the proteoglycan degrading activity of the deletion and substitution mutant polypeptides of the present invention can be controlled to be less, about the same, or greater than the full length proteoglycan degrading molecule has another potential advantage. A pharmaceutical composition containing the proteoglycan degrading molecules may be administered parenterally, intravenously or subcutaneously. The use of a WO 2004/110360 PCT/US2004/015662 18 hydrogel composed of biodegradable polymer enclosing the polypeptide and continuously releasing the polypeptide is limited by the amount of polypeptide that can be enclosed in the hydrogel. Using a deletion mutant of the polypeptide with higher specific activity implies that, on a molar basis, more of the active substance can be enclosed in the same volume, thereby increasing the time between successive administrations or possibly avoiding repeated administrations. [00501 Purification of the polypeptide obtained after expression is dependent on the host cell and the expression construct used. Generally, the purification of proteoglycan deletion or substitution mutants can be performed in the same way as the purification of native full length polypeptides including the use of histidine-tags. [0051] The deletion or substitution mutant proteoglycan degrading polypeptides and proteins are administered in an amount effective to degrade CSPGs. The polypeptides may be used to aid the diffusion of therapeutic and diagnostic compositions to tissues and and can be used to promote the recovery of neurological function and neurite outgrowth. Once the mutant proteoglycan degrading proteins or polypeptides in the compositions have been purified to the extent desired, they may be suspended or diluted in an appropriate physiological carrier or excipient for SCI treatment or for screening assays of compositions promoting neurite growth in vitro on suitable substrates like aggrecan. In models of SCI, effective intratheaal doses of chondroitinases in rats have been about 0.06 units on alternate days for 14 days. A dose for a 70 kilogram human may be about 17 Units. At about 100 Units / milligram, this would equal about 170 micrograms. Doses of up to 20 Units appear safe in mammalian subjects like rats. Compositions may include a proteoglycan degrading mutant polypeptide, preferably mutant chondroitinase polypeptides, and more preferably still deletion mutant chondroitinase polypeptides. These compositions may also include other proteoglycan degrading molecules and deletion and or substitution mutants of them, WO 2004/110360 PCT/US2004/015662 19 molecules which block the action of neurite growth inhibitors, molecules which promote neurite or axon adhesion, diagnostic, therapeutic, or the proteoglycan degrading molecule mutant as part of a fusion protein. The mixture or fusion protein may be added to a carrier or pharmaceutically acceptable excipient can be injected, generally at concentrations in the range of 1 ug to 500 mg/kg of subject. Administering the agent can be by bolus injection, intravenous delivery, continuous infusion, sustained release from implants, or sustained release pharmaceuticals. Administration by injection, can be intramuscularly, peritoneally, subcutaneously, intravenously, intrathecally. Oral administration may include tablets or capsules, preferably the oral dosage is a sustained release formulation for once or twice daily administration. Percutneous administration can be once per day, and is preferably less than once per day administration. Administration to the human patient or other mannalian subject may be continued until a measurable improvement in autonomic or motor function in the patient is achieved. [0052] The mutant proteoglycan degrading polypeptides or fusion polypeptides that include them may also be expressed or secreted by genetically modified cells. The expressed deletion or substitution proteoglycan degrading polypeptide or fusion polypeptides may be harvested and purified for a therapeutic compositon, or the genetically modified cells can be implanted, either free or in a capsule, at or near the site of CNS injury or a tissue into which the controlled diffusion of therapeutic or diagnostic molecule is desired. Mutant nucleic acids for expressing mutant proteoglycan degrading polypeptides are illustrated by non limiting examples of chondroitinase ABC I (SEQ ID NO: 22 and 28) which encode for substituted chondroitinase ABC I polypeptides and those without leader amino acid sequences; chondroitinase B nucleic acid mutant (SEQ ID NO: 21) which encodes for mutant polypeptide NA120 CA120 of chondroitinase B (SEQ ID NO: 21); and chondroitinase AC nucleic acid mutant (SEQ ID NO: 19) which encodes for mutant WO 2004/110360 PCT/US2004/015662 20 polypeptide NA50 CA275 of chondroitinase AC (SEQ ID NO: 11). A non-limiting example of a fusion nucleic acid includes a TAT-deletion mutant chondroitinase ABCI fusion DNA construct (SEQ ID NO: 41). Another example would be a nucleic acid for TAT chondroitinase ABCI-NA60 (SEQ ID NO: 43) for the expressed polypeptide (SEQ ID NO: 44). [00531 Once the mutant proteoglycan degrading polypeptide are administered to cells or a tissue with CSPGs, degradation of CSPGs removes the inhibitory molecules that block neurite outgrowth, and allow the regeneration of neurites into the affected area. The removal of CSPG also promotes plasticity in the CNS. For example, the full length polypeptides of chondroitinase AC (SEQ ID NO: 5), and chondroitinase B, (SEQ ID NO: 12), degrade CS and DS, respectively, resulting in unsaturated sulfated disaccharides. Chondroitinase AC (SEQ UD NO: 5), cleaves CS at 1, 4 glycosidic linkages between N acetylgalactosamine and glucuronic acid in the polysaccharide backbone of CS. Cleavage occurs through beta-elimination in a random endolytic action pattem. Chondroitinase B (SEQ ID NO: 12) cleaves the 1, 4 galactosamine iduronic acid linkage in the polysaccharide backbone of DS. The cleavage of both CS and DS occurs through a beta-elimination process which differentiates these enzymatic mechanisms from mammalian GAG degrading enzyme& Chondroitinase ABC I (SEQ ID NO: 1), chondroitinase ABC II (SEQ ID NO: 27), are exo and endo lyases that cleave both CS and DS. The removal of CS and DS from a glial scar permits the regeneration of neurite outgrowths into the injured area and promotes plasticity. For example, the proteoglycan degrading molecules illustrated in FIG. 2, Chondroitinase AC (SEQ ID NO: 5) and various mutant Chondroitinase AC (SEQ ID NO: 6-11) degrade a model proteoglycan substrate at by various amounts. Similar results are shown by in vitro zymograph for chondroitinase B (SEQ ID NO: 12) and illustrative mutants (SEQ ID NO: 13-17) in FIG. 6. It is reasonable to expect that since a proteoglycan WO 2004/110360 PCT/US2004/015662 21 degrading molecule like Chondroitinase ABC I (SEQ ID NO: 1) improves functional recovery in rats with contusive spinal cord injury and also facilitates the diffusion of model compounds into brain tissue, that mutant proteoglycan degrading polypeptides and compositions containing them can also improve functional recovery in mammalian subjects like rats with contusive spinal cord injury and may also facilitates the diffusion of model compounds into brain tissue. [0054] The regeneration of the nerve cells and restoration of plasticity in the affected CNS area allows the return of motor and sensory function. Clinically relevant improvement will range from a detectable improvement to a complete restoration of an impaired or lost nervous function, varying with the individual patients and injuries. The degree of functional recovery can be demonstrated by improved corticospinal tract conduction, improved tape removal, beam walling, grid walking and paw-placement following chondroitinase treatment of a dorsal column lesion. Motor skill improvement as well as autonomic function: bowel, bladder, sensory and sexual function may also be used as measures of function improvement and related to molecular structure and components in the compositions of the present invention. [0055] A series of polynucleotides that include coding for deletion or substition mutants of protedglycan degrading polypeptides may be generated by PCR using the full length cDNAs for the proteoglycans as templates and cloned into an expression vector such as pET15b at the NdeI and BamHI sites for expression in E. Coli. After induction of gene expression with isopropyl-p-D-thiogalactopyranoside (IPTG), the bacteria can lysed by sonication with the concomitant extraction of the mutant polypeptide with a surfactant such as Triton X-1 14/PBS. The majority of recombinant proteoglycan degrading polypeptide may be found in the cytosolic fraction of the bacterial cell lysate and chondroitinase purification protocols can be used to obtain the mutant proteoglycan degrading enzyme with high activity WO 2004/110360 PCT/US2004/015662 22 at high yields. This protocol may include purification by a column having anti-His antibody to selectively bind His-tagged mutant proteoglycan degrading polypeptides and may also includes cation-exchange chromatography as a capture step and gel filtration as a polishing step. After these steps, anion exchange membrane filtration, for example Intercept Q, Millipore, can be used for endotoxin and host DNA removal. Following filtration, the proteoglycan degrading mutant polypeptides can be dialyzed into volatile buffer, pH 8.0 and lyophilized to dryness. The final product is expected to be stable at -704C for long term storage. The p1 of the purified basic proteoglycan degrading mutant polypeptide may be determined by IEF-PAGE analysis of the samples from the crude cell lysate. [0056] A variety of analytical methods can be used to compare the enzymatic activity of the recombinant version the deletion or substitution mutants of proteoglycan degrading polypeptides with those of full length proteoglycan degrading molecules like chondroitinase ABC I (SEQ ID NO: 37) or a commercially available form of the enzyme. The methods may also be adapted to evaluate the activity of fusion proteins including a mutant proteoglycan degrading polypeptide portion. Specific activity measurements may be obtained using an accepted spectrophotometric assay that measures the change in absorbance due to the produdion of reaction products from the degradation of proteoglycans. Size exclusion chromatography can be used to compare the hydrodynamic properties of the mutant enzymes. [00571 A form of zymography can used to characterize the mature proteoglycan degrading enzyme and may be adapted for characterization of the mutants proteoglycan degrading polypeptides. Polyacrylamide gels can be polymerized in the presence of aggrecan, a substrate for proteoglycan degrading molecules like chondroitinase ABCI. The mutant proteoglycan degrading polypeptides, enzyme samples, may be resolved on the aggrecan-impregnated gels by electrophoresis in the presence of SDS. The gels can then be WO 2004/110360 PCT/US2004/015662 23 subjected to a renaturation step wherein the SDS can be extracted and the enzymes allowed to refold. The refolded enzyme regains activity then digests aggrecan within the gel and the resulting loss of carbohydrate in that region of the gel that can be visualized by a carbohydrate-specific stain. A similar loss of carbohydrate in the gel would be expected for equally active forms and concentration of the mutant proteoglycan degrading molecules. In the case of recombinant Chondroitinase ABCI, its activity can be visualized as a clear spot in the zymogran. The zymography results are consistent with the spectrophotometric analysis. [0058] HPLC methods may be used for detecting the four and six sulphated disaccharides (A4DS and A6DS, respectively) liberated as a result of mutant proteoglycan degrading polypeptide digestion of CSPG. The two disaccharides can be effectively resolved by anion exchange chromatography. The HPLC assay for the quantitation of A4DS and A6DS from chromatograms is expected to yield a linear relationship proportional to the amounts injected into the HPLC. Production of A4DS and A6DS from CSPG digestion is directly related to the amount of chondroitinase specific activity as determined by the spectrophotometric assay. This assay may be used as a sensitive and accurate method to independently quantitate A4DS and A6DS released by mutant proteoglycan degrading polypeptide digestion of a variety of substrates and may also be used to determine the activity of mutant proteoglycan degrading polypeptides and fusion proteins including them. [00591 Another functional assay that can be performed to characterize mutant proteoglycan polypeptide activity is where dorsal root ganglian (DRG) neurons are plated on aggrecan or aggrecan treated with a deletion or substitution mutant proteoglycan degrading polypeptide . It is expected that neurons plated on aggrecan will fail to adhere to the plate and extend axons. In contrast, neurons plated on aggrecan treated with a mutant proteoglycan degrading polypeptide in a composition or as part of a fusion polypeptide would be expected to adhere to the surface and extend axons. The extensive axon growth, which is observed for WO 2004/110360 PCT/US2004/015662 24 chondroitinase ABC I (SEQ ID NO:37) is believed to be due to the digestion of the carbohydrates on the aggrecan core protein which creates a more permissive substrate for axon growth. [0060] Various aspects of the invention may be understood with reference to the following non-limiting examples. EXAMPLE 1 [00611 This prophetic example illustrates the diffusion of molecules into cells and tissue using a deletion or substitution mutant of a proteoglycan degrading polypeptide in a composition. [0062] A brain from an adult Sprague Dawley rat may be removed from the skull and hemispheres may be soaked in buffer alone or containing about 33U/ml of a mutant proteoglycan degrading polypeptide such as (SEQ ID NO: 9) NA50 CA200 AC (1 74

-T

5 o) protein for 2 hours at 37 *C. Hemispheres can be rinsed and immediately placed in dye such as Eosin Y (Sigma) or a saturated solution of Congo Red (Sigma) in 70% ethanol. Slabs of tissue may be cut and images acquired on a scanner. The penetration of the dyes into the brain tissue may be used as an indication of the proteoglycan degrading activity of a mutant proteoglycan degrading molecule and expectant penetration or diffusion of therapeutic and diagnostic molecules into the same type of tissue. EXAMPLE 2 [0063] This prophetic example illustrates a Chondroitinase ABC I Assay Protocol which may be modified to measure the activity of a mutant proteoglycan degrading molecule, WO 2004/110360 PCT/US2004/015662 25 for example a Chondroitinase ABCI deletion mutant or a fusion proteins including a deletion and or substitution mutant of a proteoglycan degrading polypeptide. [0064] The production of reaction products from the catalytic activity of a proteoglycan degrading molecule or fusion protein can be detennined by a measurement of the absorbance of the proteoglycan degradation product at a wavelength of 232 m. A typical reaction mixture consisted of 120 pl of reaction mixture (40mM Tris, pH 8.0, 40mM NaAcetate, 0.002% casein) combined with a substrate (5 p1 of 50 mM chondroitin C (MW 521), chondroitin 6 S04, or dermatan sulfate) and 1.5 pl of chondroitinase ABCI (SEQ ID NO:1) or a mutant of chondroitinase like (SEQ ID NO:2). Reaction mixture aliquots of about 120 pl can be prepared at 30-37'C for 3 min or longer. The product formation is monitored as an increase in absorbance at 232 nm as a function of time at a wavelength of 232 nm using a spectrometer. The reaction may be stopped by addition of 0.1% SDS followed by boiling for 5 minutes. The observed activity may be converted to units (gmoles of product formed per minute) using the molar absorption coefficient for the C4-C5 double bond formed in the reaction (3800 cnf' min7'). [00651 Knowing the molar absorption coefficient for the reaction product, measuring the change in the absorbance of the reaction product at 232 nm reading over time upon addition of a known amount of the Chondroitinase ABCI (SEQ ID NO:1) or other other mutant proteoglycan degrading polypeptide to the 120 pl reaction mixture with 0002% casein and a chondroitin substrate added, the specific activity in umol/min/mg of the mutant proteoglycan degrading polypeptide can be determined. Seikagaku Chondroitinase ABC I has a specific activity under these assay conditions of about 450 pamole/min/mg. [0066J A proteoglycan degrading molecule like Chondroitinase ABC I (SEQ ID NO:37), digests axon growth inhibiting chondroitin present in CNS tissue and improves functional recovery in rats having contusion spinal cord injuries. It is reasonable to expect WO 2004/110360 PCT/US2004/015662 26 that mutants of proteoglycan degrading molecules, such as (SEQ ID NO: 11) NA50 CA275 AC (T74-T42) polypeptide that show proteoglycan degrading activity may also show some regeneration of nerves, stimulate plasticity and be useful for diffusion of agents into tissues. The mode of administration, the timing of administration and the dosage are carried out such that the functional recovery from impairment of the CNS is enhanced by the promotion of neurite outgrowth and plasticity. It is reasonable to expect that once the deletion or substitution mutants of proteoglycan degrading molecules such as (SEQ ID NO: 11) NA50 CA275 AC (T74-T426) protein are administered, the degradation of CSPGs can remove the inhibitory molecules in tissue that block drug diffusion, block neurite outgrowth, and promote the regeneration of neurites or other therapeutics into the affected area. The regeneration and plasticity of the nerve cells into the affected CNS area may allow the return of motor and sensory function. Clinically relevant improvements will range from a detectable improvement to a complete restoration of an impaired or lost nervous function, varying with the individual patients and injuries. EXAMPLE 3 [0067] This example shows that deletion mutants of chondroitinase are biologically active. [00681 Recombinantly produced chondroitinases AC and B have shown efficacy in vitro by overcoming the barrier of an inhibitory substrate border, such as aggrecan and result in neurite extension for rat cortical neurons. To facilitate effective transport of the above enzymes to the injury site, deletion mutants of these chondroitinases were prepared to determine the minimally-sized polypeptides capable of degrading CSPGs. The cleavage activity of all these mutants have been screened in vitro by zymographic assay using aggrecan as substrate. A truncated polypeptide of chondroitinase AC (nA50-cA275) (SEQ WO 2004/110360 PCT/US2004/015662 27 ID NO:11) lacking 50 and 275 amino acids from the amino and carboxy terinini respectively having a molecular weight of 38 kDa compared to 75kDa of the full length protein was found to be about the minimal size mutant chondroitinase AC that retains activity as tested by zymography assay FIG. 4(B). However, an even smaller mutant, the deletion mutant of chondroitinase B (nA 120-cA 120) (SEQ ID NO:17) lacking 120 amino acids from each of the amino and carboxy termini, having a molecular weight of 26 kDa compared to 52 kDa of the full length protein has also shown to retain activity as well in zymography assay FIG. 6(B). These and other even smaller deletion mutants could be used as potential therapeutics with lesser immunogenicity and similar or higher tissue penetration ability compared to the mature enzyme and may be used for treatment of spinal cord injury. [00691 A series of chondroitinase AC and B deletion mutants were generated by PCR using the full-length cDNAs for chondroitinases AC and B as templates and cloned in the pET15b expression vector at the NdeI and BamHI sites. Full length and deletion mutants were constructed with Histidine-tags for ease of detection and purification. Each of these cDNAs was induced by Isopropyl-J-D-Thiogalactopyranoside (IPTG,) and the expression was confirmed by Western blotting using anti-His antibody (Novagen). FIG. 3(A) show various non-limiting deletion mutants schematically, and FIG 3(B) shows confirmation of expression of these chondroitinase AC mutant polypeptides by anti-histidine tag Western blotting. Figures 5 and 6 show the same information for chondroitinase B deletions. Western blots demonstrate proteins of predicted size. Zymographic PAGE of deletion mutants show intense bands of substrate digestion (light) and negative carbohydrate staining. [0070] Zymography assay. SDS-polyacrylamide gels were poured with aggrecan (85 ptg/ml) polymerized into it. Crude extracts of deletion mutants of chondroitinases AC and B were run and renatured at 37 *C overnight. After separation the gel is incubated in 0.2% Cetylpyridinium for 90 minutes at room temperature. The digestion of the WO 2004/110360 PCT/US2004/015662 28 proteoglycans by the chondroitinases is visualized by staining the gel with 0.2% Toludene Blue in ethanol-H 2 0-acetic acid (50:49:1 v/v/v) for 30 minutes and destained with ethanol

H

2 0-acetlc acid (50:49:1 v/v/v). Following destaining the gel is incubated overnight in a 50 .g/ml solution of Stains-all in 50% ethanol in the dark and destained with H20. Appearance of clear bands on the gel shows the digestion of carboyhydrates by the chondroitinases of the CSPG leaving the core protein which remains unstained (FIG 4.and FIG. 6). EXAMPLE 4 [0071] This example describes the linking of a His tag to a mutant proteoglycan degrading polypeptide. [0072] Deletion mutants of the chondroitinase ABC I enzyme where the mutant is missing a certain number of amino acids from the N-terminal and maintains proteoglycan degrading activity can be generated (SEQ ID NO:2-4). These N-terminal deletion maintain a histidine-tag that is attached to the N-terminus; however similarly tagged full length chondroitinase ABC I (SEQ ID NO:1) did not maintain the histidine-tag after experession. (0073] Catalytically active deletion mutants of chondroitinase ABC I can be prepared for example but not limited to deleting 20, and 60 amino acids respectively from the N-terminus of the mature ABC I protein as shown in FIG. 7. A mutant polypeptide with both N and C terminal deletions such as chondroitinase ABC I-NA60-CA80 (SEQ ID NO:4) can also be made. 10074] These chondroitinase deletion mutants and mutants of other proteoglycan degrading molecules may used for construction of N-terminal fusion chimeric protein. Assay tests with these fusion polypeptides for chondroitin degradation and may be used to determine the efficacy of mature ABCI versus various deletion mutant in compositions and fusion proteins with respect to the substrate specificity, substrate binding and tissue WO 2004/110360 PCT/US2004/015662 29 penetration. Functional assay that can be performed to characterize the activity of mutant proteoglycan polypeptide or fusion polypeptides including them. In this functional assay, dorsal root ganglian (DRG) neurons can be plated on aggrecan or aggrecan treated with a mutant proteoglycan degrading polypeptide or a fusion polypeptide including the mutant . It is expected that neurons plated on aggrecan will failed to adhere to the plate and extend axons. In contrast, neurons plated on aggrecan treated with a mutant proteoglycan degrading polypeptide or a fusion polypeptide including the mutant in a composition or as part of a fusion polypeptide would be expected to adhere to the surface and extend axons. The extensive axon growth, which is observed for a chondroitinase like chondroitinase ABC I (SEQ ID NO: I or 37) treated aggrecan substrate is believed to be due to the digestion of the carbohydrates on the aggrecan core protein which creates a more permissive substrate for axon growth. EXAMPLE 5 [00751 This phrophetic example describes a mutant of chondroitinase ABC I that has native protein structure, but lacks proteoglycan degrading catalytic activity. [00761 This mutant may be prepared as a null or a negative control for bioassays and SCI studies. Based on the crystal structure of chondroitinase ABC I a site-specific mutant designated H501a and Y508a (SEQ ID NO: 36) to knock out catalytic activity in the putative active site can be prepared. Such mutants can be tested for inactivation of catalytic activity and SEC to compare to the wild-type enzyme. The null activity mutant can also be used to provide a negative control for the various proteoglycan degrading fusion proteins for use in bioassays and ultimately in SCI animal studies.

WO 2004/110360 PCT/US2004/015662 30 EXAMPLE 6 [0077] This example illustrates examples of mutant proteoglycan degrading polypeptides that include both substitution and deletions from polypeptides of the present invention. [0078] The chondroitinase ABC I sequence (SEQ ID NO: 37) is a published sequence for a mature chondroitinase ABC I peptide and includes the leader sequence. Chondroitinase ABC I sequence (SEQ ID NO: 37) is similar to (SEQ ID NO: 1 or 29), however (SEQ ID NO: 1) does not have the first 25 amino acids of (SEQ ID NO: 37), and amino acids at positions 154 and 195 of (SEQ ID NO: 37) differ from those (substitutions) found in similar positions when (SEQ ID NO: 1) and (SEQ ID NO: 37) are aligned. [0079] (SEQ ID NO: 38-40) illustrate deletions from either the N or C terminal of the (SEQ ID NO: 37) polypeptide and substitutions relative to (SEQ ID NO: 1). These mutant polypeptides are NA20 (SEQ ID NO: 38), NA60 (SEQ ID NO: 39) and NA60 CA80 (SEQ ID NO: 40). EXAMPLE 7 [0080] This example illustrates non-limiting illustrations of mutant polypeptides of the present invention fused with a membrane transduction polypeptide such as but not limited to a polypeptide portion of a HIV TAT protein. Full sequence listings for the mutants fusion polypeptides are provided in the Sequence listing included in the specification. [0081] A nucleotide sequence for TAT-chondroitinase ABCI-nA20 (SEQ ID NO. 41), a portion of which is illustrated below, shows the TAT sequence nucleotides highlighted by underlining linked to chondroitinase nucleotides. 1 ggtc gtaaaaagcg tcgtcaacgt cgtcgtcctc ctcaatgcgc acaaaataac 61 ccattagcag acttetcatc agataaaaac tcaatactaa cgttatctga taaacgtagc WO 2004/110360 PCT/US2004/015662 31 [00821 The underlined nucleotides in this portion of the nucleic acid sequence denote a TAT sequence attached to the 5' of chondroitinase ABC I-NA20 nucleic acid (SEQ ID NO. 47). [0083] An amino acid sequence for TAT-chondroitinase ABCI-nA20 (SEQ ID NO. 42), a portion of which is shown below, illustrates the TAT sequence amino acids highlighted by underlining at the N-terminus of chondroitinase ABCI-NA20 (SEQ ID NO. 2). rkkrrrmpgcaqnnpladfssdnsiltlsdlasimgnqslwkwkggssftlkl-divptdkeaskawgrsstpvfsfwly nekpidgyltidfgeklistseaqagfkvkldftgwrtvgvsnndlenremtlnatntssdgtqdsigrsgakvdsirfkapsnvsq geiy [00841 A nucleotide sequence for TAT-ABCI-NA60 (SEQ ID NO. 43), a portion of which is illustrated below, shows the N-terminal TAT (SEQ ID NO. 49) nucleotides highlighted by underlining. gtcataaaaagtctcaacgtgtcatctctaatgetttactttacataaaaaactgattgtcccacegataaagaagcatcta aagcatggggacgctcatccacccccgttttctcattttggctttacaatgaaaaaccgattgatggttatcttactatgatttcgg...... [0085] Amino acid sequence for TAT-ABCI-nA60 (SEQ ID NO. 44) a portion of which is shown below, illustrates the TAT sequence (SEQ ID NO. 50) highlighted by underlining at the N-terminus of chondroitinase ABC I -NA60 (SEQ ID NO. 3). rkkrq ppfthklivptdkeaskawgrsspvfsfwlynekpidgyltidfgeklistseaqagfkvkldftgwrtvgvsl nndlenremtlnatntssdgtqdsigrslgakvdsirfkapsnvsqgeiyidrimfsvddaryqwsdyqvktrlsepeiqf.... [00861 INucleotide sequence for ABCI-TAT-C (SEQ ID NO. 45), a portion of which is illustrated below, shows the C-tenninal TAT sequence nucleotides highlighted by underlining. The stop codon from chondroitinase ABC I (SEQ ID NO. 28) was replaced by the TAT sequence and was placed at the 3'end of the TAT sequence.

WO 2004/110360 PCT[US2004/015662 32 ... gattaatggcaaatggcaatctgctgataaaaatagtgaagtgaaatatcaggttttggtgataacactgaactgacgtttacgagtt actttggtattceacaagaaatcaaactctcgccactccct ggtcgtaaaaagcatcatcaacgtcgtcetctcctcaatgctag [00871 Amino acid sequence for ABCI-TAT-C (SEQ ID NO. 46), a portion of which is shown below, illustrates the TAT sequence, highlighted by underlining, linked to the chondroitinase polypeptide at the C-terminus of the mature chondroitinase ABC I (SEQ ID NO. 1). ... aekvnvsrqhqvsaenknrqptegnfssawidhstrpkdasyeymvfldatpekmgemaqkfrennglyqvrkdlcdvhi ildklsnvtgyafyqpasiedkwikknkpaivmthrqkdtlivsavtpdlntrqkaatpvtinvtingkwqsadknsevkyq vsgdnteltftsyfgipqeillsplparkkrrArrrppac EXAMPLE 8 [0088] This example illustrates the sequence of chondroitinase nucleic acid and polypeptides which may be used for deletions or substitutions in mutants of the present invention. In these sequence, discrepancies from published sequences are highlighted in bold text at both the nucleotide level and at the amino acid level. These are illustrative of substitutions in the present invention. SEQ ID NO: 26 Present invention Chondroitinase ABC II Nucleic acid > ABC II mature 2973 nt vs. > ABC II (present invention) 2974 nt scoring matrix; , gap penalties: -12/-2 99.0% identity; Global alignment score: 11684 10 20 30 40 50 60 806559 TTACCCACTCTGTCTCATGAAGCTTTCGGCGATATTTATCTTTTTGAAGGTGAATTACCC TTACCCACTCTGTCTCATGAAGCTTTCGGCGATATTTATCTTTTTGAAGGCGAATTACCC 10 20 30 40 50 60 70 80 90 100 110 120 806559 AATACCCTTACCACTTCAAATAATAATCAATTATCGCTAAGCAAACAGCATGCTAAAGAT AATATCCTTACCACTTCAAATAATAATCAATTATCGCTAAGCAAACAGCATGCTAAAGAT 70 80 90 100 110 120 WO 2004/110360 PCT/US2004/015662 33 130 140 150 160 170 180 806559 GGTGAACAATCACTCAAATGGCAATATCAACCACAAGCAACATTAACACTAAATAATATT GGTGAACAATCACTCAAATGGCAATATCAACCACAAGCAACATTAACACTAAATAATATT 130 140 150 160 170 180 190 200 210 220 230 240 806559 GTTAATTACCAAGATGATAAAAATACAGCCACACCACTCACTTTTATGATGTGGATTTAT GTTAATTACCAAGATGATAAAAATACAGCCACACCACTCACTTTTATGATGTGGATTTAT 190 200 210 220 230 240 250 260 270 280 290 300 806559 AATGAAAAACCTCAATCTTCCCCATTAACGTTAGCATTTAAACAAAATAATAAAATTGCA .......................................... AATGAAAAACCTCAATCTTCCCCATTAACGTTAGCATTTAAACAAAATAATAAAATTGCA 250 260 270 280 290 300 310 320 330 340 350 360 806559 CTAAGTTTTAATGCTGAACTTAATTTTACGGGGTGGCGAGGTATTGCTGTTCCTTTTCGT CTAAGTTTTAATGCTGAACTTAATTTTACGGGGTGGCGAGGTATTGCTGTTCCTTTTCGT 310 320 330 340 350 360 370 380 390 400 410 420 806559 GATATGCAAGGCTCTGTGACAGGTCAACTTGATCAATTAGTGATCACCGCTCCAAACCAA GATATGCAAGGCTCTGCGACAGGTCAACTTGATCAATTAGTGATCACCGCTCCAAACCAA 370 380 390 400 410 420 430 440 450 460 470 480 806559 GCCGGAACACTCTTTTTTGATCAAATCATCATGAGTGTACCGTTAGACAATCGTTGGGCA GCCGGAACACTCTTTTTTGATCAAATCATCATGAGTGTACCGTTAGACAATCGTTGGGCA 430 440 450 460 470 480 490 500 510 520 530 540 806559 GTACCTGACTATCAAACACCTTACGTAAATAACGCAGTAAACACGATGGTTAGTAAAAAC GTACCTGACTATCAAACACCTTACGTAAATAACGCAGTAAACACGATGGTTAGTAAAAAC 490 500 510 520 530 540 550 560 570 580 590 600 806559 TGGAGTGCATTATTGATGTACGATCAGATGTTTCAAGCCCATTACCCTACTTTAAACTTC TGGAGTGCATTATTGATGTACGATCAGATGTTTCAAGCCCATTACCCTACTTTAAACTTC 550 560 570 580 590 600 610 620 630 640 650 660 806559 GATACTGAATTTCGCGATGACCAAACAGAAATGGCTTCGAGGTATCAGCGCTTTGAATAT GATACTGAATTTCGCGATGACCAAACAGAAATGGCTTCGATTTATCAGCGCTTTGAATAT 610 620 630 640 650 660 670 680 690 700 710 720 806559 TATCAAGGAATTCGTAGTGATAAAAAAATTACTCCAGATATGCTAGATAAACATTTAGCA TATCAAGGAATTCGTAGTGATAAAAAAATTACTCCAGATATGCTAGATAAACATTTAGCG 670 680 690 700 710 720 WO 2004/110360 PCT/US2004/015662 34 730 740 750 760 770 780 806559 TTATGGGAAAAATTGGTGTTAACACAACACGCTGATGGTTCAATCACAGGAAAAGCCCTT TTATGGGAAAAATTGGGGTTAACACAACACGCTGATGGCTCAATCACAGGAAAAGCCCTT 730 740 750 760 770 780 790 800 810 820 830 840 806559 GATCACCCTAACCGGCAACATTTTATGAAAGTCGAAGGTGTATTTAGTGAGGGGACTCAA GATCACCCTAACCGGCAACATTTTATGAAAGTCGAAGGTGTATTTAGTGAGGGGACTCAA 790 800 810 820 830 840 850 860 870 880 890 900 806559 AAAGCATTACTTGATGCCAATATGCTAAGAGATGTGGGCAAAACGCTTCTTCAAACTGCT AAAGCATTACTTGATGCCAATATGCTAAGAGATGTGGGCAAAACGCTTCTTCAAACTGCT 850 860 870 880 890 900 910 920 930 940 950 960 806559 ATTTACTTGCGTAGCGATTCATTATCAGCAACTGATAGAAAAAAATTAGAAGAGCGCTAT ATTTACTTGCGTAGCGATTCATTATCAGCAACTGGTAGAAAAAAATTAGAAGAGCGCTAT 910 920 930 940 950 960 970 980 990 1000 1010 1020 806559 TTATTAGGTACTCGTTATGTCCTTGAACAAGGTTTTCACCGAGGAAGTGGTTATCAAATT TTATTAGGTACTCGTTATGTCCTTGAACAAGGTTTTACACGAGGAAGTGGTTATCAAATT 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080 806559 ATTAGCCATGTTGGTTACCAAACCAGAGAACTTTTTGATGCATGGTTTATTGGTCGTCAT ATTACTCATGTTGGTTACCAAACCAGAGAACTTTTTGATGCATGGTTTATTGGCCGTCAT 1030 1040 1050 1060 1070 1080 1090 1100 1110 1120 1130 1140 806559 GTTCTTGCAAAAAATAACCTTTTAGCCCCCACTCAACAAGCTATGATGTGGTACAACGCC GTTCTTGCAAAAAATAACCTTTTAGCCCCCACTCAACAAGCTATGATGTGGTACAACGCC 1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200 806559 ACAGGACGTATTTTTGAAAAAAATAATGAAATTGTTGATGCAAATGTCCATATTCTCAAT ACAGGACGTATTTTTGAAAAAGATAATGAAATTGTTGATGCAAATGTCGATATTCTCAAT 1150 1160 1170 1180 1190 1200 1210 1220 1230 1240 1250 1260 806559 ACTCAATTGCAATGGATGATAAAAAGCTTATTGATGCTACCGGATTATCAACAACGTCAA ACTCAATTGCAATGGATGATAAAAAGCTTATTGATGCTACCGGATTATCAACAACGTCAA 1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320 806559 CAAGCCTTAGCGCAACTGCAACGTTGGCTAAATAAAACCATTCTAAGCTCAAAAGGTGTT CAAGCCTTAGCGCAACTGCAAAGTTGGCTAAATAAAACCATTCTAAGCTCAAAAGGTGTT 1270 1280 1290 1300 1310 1320 1330 1340 1350 1360 1370 1380 WO 2004/110360 PCT/US2004/015662 35 806559 GCTGGCGGTTTCAAATCTGATGGTTCTATTTTTCACCATTCACAACATTACCCCGCTTAT GCTGGCGGTTTCAAATCTGATGGTTCTATTTTTCACCATTCACAACATTACCCCGCTTAT 1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440 806559 GCTAAAGATGCATTTGGTGGTTTAGCACCCAGTGTTTATGCATTAAGTGATTCACCTTTT GCTAAAGATGCATTTGGTGGTTTAGCACCCAGTGTTTATGCATTAAGTGATTCACCTTTT 1390 1400 1410 1420 1430 1440 1450 1460 1470 1480 1490 1500 806559 CGCTTATCTACTTCAGCACATGAGCGTTTAAAAGATGTTTTGTTAAAAATGCGGATCTAC CGCTTATCTACTTCAGCACATGAGCATTTAAAAGATGTTTTGTTAAAAATGCGGATCTAC 1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560 806559 ACCAAAGAGACACAAATTCCTGCTGTATTAAGTGGTCGTCATCCAACTGGGTTGCATAAA ACCAAAGAGACACAAATTCCTGTGGTATTAAGTGGTCGTCATCCAACTGGGTTGCATAAA 1510 1520 1530 1540 1550 1560 1570 1580 1590 1600 1610 1620 806559 ATAGGGATCGCGCCATTTAAATGGATGGCATTAGCAGGAACCCCAGATGGCAAACAAAAG ATAGGGATCGCGCCATTTAAATGGATGGCATTAGCAGGAACCCCAGATGGCAAACAAAAG 1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670 1680 806559 TTAGATACCACATTATCCGCCGCTTATGCAAAATTAGACAACAAAACGCATTTTGAAGGC TTAGATACCACATTATCCGCCGCTTATGCAAACTTAGACAACAAAACGCATTTTGAAGGC 1630 1640 1650 1660 1670 1680 1690 1700 1710 1720 1730 1740 806559 ATTAAGGCTGAAAGTGAGCCAGTCGGCGCATGGGCAATGAATTATGCATCAATGGCAATA ATTAACGCTGAAAGTGAGCCAGTCGGCGCATGGGCAATGAATTATGCATCAATGGCAATA 1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 1800 806559 CAACGAAGAGCATCGACCCAATCACCACAACAAAGCTGGCTCGCCATAGCGCGCGGTTTT CAACGAAGAGCATCGACCCAATCACCACAACAAAGCTGGCTCGCCATAGCGCGCGGTTTT 1750 1760 1770 1780 1790 1800 1810 1820 1830 1840 1850 1860 806559 AGCCGTTATCTTGTTGGTAATGAAAGCTATGAAAATAACAACCGTTATGGTCGTTATTTA AGCCGTTATCTTGTTGGTAATGAAAGCTATGAAAATAACAACCGTTATGGTCGTTATTTA 1810 1820 1830 1840 1850 1860 1870 1880 1890 1900 1910 1920 806559 CAATATGGACAATTGGAAATTATTCCAGCTGATTTAACTCAATCAGGGTTTAGCCATGCT CAATATGGACAATTGGAAATTATTCCAGCTGATTTAACTCAATCAGGGTTTAGCCATGCT 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 806559 GGATGGGATTGGAATAGATATCCAGGTACAACAACTATTCATCTTCCCTATAACGAACTT WO 2004/110360 PCTIUS2004/015662 36 GGATGGGATTGGAATAGATATCCAGGTACAACAACTATTCATCTTCCCTATAACGAACTT 1930 1940 1950 1960 1970- 1980 1990 2000 2010 2020 2030 2040 806559 GAAGCAAAACTTAATCAATTACCTGCTGCAGGTATTGAAGAAATGTTGCTTTCAACAGAA GAAGCAAAACTTAATCAATTACCTGCTGCAGGTATTGAAGAAATGTTGCTTTCAACAGAA 1990 2000 2010 2020 2030 2040 2050 2060 2070 2080 2090 2100 806559 AGTTACTCTGGTGCAAATACCCTTAATAATAACAGTATGTTTGCCATGAAATTACACGGT AGTTACTCTGGTGCAAATACCCTTAATAATAACAGTATGTTTGCCATGAAATTACACGGT 2050 2060 2070 2080 2090 2100 2110 2120 2130 2140 2150 2160 806559 CCAAGTAAATATCAACAACAAAGCTTAAGGGCAAATAAATCCTATTTCTTATTTGATAAT CACAGTAAATATCAACAACAAAGCTTAAGGGCAAATAAATCCTATTTCTTATTTGATAAT 2110 2120 2130 2140 2150 2160 2170 2180 2190 2200 2210 2220 806559 AGAGTTATTGCTTTAGGCTCAGGTATTGAAAATGATGATAAACAACATACGACCGAAACA AGAGTTATTGCTTTAGGCTCAGGTATTGAAAATGATGATAAACAACATACGACCGAAACA 2170 2180 2190 2200 2210 2220 2230 2240 2250 2260 2270 2280 806559 ACACTATTCCAGTTTGCCGTCCCTAAATTACAGTCAGTGATCATTAATGGCAAAAAGGTA ACACTATTCCAGTTTGCCGTCCCTAAATTACAGTCAGTGATCATTAATGGCAAAAAGGTA 2230 2240 2250 2260 2270 2280 2290 2300 2310 2320 2330 2340 806559 AATCAATTAGATACTCAATTAACTTTAAATAATGCAGATACATTAATTGATCCTGCCGGC AATCAATTAGATACTCAATTAACTTTAAATAATGCAGATACATTAATTGATCCTGCCGGC 2290 2300 2310 2320 2330 2340 2350 2360 2370 23BO 2390 2400 806559 AATTTATATAAGCTCACTAAAGGACAAACTGTAAAATTTAGTTATCAAAAACAACATTCA AATTTATATAAGCTCACTAAAGGACAAACTGTAAAATTTAGTTATCAAAAACAACATTCA 2350 2360 2370 2380 2390 2400 2410 2420 2430 2440 2450 2460 806559 CTTGATGATAGAAATTCAAAACCAACAGAACAATTATTTGCAACAGCTGTTATTTCTCAT CTTGATGATAGAAATTCAAAACCAACAGAACAATTATTTGCAACAGCTGTTATTTCTCAT 2410 2420 2430 2440 2450 2460 2470 2480 2490 2500 2510 2520 806559 GGTAAGGCACCGAGTAATGAAAATTATGAATATGCAATAGCTATCGAAGCACAAAATAAT GGTAAGGCACCGAGTAATGAAAATTATGAATATGCAATAGCTATCGAAGCACAAAATAAT 2470 2480 2490 2500 2510 2520 2530 2540 2550 2560 2570 2580 806559 AAAGCTCCCGAATACACAGTATTACAACATAATGATCAGCCCCATGCGGTAAAAGATAAA WO 2004/110360 PCT/US2004/015662 37 AAAGCTCCCAAATACACAGTATTACAACATAATGATCAGCTCCATGCGGTAAAAGATAAA 2530 2540 2550 2560 2570 2580 2590 2600 2610 2620 2630 806559 ATAACCCAAGAAGAGGGATATGCTTTTTTTGAAGCCACTAAGTTAAAATCAGCGGATGC ATAACCCAAGAAGAGGGATATGGTTTTTTTGAAGCCACTAAGTTAAAATCAGCGGATGC 2590 2600 2610 2620 2630 2640 2640 2650 2660 2670 2680 2690 806559 AACATTATTATCCAGTGATGCGCCGGTTATGGTCATGGCTAAAATACAAAATCAGCAATT AACATTATTATCCAGTGATGCGCCGGTTATGGTCATGGCTAAAATACAAAATCAGCAATT 2650 2660 2670 2680 2690 2700 2700 2710 2720 2730 2740 2750 806559 AACATTAAGTATTGTTAATCCTGATTTAAATTTATATCAAGGTAGAGAAAAAGATCAATT AACATTAAGTATTGTTAATCCTGATTTAAATTTATATCAAGGTAGAGAAAAAGATCAATT 2710 2720 2730 2740 2750 2760 2760 2770 2780 2790 2800 2810 806559 TGATGATAAAGGTAATCAAATCGAAGTTAGTGTTTATTCTCGTCATTGGCTTACAGCAGA TGATGATAAAGGTAATCAAATCGAAGTTAGTGTTTATTCTCGTCATTGGCTTACAGCAGA 2770 2780 2790 2800 2810 2820 2820 2830 2840 2850 2860 2870 806559 ATCGCAATCAACAAATAGTACTATTACCGTAAAAGGAATATGGAAATTAACGACACCTCA ATCGCAATCAACAAATAGTACTATTACCGTAAAAGGAATATGGAAATTAACGACACCTCA 2830 2840 2850 2860 2870 2880 2880 2890 2900 2910 2920 2930 806559 ACCCGGTGTTATTATTAAGCACCACAATAACAACACTCTTATTACGACAACAACCATACA ACCCGGTGTTATTATTAAGCACCACAATAACAACACTCTTATTACGACAACAACCATACA 2890 2900 2910 2920 2930 2940 2940 2950 2960 2970 806559 GGCAACACCTACTGTTATTAATTTAGTTAAGTAA GGCAACACCTACTGTTATTAATTTAGTTAAGTAA 2950 2960 2970 The above discrepancies, bold text, at the nucleotide level resulted in 98.3% identity at the amino acid level and the substituted residues are marked in bold text in the following. SEQ ID NO: 27 Present Invention Chondroitinase ABC II protein >_ ABC (present invention) 990 aa vs. >- ABC (mature) 990 aa scoring matrix: , gap penalties: -12/-2 98.3% identity; Global alignment score: 6393 WO 2004/110360 PCT/US2004/015662 38 10 20 30 40 50 60 457676 LPTLSHEAFGDIYLFEGELPNILTTSNNNQLSLSKQIAKDGEQSLKWQYQPQATLTLNNI LPTLS..EAFGDIYLFEGELPNTLTTSNNNQLSLSKQHAKDGEQSLKWQYQPQATLTLNNI 10 20 30 40 50 60 70 80 90 100 110 120 457676 VNYQDDKNTATPLTFMMWIYNEKPQSSPLTLAFKQNNKIALSFNAELNFTGWRGIAVPFR VNYQDDKNTATPLTFMMWIYNEKPQSSPLTLAFKQNNKIALSFIAELNFTGWRGIAVPFR 70 80 90 100 110 120 130 140 150 160 170 180 457676 DMQGSATGQLDQLVITAPNQAGTLFFDQIIMSVPLDNRWAVPDYQTPYVNNAVNTMVSKN DMQGSVTGQLDQLVITAPNQAGTLFFDQIIMSVPLDNRWAVPDYQTPYVNNAVNTMVSKN 130 140 150 160 170 180 190 200 210 220 230 240 457676 WSALLMYDQMFQARYPTLNFDTEFRDDQTEMASIYQRFEYYQGIRSDKKITPDMLDKHLA WSALLMYDQMFQAHYPTLNFDTEFRDDQTEMASRYQRFEYYQGIRSDKITPDMLDKHLA 190 200 210 220 230 240 250 260 270 280 290 300 457676 LWEKLGLTQHADGSITGKALDHPNRQHFMKVEGVFSEGTQKALLDANMLRDVGKTLLQTA LWEXLVLTQHADGSITGKALDHPNRQHFMKVEGVFSEGTQKALLDANMLRDVGKTLLQTA 250 260 270 280 290 300 310 320 330 340 350 360 457676 IYLRSDSLSATGRKKLEERYLLGTRYVLEQGFTRGSGYQIITHVGYQTRELFDAWFIGRH IYLRSDSLSATDRKKLEERYLLGTRYVLEQGFHRGSGYQIISHVGYQTRELFDAWFIGRH 310 320 330 340 350 360 370 380 390 400 410 420 457676 VLAKNNLLAPTQQAMWYNATGRIFEKDNEIVDANVDILNTQLQWMIKSLLMLPDYQQRQ VLAKNNLLAPTQQAMMWYNATGRIFEKNNEIVDANVDILNTQLQWMIKSLLMLPDYQQRQ 370 380 390 400 410 420 430 440 450 460 470 480 457676 QALAQLQSWLNKTILSSKGVAGGFKSDGSIFHHSQHYPAYAKDAFGGLAPSVYALSDSPF QALAQLQRWLNKTILSSKGVAGGFKSDGSIFHHSQHYPAYAKDAFGGLAPSVYALSDSPF 430 440 450 460 470 480 490 500 510 520 530 540 457676 RLSTSAHEHLKDVLLKMRIYTKETQIPVVLSGRHPTGLHKIGIAPFKWMALAGTPDGKQK RLSTSAHERLKDVLLKMRIYTKETQIPAVLSGRHPTGLHKIGIAPFKWMALAGTPDGKQK 490 500 510 520 530 540 550 560 570 580 590 600 457676 LDTTLSAAYANLDNKTHFEGINAESEPVGAWAMNYASMAIQRRASTQSPQQSWLAIARGF LDTTLSAAYAKLDNKTHFEGIKAESEPVGAWAMNYASMAIQRRASTQSPQQSWLAIARGF 550 560 570 580 590 600 610 620 630 640 650 660 WO 2004/110360 PCT/US2004/015662 39 457676 SRYLVGNESYENNNRYGRYLQYGQLEIIPADLTQSGFSHAGWDWNRYPGTTTIHLPYNEL SRYLVGNESYENNNRYGRYLQYGQLEIIPADLTQSGFSHAGWDWNRYPGTTTIHLPYNEL 610 620 630 640 650 660 670 680 690 700 710 720 457676 EAKLNQLPAAGIEEMLLSTESYSGANTLNNNSMFAMKLHGHSKYQQQSLRANKSYFLFDN EAKLNQ;PAAGIEEMLLSTESYSGANTLNNNSMFAMKLHGPSKYQQQSLRANKSYFLFDN 670 680 690 700 710 720 730 740 750 760 770 780 457676 RVIALGSGIENDDKQHTTETTLFQFAVPKLQSVIINGKKVNQLDTQLTLNNADTLIDPAG RVIALGSGIENDDKQHTTETTLFQFAVPKLQSVIINGKKVNQLDTQLTLNNADTLIDPAG 730 740 750 760 770 780 790 800 810 820 830 840 457676 NLYKLTKGQTVKFSYQKQHSLDDRNSKPTEQLFATAVISHGKAPSNENYEYAIAIEAQNN NLYKLTKGQTVKFSYQKQHSLDDRNSKPTEQLFATAVISHGKAPSNENYEYAIAIEAQNN 790 800 810 820 830 840 850 860 870 880 890 900 457676 KAPKYTVLQHNDQLHAVKDKITQEEGYGFFEATKLKSADATLLSSDAPVMVMAKIQNQQL KAPEYTVLQHNDQPHAVKDKITQEEGYAFFEATKLKSADATLLSSDAPVMMKIQNQQL -850 860 870 880 890 900 910 920 930 940 950 960 457676 TLSIVNPDLNLYQGREEDQFDDKGNQIEVSVYSRHWLTAESQSTNSTITVKGIWKLTTPQ TLSIVNPDLNLYQGREKDQFDDKGNQIEVSVYSRHWLTAESQSTNSTITVKGIWKLTTPQ 910 920 930 940 950 960 970 980 990 457676 PGVIIKHHNNNTLITTTTIQATPTVINLVK PGVIIKHHNNNTLITTTTIQATPTVINLVK 970 980 990 SEQ ID NO: 28 Present Invention Chondroitinase ABC I nucleic acid >_ ABCI present invention 2994 nt vs. >- ABCI mature 2994 nt scoring matrix: , gap penalties: -12/-2 99.7% identity; Global alignment score: 11909 10 20 30 40 50 60 806559 GCCACCAGCAATCCTGCATTTGATCCTAAAAATCTGATGCAGTCAGAAATTTACCATTTT GCCACCAGCAATCCTGCATTTGATCCTAAAAATCTGATGCAGTCAGAAATTTACCATTTT 10 20 30 40 50 60 70 80 90 100 110 120 806559 GCACAAAATAACCCATTAGCAGACTTCTCATCAGATAAAAACTCAATACTAACGTTATCT GCACAAAATAACCCATTAGCAGACTTCTCATCAGATAAAAACTCAATACTAACGTTATCT 70 80 90 100 110 120 WO 2004/110360 PCT/US2004/015662 40 130 140 ISO 160 170 180 806559 GATAAACGTAGCATTATGGGAAACCAATCTCTTTTATGGAAATGGAAAGGTGGTAGTAGC GATAAACGTAGCATTATGGGAAACCAATCTCTTTTATGGAAATGGAAAGGTGGTAGTAGC 130 140 150 160 170 180 190 200 210 220 230 240 806559 TTTACTTTACATAAAAAACTGATTGTCCCCACCGATAAAGAAGCATCTAAAGCATGGGGA TTTACTTTACATAAAAAACTGATTGTCCCCACCGATAAAGAAGCATCTAAAGCATGGGGA 190 200 210 220 230 240 250 260 270 280 290 300 806559 CGCTCATCCACCCCCGTTTTCTCATTTTGGCTTTACAATGAAAAACCGATTGATGGTTAT CGCTCATCTACCCCCGTTTTCTCATTTTGGCTTTACAATGAAAAACCGATTGATGGTTAT 250 260 270 280 290 300 310 320 330 340 350 360 806559 CTTACTATCGATTTCGGAGAAAAACTCATTTCAACCAGTGAGGCTCAGGCAGGCTTTAAA CTTACTATCGATTTCGGAGAAAAACTCATTTCAACCAGTGAGGCTCAGGCAGGCTTTAAA 310 320 330 340 350 360 370 380 390 400 410 420 806559 GTAAAATTAGATTTCACTGGCTGGCGTACTGTGGGAGTCTCTTTAAATAACGATCTTGAA GTAAAATTAGATTTCACTGGCTGGCGTGCTGTGGGAGTCTCTTTAAATAACGATCTTGAA 370 380 390 400 410 420 430 440 450 460 470 480 806559 AATCGAGAGATGACCTTAAATGCAACCAATACCTCCTCTGATGGTACTCAAGACAGCATT AATCGAGAGATGACCTTAAATGCAACCAATACCTCCTCTGATGGTACTCAAGACAGCATT 430 440 450 460 470 480 490 500 510 520 530 540 806559 GGGCGTTCTTTAGGTGCTAAAGTCGATAGTATTCGTTTTAAAGCGCCTTCTAATGTGAGT GGGCGTTCTTTAGGTGCTAAAGTCGATAGTATTCGTTTTAAAGCGCCTTCTAATGTGAGT 490 500 510 520 530 540 550 560 570 580 590 600 806559 CAGGGTGAAATCTATATCGACCGTATTATGTTTTCTGTCGATGATGCTCGCTACCAATGG CAGGGTGAAATCTATATCGACCGTATTATGTTTTCTGTCGATGATGCTCGCTACCAATGG 550 560 570 580 590 600 610 620 630 640 650 660 806559 TCTGATTATCAAGTAAAAACTCGCTTATCAGAACCTGAAATTCAATTTCACAACGTAAAG TCTGATTATCAAGTAAAAACTCGCTTATCAGAACCTGAAATTCAATTTCACAACGTAAAG 610 620 630 640 650 660 670 680 690 700 710 720 806559 CCACAACTACCTGTAACACCTGAAAATTTAGCGGCCATTGATCTTATTCGCCAACGTCTA CCACAACTACCTGTAACACCTGAAAATTTAGCGGCCATTGATCTTATTCGCCAACGTCTA 670 680 690 700 710 720 WO 2004/110360 PCT/US2004/015662 41 730 740 750 760 770 780 806559 ATTAATGAATTTGTCGGAGGTGAAAAAGAGACAAACCTCGCATTAGAAGAGAATATCAGC ATTAATGAATTTGTCGGAGGTGAAAAAGAGACAAACCTCGCATTAGAAGAGAATATCAGC 730 740 750 760 770 780 790 800 810 820 830 840 806559 AAATTAAAAAGTGATTTCGATGCTCTTAATACTCACACTTTAGCAAATGGTGGAACGCAA AAATTAAAAAGTGATTTCGATGCTCTTAATATTCACACTTTAGCAAATGGTGGAACGCAA 790 800 810 820 830 840 850 860 870 880 890 900 806559 GGCAGACATCTGATCACTGATAAACAAATCATTATTTATCAACCAGAGAATCTTAACTCT GGCAGACATCTGATCACTGATAAACAAATCATTATTTATCAACCAGAGAATCTTAACTCC 850 860 870 880 890 900 910 920 930 940 950 960 806559 CAAGATAAACAACTATTTGATAATTATGTTATTTTAGGTAATTACACGACATTAATGTTT CAAGATAAACAACTATTTGATAATTATGTTATTTTAGGTAATTACACGACATTAATGTTT 910 920 930 940 950 960 970 980 990 1000 1010 1020 806559 AATATTAGCCGTGCTTATGTGCTGGAAAAAGATCCCACACAAAAGCCGCAACTAAAGCAG AATATTAGCCGTGCTTATGTGCTGGAAAAAGATCCCACACAAAAGGCGCAACTAAAGCAG 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080 806559 ATGTACTTATTAATGACAAAGCATTTATTAGATCAAGGCTTTGTTAAAGGGAGTGCTTTA ATGTACTTATTAATGACAAAGCATTTATTAGATCAAGGCTTTGTTAAAGGGAGTGCTTTA 1030 1040 1050 1060 1070 1080 1090 1100 1110 1120 1130 1140 806559 GTGACAACCCATCACTGGGGATACAGTTCTCGTTGGTGGTATATTTCCACGTTATTAATG GTGACAA.CCCATCACTGGGGATACAGTTCTCGTTGGTGGTATATTTCCACGTTATTAATG -1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200 806559 TCTGATGCACTAAAAGAAGCGAACCTACAAACTCAAGTTTATGATTCATTACTGTGGTAT TCTGATGCACTAAAAGAAGCGAACCTACAAACTCAAGTTTATGATTCATTACTGTGGTAT 1150 1160 1170 1180 1190 1200 1210 1220 1230 1240 1250 1260 806559 TCACGTGAGTTTAAAAGTAGTTTTGATATGAAAGTAAGTGCTGATAGCTCTGATCTAGAT TCACGTGAGTTTAAAAGTAGTTTTGATATGAAAGTAAGTGCTGATAGCTCTGATCTAGAT 1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320 806559 TATTTCAATACCTTATCTCGCCAACATTTAGCCTTATTACTACTAGAGCCTGATGATCAA TATTTCAATACCTTATCTCGCCAACATTTAGCCTTATTATTACTAGAGCCTGATGATCAA 1,270 1280 1290 1300 1310 1320 1330 1340 1350 1360 1370 1380 WO 2004/110360 PCT/US2004/015662 42 806559 AAGCGTATCAACTTAGTTAATACTTTCAGCCATTATATCACTGGCGCATTAACGCAAGTG AAGCGTATCAACTTAGTTAATACTTTCAGCCATTATATCACTGGCGCATTAACGCAAGTG 1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440 806559 CCACCGGGTGGTAAAGATGGTTTACGCCCTGATGGTACAGCATGGCGACATGAAGGCAAC CCACCGGGTGGTAAAGATGGTTTACGCCCTGATGGTACAGCATGGCGACATGAAGGCAAC 1390 1400 1410 1420 1430 1440 1450 1460 1470 1480 1490 1500 806559 TATCCGGGCTACTCTTTCCCAGCCTTTAAAAATGCCTCTCAGCTTATTTATTTATTACGC TATCCGGGCTACTCTTTCCCAGCCTTTAAAAATGCCTCTCAGCTTATTTATTTATTACGC 1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560 806559 GATACACCATTTTCAGTGGGTGAAAGTGGTTGGAATAGCCTGAAAAAAGCGATGGTTTCA GATACACCATTTTCAGTGGGTGAAAGTGGTTGGAATAACCTGAAAAAAGCGATGGTTTCA 1510 1520 1530 1540 1550 1560 1570 1580 1590 1600 1610 1620 806559 GCGTGGATCTACAGTAATCCAGAAGTTGGATTACCGCTTGCAGGAAGACACCCTCTTAAC GCGTGGATCTACAGTAATCCAGAAGTTGGATTACCGCTTGCAGGAAGACACCCTTTTAAC 1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670 1680 806559 TCACCTTCGTTAAAATCAGTCGCTCAAGGCTATTACTGGCTTGCCATGTCTGCAAAATCA TCACCTTCGTTAAAATCAGTCGCTCAAGGCTATTACTGGCTTGCCATGTCTGCAAAATCA 1630 1640 1650 1660 1670 1680 1690 1700 1710 1720 1730 1740 806559 TCGCCTGATAAAACACTTGCATCTATTTATCTTGCGATTAGTGATAAAACACAAAATGAA TCGCCTGATAAAACACTTGCATCTATTTATCTTGCGATTAGTGATAAAACACAAAATGAA 1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 1800 806559 TCAACTGCTATTTTTGGAGAAACTATTACACCAGCGTCTTTACCTCAAGGTTTCTATGCC TCAACTGCTATTTTTGGAGAAACTATTACACCAGCGTCTTTACCTCAAGGTTTCTATGCC 1750 1760 1770 1780 1790 1800 1810 1820 1830 1840 1850 1860 806559 TTTAATGGCGGTGCTTTTGGTATTCATCGTTGGCAAGATAAAATGGTGACACTGAAAGCT TTTAATGGCGGTGCTTTTGGTATTCATCGTTGGCAAGATAAAATGGTGACACTGAAAGCT 1810 1820 1830 1840 1850 1860 1870 1880 1890 1900 1910 1920 806559 TATAACACCAATGTTTGGTCATCTGAAATTTATAACAAAGATAACCGTTATGGCCGTTAC TATAACACCAATGTTTGGTCATCTGAAATTTATAACAAAGATAACCGTTATGGCCGTTAC 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 806559 CAAAGTCATGGTGTCGCTCAAATAGTGAGTAATGGCTCGCAGCTTTCACAGGGCTATCAG WO 2004/110360 PCT/US2004/015662 43 CAAAGTCATGGTGTCGCTCAAATAGTGAGTAATGGCTCGCAGCTTTCACAGGGCTATCAG 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 2030 2040 806559 CAAGAAGGTTGGGATTGGAATAGAATGCCAGGGGCAACCACTATCCACCTTCCTCTTAAA CAAGAAGGTTGGGATTGGAATAGAATGCAAGGGGCAACCACTATTCACCTTCCTCTTAAA 1990 2000 2010 2020 2030 2040 2050 2060 2070 2080 2090 2100 806559 GACTTAGACAGTCCTAAACCTCATACCTTAATGCAACGTGGAGAGCGTGGATTTAGCGGA GACTTAGACAGTCCTAAACCTCATACCTTAATGCAACGTGGAGAGCGTGGATTTAGCGGA 2050 2060 2070 2080 2090 2100 2110 2120 2130 2140 2150 2160 806559 ACATCATCCCTTGAAGGTCAATATGGCATGATGGCATTCGATCTTATTTATCCCGCCAAT ACATCATCCCTTGAAGGTCAATATGGCATGATGGCATTCGATCTTATTTATCCCGCCAAT 2110 2120 2130 2140 2150 2160 2170 2180 2190 2200 2210 2220 806559 CTTGAGCGTTTTGATCCTAATTTCACTGCGAAAAAGAGTGTATTAGCCGCTGATAATCAC CTTGAGCGTTTTGATCCTAATTTCACTGCGAAAAAGAGTGTATTAGCCGCTGATAATCAC 2170 2180 2190 2200 2210 2220 2230 2240 2250 2260 2270 2280 806559 TTAATTTTTATTGGTAGCAATATAAATAGTAGTGATAAAAATAAAAATGTTGAAACGACC TTAATTTTTATTGGTAGCAATATAAATAGTAGTGATAAAAATAAAAATGTTGAAACGACC 2230 2240 2250 2260 2270 2280 2290 2300 2310 2320 2330 2340 806559 TTATTCCAACATGCCATTACTCCAACATTAAATACCCTTTGGATTAATGGACAAAAGATA TTATTCCAACATGCCATTACTCCAACATTAAATACCCTTTGGATTAATGGACAAAAGATA 2290 2300 2310 2320 2330 2340 2350 2360 2370 2380 2390 2400 806559 GAAAACATGCCTTATCAAACAACACTTCAACAAGGTGATTGGTTAATTGATAGCAATGGC GAAAACATGCCTTATCAAACAACACTTCAACAAGGTGATTGGTTAATTGATAGCAATGGC 2350 2360 2370 2380 2390 2400 2410 2420 2430 2440 2450 2460 806559 AATGGTTACTTAATTACTCAAGCAGAAAAAGTAAATGTAAGTCGCCAACATCAGGTTTCA AATGGTTACTTAATTACTCAAGCAGAAAAAGTAAATGTAAGTCGCCAACATCAGGTTTCA 2410 2420 2430 2440 2450 2460 2470 2480 2490 2500 2510 2520 806559 GCGGAAAATAAAAATCGCCAACCGACAGAAGGAAACTTTAGCTCGGCATGGATCGATCAC GCGGAAAATAAAAATCGCCAACCGACAGAAGGAAACTTTAGCTCGGCATGGATCGATCAC 2470 2480 2490 2500 2510 2520 2530 2540 2550 2560 2570 2580 806559 AGCACTCGCCCCAAAGATGCCAGTTATGAGTATATGGTCTTTTTAGATGCGACACCTGAA WO 2004/110360 PCT/US2004/015662 44 AGCACTCGCCCCAAAGATGCCAGTTATGAGTATATGGTCTTTTTAGATGCGACACCTGAA 2530 2540 2550 2560 2570 2580 2590 2600 2610 2620 2630 2640 806559 AAAATGGGAGAGATGGCACAAAAATTCCGTGAAAATAATGGGTTATATCAGGTTCTTCGT AAAATGGGAGAGATGGCACAAAAATTCCGTGAAAATAATGGGTTATATCAGGTTCTTCGT 2590 2600 2610 2620 2630 2640 2650 2660 2670 2680 2690 2700 806559 AAGGATAAAGACGTTCATATTATTCTCGATAAACTCAGCAATGTAACGGGATATGCCTTT AAGGATAAAGACGTTCATATTATTCTCGATAAACTCAGCAATGTAACGGGATATGCCTTT 2650 2660 2670 2680 2690 2700 2710 2720 2730 2740 2750 2760 806559 TATCAGCCAGCATCAATTGAAGACAAATGGATCAAAAAGGTTAATAAACCTGCAATTGTG TATCAGCCAGCATCAATTGAAGACAAATGGATCAAAAAGGTTAATAAACCTGCAATTGTG 2710 2720 2730 2740 2750 2760 2770 2780 2790 2800 2810 2820 806559 ATGACTCATCGACAAAAAGACACTCTTATTGTCAGTGCAGTTACACCTGATTTAAATATG ATGACTCATCGACAAAAAGACACTCTTATTGTCAGTGCAGTTACACCTGATTTAAATATG 2770 2780 2790 2800 2810 2820 2830 2840 2850 2860 2870 2880 806559 ACTCGCCAAAAAGCAGCAACTCCTGTCACCATCAATGTCACGATTAATGCATGGCAA ACTCGCCAAAAAGCAGCAACTCCTGTCACCATCAATGTCACGATTAATGGCAAATGGCAA 2830 2840 2850 2860 2870 2880 2890 2900 2910 2920 2930 2940 B06559 TCTGCTGATAAAAATAGTGAAGTGAAATATCAGGTTTCTGGTGATAACACTGAACTGACG TCTGCTGATAAAAATAGTGAAGTGAAATATCAGGTTTCTGGTGATAACACTGAACTGACG 2890 2900 2910 2920 2930 2940 2950 2960 2970 2980 2990 806559 TTTACGAGTTACTTTGGTATTCCACAAGAAATCAAACTCTCGCCACTCCCTTGA TTTACGAGTTACTTTGGTATTCCACAAGAAATCAAACTCTCGCCACTCCCTTGA 2950 2960 2970 2980 2990 The sequence identity at the amino acid level is shown below: SEQ ID NO: 29 Present Invention Chondroitinase ABC I protein > ABC Present invention 997 aa vs. >- ABC[ mature 997 aa scoring matrix: , gap penalties: -12/-2 99.5% identity; Global alignment score: 6595 WO 2004/110360 PCT/US2004/015662 45 10 20 30 40 50 60 365019 ATSNPAFDPKNLMQSEYHFAQNNPLADFSSDKNSlLTLSDKRSIMGNQSLLWKWKGGSS ATSNPAFDPKNLMQSEIYHFAQNNPLADFSSDKNSILTLSDKRSIMGNQSLLWKWKGGSS 10 20 30 40 50 60 70 80 90 100 110 120 365019 FTLHKKLIVPTDKEASKAWGRSSTPVFSFWLYNEKPIDGYLTIDFGEKLISTSEAQAGFK FTLHKKL[VPTDKEASKAWGRSSTPVFSFWLYNEKPIDGYLTIDFGEKLISTSEAQAGFK 70 80 90 100 110 120 130 140 150 160 170 180 365019 VKLDFTGWRTVGVSLNNDLENREMTLNATNTSSDGTQDSIGRSLGAKVDSIRFKAPSNVS VKLDFTGWRAVGVSLNNDLENREMTLNATNTSSDGTQDSIGRSLGAKVDSIRFKAPSNVS 130 140 150 160 170 180 190 200 210 220 230 240 365019 QGEYIDRIMFSVDDARYQWSDYQVKTRLSEPEIQFHNVKPQLPVTPENLAAIDLIRQRL QGEIYIDRIMFSVDDARYQWSDYQVKTRLSEPEIQFHNVKPQLPVTPENLAAIDLIRQRL 190 200 210 220 230 240 250 260 270 280 290 300 365019 INEFVGGEKETNLALEENISKLKSDFDALNTHTLANGGTQGRHLITDKQIIIYQPENLNS INEFVGGEKETNLALEENISKLKSDFDALNIHTLANGGTQGRHLITDKQIIIYQPENLNS 250 260 270 280 290 300 310 320 330 340 350 360 365019 QDKQLFDNYVI LGNYTTLMFN ISRAYVLEKDPTQKAQLKQMYLLMTKH LLDQGFVKGSAL QDKQLFDNYVILGNYTTLMFNISRAYVLEKDPTQKAQLKQMYLLMTKHLLDQGFVKGSAL 310 320 330 340 350 360 370 380 390 400 410 420 365019 VTTHHWGYSSRWWYISTLLMSDALKEANLQTQVYDSLLWYSREFKSSFDMKVSADSSDLD

VTTHHWGYSSRWWYISTLLMSDALKEANLQTQVYDSLLWYSREFKSSFDMKVSADSSDLD

WO 2004/110360 PCT/US2004/015662 46 370 380 390 400 410 420 430 440 450 460 470 480 365019 YFNTLSRQHLALLLLEPDDQKRINLVNTFSHYITGALTQVPPGGKDGLRPDGTAWRHEGN YFNTLSRQHLALLLLEPDDQKRINLVNTFSHYTGALTQVPPGGKDGLRPDGTAWRHEGN 430 440 450 460 470 480 490 500 510 520 530 540 365019 YPGYSFPAFKNASQLIYLLRDTPFSVGESGWNSLKKAMVSAWIYSNPEVGLPLAGRHPLN YPGYSFPAFKNASQLIYLLRDTPFSVGESGWNNLKKAMVSAWIYSNPEVGLPLAGRHPFN 490 500 510 520 530 540 550 560 570 580 590 600 365019 SPSLKSVAQGYYWLAMSAKSSPDKTLASIYLAISDKTQNESTAIFGETITPASLPQGFYA SPSLKSVAQGYYWLAMSAKSSPDKTLASIYLAISDKTQNESTAIFGETITPASLPQGFYA 550 560 570 580 590 600 610 620 630 640 650 660 365019 FNGGAFGIHRWQDKMVTLKAYNTNVWSSEYNKDNRYGRYQSHGVAQIVSNGSQLSQGYQ FNGGAFGIHRWQDKMVTLKAYNTNVWSSEIYNKDNRYGRYQSHGVAQVSNGSQLSQGYQ 610 620 630 640 650 660 670 680 690 700 710 720 365019 QEGWDWNRMPGATTIHLPLKDLDSPKPHTLMQRGERGFSGTSSLEGQYGMMAFDLIYPAN QEGWDWNRMQGATTHLPLKDLDSPKPHTLMQRGERGFSGTSSLEGQYGMMAFDLiYPAN 670 680 690 700 710 720 730 740 750 760 770 780 365019 LERFDPNFTAKKSVLAADNHLIFIGSNINSSDKNKNVETTLFQHAITPTLNTLWINGQKI LERFDPNFTAKKSVLAADNHLIFIGSNINSSDKNKNVETTLFQHAITPTLNTLWINGQKI 730 740 750 760 770 780 790 800 810 820 830 840 365019 ENMPYQTTLQQGDWLIDSNGNGYLITQAEKVNVSRQHQVSAENKNRQPTEGNFSSAWIDH WO 2004/110360 PCT/US2004/015662 47 ENMPYQTTLQQGDWLIDSNGNGYLITQAEKVNVSRQHQVSAENKNRQPTEGNFSSAWIDH 790 800 810 820 830 840 850 860 870 880 890 900 365019 STRPKDASYEYMVFLDATPEKMGEMAQKFRENNGLYQVLRKDKDVHlILDKLSNVTGYAF STRPKDASYEYMVFLDATPEKMGEMAQKFRENNGLYQVLRKDKDVHilLDKLSNVTGYAF 850 860 870 880 890 900 910 920 930 940 950 960 365019 YQPASIEDKWIKKVNKPAIVMTHRQKDTLIVSAVTPDLNMTRQKAATPVTINVTINGKWQ YQPASIEDKWIKKVNKPAIVMTHRQKDTLIVSAVTPDLNMTRQKAATPVTINVTINGKWQ 910 920 930 940 950 960 970 980 990 365019 SADKNSEVKYQVSGDNTELTFTSYFGIPQEIKLSPLP SADKNSEVKYQVSGDNTELTFTSYFGIPQEIKLSPLP 970 980 990 WO 2004/110360 PCT/US2004/015662 48 REFERENCES 1. Fetbiere J, Eggimann B, Cygler M (1999) Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. J Mol Biol. 288:635-47. 2. Pojasek K, Shriver Z, Kiley, P Venkataraman G and Sasisekharan R. (2001) Biochem Biophys Res Commun. 286:343-51. 3. Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M. (1999) Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution. J Mol Biol. 294:1257-69. 4. Miura RO, Yamagata S, Miura Y, Harada T and Yamagata T. (1995) Anal Biochem. 225:333-40. 5. Yamagata T, Saito H, Habuchi 0 and Suzuki S. (1968) J Biol Chem. 243:1536-42. [0089] Although the present invention has been described in considerable detail with reference to certain preferred embodiments thereof, other versions are possible. Therefore the spirit and scope of the appended claims should not be limited to the description and the preferred versions contain within this specification.

Claims (19)

1. A composition comprising a deletion mutant of full-length chondroitinase AC protein (SEQ ID NO: 5), wherein the deletion mutant chondroitinase AC protein is truncated up to 100 amino acids at the N-terminus when compared to the full-length chondroitinase AC protein, and wherein the deletion mutant retains the proteoglycan degrading activity.

2. The composition of claim 1, wherein the deletion mutant chondroitinase AC protein further comprises a truncation of up to 275 amino acids at the C-terminus.

3. A composition comprising a deletion mutant of full-length chondroitinase AC protein (SEQ ID NO: 5), wherein the deletion mutant chondroitinase AC protein is truncated up to 275 amino acids at the C-terminus when compared to the full-length chondroitinase AC protein, and wherein the deletion mutant retains the proteoglycan degrading activity.

4. The composition of claims 1-3, wherein the deletion mutant chondroitinase AC protein is selected from SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11.

5. The composition of any of claims 1-4 further comprising compounds that facilitate plasticity, neurite growth and regeneration; molecules that overcome neurite outgrowth inhibition or promote nerve growth; therapeutic molecules; diagnostic molecules or a combination of these.

6. The composition of claim 5, wherein the compounds that facilitate plasticity, neurite growth and regeneration are selected from soluble NOGO antagonists, neural cell adhesion molecules, neurotrophic factors, growth factors, phosphodiesterase inhibitors, inhibitors of MAG, inhibitors of MOG, neuregulins, and antibodies that promote remyelination.

7. A purified deletion mutant of full-length chondroitinase AC protein (SEQ ID NO: 5), wherein the deletion mutant chondroitinase AC protein is truncated up to 100 amino acids at the N-terminus when compared to the full-length chondroitinase AC protein, and wherein the deletion mutant retains the proteoglycan degrading activity. 50

8. The purified deletion mutant of chondroitinase AC protein of claim 7, wherein the deletion mutant chondroitinase AC protein further comprises a truncation of up to 275 amino acids at the C-terminus.

9. A purified deletion mutant of full-length chondroitinase AC protein (SEQ ID NO: 5), wherein the deletion mutant chondroitinase AC protein is truncated up to 275 amino acids at the C-terminus when compared to the full-length chondroitinase AC protein, and wherein the deletion mutant retains the proteoglycan degrading activity.

10. The purified deletion mutant of chondroitinase AC protein of claims 7-9, wherein the deletion mutant chondroitinase AC protein is selected from SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11.

11. A genetically modified cell that expresses the purified chondroitinase AC deletion mutant protein of any of claims 7-10.

12. A nucleic acid sequence that encodes a chondroitinase AC deletion mutant of any of claims 7-10.

13. An expression vector comprising a nucleic acid sequence that encodes a chondroitinase AC deletion mutant of any of claims 7-10.

14. A method of treating a central nervous system tissue comprising administering a mutant proteoglycan degrading polypeptide composition to the tissue, wherein the polypeptide is a deletion mutant comprising an amino acid sequence of chondroitinase AC SEQ ID NO: 5 truncated by a deletion up to 100 amino acids from the N-terminus of chondroitinase AC, and wherein the deletion mutant retains the proteoglycan degrading activity.

15. The method of claim 14, wherein the deletion mutant chondroitinase AC protein further comprises a truncation of up to 275 amino acids at the C-terminus.

16. The method of claims 14 or 15, wherein the composition further comprises compounds that facilitate plasticity, neurite growth and regeneration; molecules that overcome neurite outgrowth 51 inhibition or promote nerve growth; therapeutic molecules; diagnostic molecules or a combination of these.

17. A method of treating a central nervous system tissue comprising administering a mutant proteoglycan degrading polypeptide composition to the tissue, wherein the polypeptide is a deletion mutant comprising an amino acid sequence of chondroitinase AC SEQ ID NO: 5 truncated by a deletion up to 275 amino acids from the C-terminus of chondroitinase AC, and wherein the deletion mutant retains the proteoglycan degrading activity.

18. The method of claims 14-17, wherein the deletion mutant chondroitinase AC protein is selected from SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 11.

19. The method of claims 17 or 18, wherein the composition further comprises compounds that facilitate plasticity, neurite growth and regeneration; molecules that overcome neurite outgrowth inhibition or promote nerve growth; therapeutic molecules; diagnostic molecules or a combination of these.