# Patent

## Title
Proteoglycan degrading mutants for the treatment of CNS

## 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.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit and priority of U.S. Provisional Application Ser. No. 60/471,240, filed May 16, 2003; U.S. Provisional Application Ser. No. 60/471,239, filed May 16, 2003; U.S. Provisional Application Ser. No. 60/471,300, filed May 16, 2003; U.S. Provisional Application Ser. No. 60/474,372 filed May 16, 2003; and U.S. patent application entitled FUSION PROTEINS FOR TREATMENT OF CNS, filed cocurrently herewith on May 17, 2004, U.S. patent application Ser. No. 10/848,564 the contents of each of these references incorporated herein by reference in their entirety.


L. SEQUENCE LISTING
The file of this patent contains a Sequence Listing, identified as Seq. ID. Nos. 1-50. The Sequence Listing is contained in paper format (110 sheets) and in electronic format (2 CD-R 221KB). The CD-R formats can be identified as follows:
BACKGROUND AND SUMMARY
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.
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.
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.
P. vulgaris chondroitinase ABC I SEQ ID NO: 1 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: 1.
Chondroitinase ABC II, SEQ ID NO: 26, has also been isolated and purified from P. vulgaris, Chondroitinase ABC II, SEQ ID NO: 26, 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: 26, has an isoelectric point of 8.4-8.45. Its enzymatic activity is distinct from, but complementary to, that of chondroitinase ABC I SEQ ID NO: 1. Chondroitinase ABC I, SEQ ID NO: 1, 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: 26, digests at least one of these tetrasaccharide products from the chondroitinase ABC I (SEQ ID NO: 1) digestion of proteoglycan.
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.
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.
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.
The inventors have discovered through a deletion analysis based on the available crystal structures, the minimally sized polypeptides capable of degrading chondroitin sulfate 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 (nΔ50-cΔ275), (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 75 kDa 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 (nΔ120-cΔ120), (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 52 kDa 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.
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.
Polypeptide mutants of chondroitinase ABC Type I, SEQ ID NO: 1, Chondroitinase ABC Type II, SEQ ID NO: 26, 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: 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.
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 ABC Type I, SEQ ID NO: 1, Chondroitinase ABC Type II, SEQ ID NO: 26, 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. 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.
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 chondroitinase ABC Type I, SEQ ID NO: 1, Chondroitinase ABC Type II, SEQ ID NO: 26, 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 chondroitinases and or hyaluronidases; the composition may include one or more of the deletion and substitution mutants from different proteoglycan degrading polypeptides.
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 1-120 amino acids and/or the C-terminus, about 1-275 amino acids, more preferably the deletions are from a chondroitinase.
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.
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 therewith.
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.
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 therapeutic 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 therapeutics with lesser immunogenicity and similar or higher tissue penetration ability for the treatment of CNS injury.
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.
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.
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.



A BRIEF DESCRIPTION OF THE FIGURES
FIG. 1(A) shows Anti-His-tag Western Blot (top) and zymogram (bottom) demonstrating chondroitinase B deletion NΔ120 CΔ120 mutant (SEQ ID NO: 17) expression activity; FIG. 1(B) shows Anti-His-tag Western Blot (top) and zymogram (bottom) demonstrating chondroitinase AC deletion NΔ50 CΔ275 mutant (SEQ ID NO: 11) expression activity;
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;
FIG. 3(A) shows a schematic of deletion mutant polypeptides of chondroitinase AC (SEQ ID NO: 6-11); FIG. 3(B) shows confirmation of chondroitinase AC deletion mutants by Western blotting;
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;
FIG. 5 shows a schematic of deletion mutant polypeptides (SEQ ID NO: 13-17) of chondroitinase B (SEQ ID NO: 12);
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;
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
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.
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. 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.
“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.
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 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.
The mutants of the proteoglycan degrading molecules s can be used to treat mammalian CNS injuries, typically caused by trauma or disease. In particular, a deletion mutant of a proteoglycan degrading molecule like chondroitinase ABC Type I, (SEQ ID NO: 1), Chondroitinase ABC Type II, (SEQ ID NO: II), 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.
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 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/IU enzyme.
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.
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 NgR27-311, 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.
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.
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 controlled 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 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.
Native or wild-type P. vulgaris bacterial strains typically can be used to produce chondroitinases ABC I, (SEQ ID NO: 1), 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. Cloned chondroitinase ABC I, (SEQ ID NO: 22), chondroitinase ABC II, (SEQ ID NO: 26), and mutants of these genes in E. coli can be expressed using a heterologous expression system with an artificial inducer. Chondroitinase AC (SEQ ID NO: 22), and chondroitinase B (SEQ ID NO: 26), and their mutants may be cloned from F. heparinum and expressed in E. coli. 
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 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.
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.
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 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.
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 conformational 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.
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 polypeptides and nucleic acids having a sequence which differs from the 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.
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.
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.
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 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.
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.
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 intrathecal 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, 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 mammalian subject may be continued until a measurable improvement in autonomic or motor function in the patient is achieved.
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 B nucleic acid mutant (SEQ ID NO: 21) which encodes for mutant polypeptide NΔ120 CΔ120 of chondroitinase B (SEQ ID NO: 21) and chondroitinase AC nucleic acid mutant (SEQ ID NO: 19) which encodes for mutant polypeptide NΔ50 CΔ275 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: 23). Another example would be a nucleic acid for TAT-chondroitinase ABCI-NΔ60 SEQ ID NO: 37) and a peptide sequence for the expressed polypeptide (SEQ ID NO: 38).
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 ID 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 pattern. 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 enzymes. 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 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.
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 walking, 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.
A series of polynucleotides that include coding for deletion or substition mutants of proteoglycan 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-β-D-thiogalactopyranoside (IPTG), the bacteria can lysed by sonication with the concomitant extraction of the mutant polypeptide with a surfactant such as Triton X-114/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 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 −70° C. for long term storage. The pI of the purified basic proteoglycan degrading mutant polypeptide may be determined by IEF-PAGE analysis of the samples from the crude cell lysate.
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: 1) 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 production of reaction products from the degradation of proteoglycans. Size exclusion chromatography can be used to compare the hydrodynamic properties of the mutant enzymes.
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 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 zymogram. The zymography results are consistent with the spectrophotometric analysis.
HPLC methods may be used for detecting the four and six sulphated disaccharides (Δ4DS and Δ6DS, 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 Δ4DS and Δ6DS from chromatograms is expected to yield a linear relationship proportional to the amounts injected into the HPLC. Production of Δ4DS and Δ6DS 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 Δ4DS and Δ6DS 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.
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 chondroitinase ABC I (SEQ ID NO:1) 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.
Various aspects of the invention may be understood with reference to the following non-limiting examples.
EXAMPLE 1
This phrophetic example illustrates the diffusion of molecules into cells and tissue using a deletion or substitution mutant of a proteoglycan degrading polypeptide in a composition.
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 33 U/ml of a mutant proteoglycan degrading polypeptide such as (SEQ ID NO: 9) NΔ50 CΔ200 AC (T74-T500) 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
This prophetic example illustrates a Chondroitinase ABC I Assay Protocol which may be modified to measure the activity of a mutant proteoglycan degrading molecule, for example a Chondroitinase ABCI deletion mutant or a fusion proteins including a deletion and or substitution mutant of a proteoglycan degrading polypeptide.
The production of reaction products from the catalytic activity of a proteoglycan degrading molecule or fusion protein can be determined by a measurement of the absorbance of the proteoglycan degradation product at a wavelength of 232 nm. A typical reaction mixture consisted of 120 μl of reaction mixture (40 mM Tris, pH 8.0, 40 mM NaAcetate, 0.002% casein) combined with a substrate (5 μl of 50 mM chondroitin C (MW 521), chondroitin 6 SO4, or dermatan sulfate) and 1.5 μl of chondroitinase ABCI (SEQ ID NO:1) or a mutant of chondroitinase like (SEQ ID NO:2). Reaction mixture aliquots of about 120 μl 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 (μmoles of product formed per minute) using the molar absorption coefficient for the C4-C5 double bond formed in the reaction (3800 cm−1min−1).
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 μl 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 μmole/min/mg.
Chondroitinase ABC I (SEQ ID NO:1), 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 that mutants of proteoglycan degrading molecules, such as (SEQ ID NO: 11) NΔ50 CΔ275 AC (T74-T426) 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) NΔ50 CΔ275 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
This example shows that deletion mutants of chondroitinase are biologically active.
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 (nΔ50-cΔ275) (SEQ ID NO:11) lacking 50 and 275 amino acids from the amino and carboxy termini respectively having a molecular weight of 38 kDa compared to 75 kDa 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 (nΔ120-cΔ120) (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.
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-β-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. FIGS. 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.
Zymography assay. SDS-polyacrylamide gels were poured with aggrecan (85 μg/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 proteoglycans by the chondroitinases is visualized by staining the gel with 0.2% Toludene Blue in ethanol-H2O-acetic acid (50:49:1 v/v/v) for 30 minutes and destained with ethanol-H2O-acetlc acid (50:49:1 v/v/v). Following destaining the gel is incubated overnight in a 50 μg/ml solution of Stains-all in 50% ethanol in the dark and destained with H2O. 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
This example describes the linking of a His tag to a mutant proteoglycan degrading polypeptide.
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 were 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 expression.
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 for ILLUSTRATIVE PURPOSES ONLY in FIG. 7. In addition, deletion of 80 amino acids from the C-terminal end (SEQ ID NO:38) yields a mutant of chondroitinase ABC I which has proteoglycan degrading activity as tested in a zymography assay. As a potential alternative to the full-length chondroitinase ABC I, a deletion mutant such as ABCI-NΔ20-CΔ80 with a predicted molecular weight of 89 kDa can also be made (SEQ ID NO:39).
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 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 chondroitinase ABC I (SEQ ID NO:1) 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
This phrophetic example describes a mutant of chondroitinase ABC I that has native protein structure, but lacks proteoglycan degrading catalytic activity.
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.
EXAMPLE 6
This example illustrates examples of mutant proteoglycan degrading polypeptides that include both substitution and deletions from polypeptides of the present invention.
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), 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.
(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 NΔ20 (SEQ ID NO: 38), NΔ60 (SEQ ID NO: 39) and NΔ60 CΔ80 (SEQ ID NO: 40).
EXAMPLE 7
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.
A nucleotide sequence for TAT-chondroitinase ABCI-nΔ20 (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 acttctcatc agataaaaac tcaatactaa cgttatctga taaacgtagc






The underlined nucleotides in this portion of the nucleic acid sequence denote a TAT sequence attached to the 5′ of chondroitinase ABC I-NΔ20 nucleic acid (SEQ ID NO. 47).
An amino acid sequence for TAT-chondroitinase ABCI-nΔ20 (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-NΔ20 (SEQ ID NO. 2).








grkkrrqrrrppqcaqnnpladfssdknsiltlsdkrsimgnqsllwkwk



ggssftlhkklivptdkeaskawgrsstpvfsfwlynekpidgyltidfg


eklistseaqagfkvkldftgwrtvgvslnndlenremtlnatntssdgt


qdsigrslgakvdsirfkapsnvsqgeiy






A nucleotide sequence for TAT-ABCI-NΔ60 (SEQ ID NO. 43), a portion of which is illustrated below, shows the N-terminal TAT (SEQ ID NO. 49) nucleotides highlighted by underlining.








ggtcgtaaaaagcgtcgtcaacgtcgtcgtcctcctcaatgctttacttt



acataaaaaactgattgtccccaccgataaagaagcatctaaagcatggg


gacgctcatccacccccgttttctcattttggctttacaatgaaaaaccg


attgatggttatcttactatcgatttcgg...






Amino acid sequence for TAT-ABCI-nΔ60 (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-NΔ60 (SEQ ID NO. 3).








grkkrrqrrrppqcftlkkklivptdkeaskawgrsstpvfsfwlynekp



idgyltidfgeklistseaqagfkvkldftgwrtvgvslnndlenremtl


natntssdgtqdsigrslgakvdsirfkapsnvsqgeiyidrimfsvdda


ryqwsdyqvktrlseqeiqf...






Nucleotide sequence for ABCI-TAT-C (SEQ ID NO. 45), a portion of which is illustrated below, shows the C-terminal 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.








...gattaatggcaaatggcaatctgctgataaaaatagtgaagtgaaat



atcaggtttctggtgataacactgaactgacgtttacgagttactttggt


attccacaagaaatcaaactctcgccactccct ggtcgtaaaaagcgtc


gtcaacgtcgtcgtcctcctcaatgctag






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 at the C-terminus of the mature chondroitinase ABC I (SEQ ID NO. 1).








...aekvnvsrqhqvsaenknrqptegnfssawidhstrpkdasyeymvf



ldatpekmgemaqkfrennglyqvlrkdkdvhiildklsnvtgyafyqpa


siedkwikkvnkpaivmthrqkdtlivsavtpdlnmtrqkaatpvtinvt


ingkwqsadknsevkyqvsgdnteltftsyfgipqeiklsplpgrkkrrq


rrrppqc






EXAMPLE 8
This example illustrates the sequence of chondroitinase polypeptides which may be used for deletions or substitutions in mutants of 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


 



       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



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
TATCAAGGAATTCGTAGTGATAAAAAAATTACTCCAGATATGCTAGATAAACATTTAGCA



       670       680       690       700       710       720


 



       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
ACAGGACGTATTTTTGAAAAAGATAATGAAATTGTTGATGCAAATGTCGATATTCTCAAT



::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::


—
ACAGGACGTATTTTTGAAAGAGATAATGAAATTGTTGATGCAAATGTCGATATTCTCAAT



      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


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



::::::::::::::::::::::  ::::::::::::::::::::::::::::::::::::


—
ACCAAAGAGACACAAATTCCTGTGGTATTAAGTGGTCGTCAPCCAACTGGGTTGCATAAA



      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



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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      2380      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



::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::


—
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 at the nucleotide level resulted in 98.3% identity at the amino acid level and the substituted residues are marked in red 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










        10        20        30        40        50        60



457676
LPTLSHEAFGDIYLFEGELPNILTTSNNNQLSLSKQHAKDGEQSLKWQYQPQATLTLNNI



::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::


—
LPTLSHEAFGDIYLFEGELPNTLTTSNNNQLSLSKQHAKDGEQSLKWQYQPQATLTLNNI



        10        20        30        40        50        60


 



        70        80        90       100       110       120


457676
VNYQDDKNTATPLTFMMWIYNEKPQSSPLTLAFKQNNKIALSFNAELNFTGWRGIAVPFR



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
VNYQDDKNTATPLTFMMWIYNEKPQSSPLTLAFKQNNKIALSFNAELNFTGWRGIAVPFR



        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
WSALLMYDQMFQAHYPTLNFDTEFRDDQTEMASIYQRFEYYQGIRSDKKIPPDMLDKHLA



::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::


—
WSALLMYDQMFQAHYPTLNFDTEFRDDQTEMASRYQRFEYYQGIRSDKKIPPDMLDKHLA



       190       200       210       220       230       240


 



       250       260       270       280       290       300


457676
LWEKLGLTQHADGSITGKALDHPNRQHFMXVEGVFSEGTQKALLDANMLRDVGKTLLQTA



::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
LWEKLVLTQHADGSITGKALDHPNRQHFMKVEGVFSEGTQKALLDANMLRDVGKTLLQTA



       250       260       270       280       290       300


 



       310       320       330       340       350       360


457676
IYLRSDSLSATGRXKLEERYLLGTRYVLEQGFTRGSGYQIITHVGYQTRELFDAWFIGRH



::::::::::: :::::::::::::::::::: :::::::::::::::::::::::::::


—
IYLRSDSLSATDRKKLEERYLLGTRYVLEQGFHRGSGYQIISHVGYQTRELFDAWFIGRH



       310       320       330       340       350       360


 



       370       380       390       400       410       420


457676
VLAKNNLLAPTQQAMMWYNATGRIFEKDNEIVDANVDILNTQLQWMIKSLLMLPDYQQRQ



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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
LDTTLSAAYANLDNKTHFEGINAESEPVGAWANNYASMAIQRRASTQSPQQSWLAIARGF



::::::::::.::::::::::.::::::::::::::::::::::::::::::::::::::


—
LDTTLSAAYAKDNKTHFEGIKAESEPVGAWANNYASMAIQRRASTQSPQQSWLAIARGF



       550       560       570       580       590       600


 



       610       620       630       640       650       660


457676
SRYLVGNESYENNNRYGRYLQYGQLEIIPADLTQSGFSHAGWDWNRYPGTTTIHLPYNEL



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
SRYLVGNESYENNNRYGRYLQYGQLEIIPADLTQSGFSHAGWDWNRYPGTTTIHLPYNEL



       610       620       630       640       650       660


 



       670       680       690       700       710       720


457676
EAKLNQLPAAGIEEMLLSTESYSGANTLNNNSMFAMKLHGHSKYQQQSLRANKSYFLFDN



:::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::


—
EAKLNQLPAAGIEEMLLSTESYSGANTLNNNSMFAMKLHGPSKYQQQSLRANKSYFLFDN



       670       680       690       700       710       720


 



       730       740       750       760       770       780


457676
RVIALGSGIENDDKQHTTEPTLFQFAVPKLQSVIINGKKVNQLDTQLTLNNADTLIDPAG



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
RVIALGSGIENDDKQHTTETTLFQFAVPKLQSVIINGRKVNQLDTQLTLNNADTLIDPAG



       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



:::.::::::::: :::::::::::::.::::::::::::::::::::::::::::::::


—
KAPEYTVLQHNDQPHAVKDKITQEEGYAFFEATRLKSADATLLSSDAPVMVMAKIQNQQL



       850       860       870       880       890       900


 



       910       920       930       940       950       960


457676
TLSIVNPDLNLYQGREKDQFDDKGNQIEVSVYSRHWLTAESQSTNSTITVKGIWKLTTPQ



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
TLSIVNPDLNLYQGREKDQFDDKGNQIEVSVYSRHWLTAESQSTNSTITVKGIWKLTTPQ



       910       920       930       940       950       960


 



       970       980       990


457676
PGVIIKHHNNNTLITPTTIQATPTVINLVK



::::::::::::::::::::::::::::::


—
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


 



       130       140       150       160       170       180


806559
GATAAACGTAGCATTATGGGAAACCAATCTCTTTTATGGAAATGGAAAGGTGGTAGTAGC



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
GATAAACGTAGCATTATGGGAAACCAATCTCTTTTATGGAAATGGAAACGTGGTAGTAGC



       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


 



       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
AATATTAGCCGTGCTTATGTGCTGGAAAAAGATCCCACACAAAAGGCGCAACTAAAGCAG



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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



:::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
GTGACAACCCATCACTGGGGATACAGTTCTCGTTGGTGGTATATTTCCACGTTATTAATG



      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



      1270      1280      1290      1300      1310      1320


 



      1330      1340      1350      1360      1370      1380


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



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
GCGTGGATCTACAGTAATCCAGAAGTTGGATTACCGCTTGCAGGAAGACACCCTCTTAAC



      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



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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
AGCACTCGCCCCAAAGATGCCAGTTATGAGTATATCGTCTTTTTAGATGCGACACCTGAA



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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
ACTCGCCAAAAAGCAGCAACTCCTGTCACCATCAATGTCACGATTAATGGCAAATGGCAA



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
ACTCGCCAAAAAGCAGCAACTCCTGTCACCATCAATGTCACGATTAATGGCAAATGGCAA



      2830      2840      2850      2860      2870      2880


 



      2890      2900      2910      2920      2930      2940


806559
TCTGCTGATAAAAATAGTGAAGTGAAATATCAGGTTTCTGGTGATAACACTGAACTGACG



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
TCTGCTGATAAAAATAGTGAAGTGAAATATCAGGTTTCTGGTGATAACACTGAACTGACG



      2890      2900      2910      2920      2930      2940


 



      2950      2960      2970      2980      2990


806559
TTTACGAGATACTTTGGTATTCCACAAGAAATCAAACTCTCGCCACTCCCTTGA



::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
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










>_ ABCI Present invention
997 aa vs.



>_ ABCI mature
997 aa    


scoring matrix: gap penalties: −12/−2


99.5% identity;      Global alignment score: 6595










        10        20        30        40        50        60



365019
ATSNPAFDPKNLMQSEIYHFAQNNPLADFSSDKNSILTLSDKRSIMGNQSLLWKWKGGSS



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
ATSNPAFDPKNLMQSEIYHFAQNNPLADFSSDKNSILTLSDKRSIMGNQSLLWKWKGGSS



        10        20        30        40        50        60


 



        70        80        90       100       110       120


365019
FTLHKKLIVPTDKEASKAWGRSSTPVFSFWLYNEKPIDGYLTIDFGEKLISTSEAQAGFK



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
FTLHKKLIVPTDKEASKAWGRSSTPVFSFWLYNEKPIDGYLTIDFGEKLISTSEAQAGFK



        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
QGEIYIDRIMFSVDDARYQWSDYQVKTRLSEPEIQFHNVKPQLPVTPENLAAIDLIRQRL



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
QGEIYIDRIMFSVDDARYQWSOYQVKTRLSEPEIQFHNVKPQLPVTPENLAAIDLIRQRL



       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
QDKQLFDNYVILGNYTTLMFNISRAYVLEKDPTQKAQLKQMYLLMTKHLLDQGFVKGSAL



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
QDKQLFDNYVILGNYTTLMFNISRAYVLEKDPTQKAQLKQMYLLMTKHLLDQGFVKGSAL



       310       320       330       340       350       360


 



       370       380       390       400       410       420


365019
VTTHHWGYSSRWWYISTLLMSDALKEANLQTQVYDSLLWYSREFKSSFDMKVSADSSDLD



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
VTTHHWGYSSRWWYISTLLMSDALKEANLQTQVYDSLLWYSREFKSSFDMKVSADSSDLD



       370       380       390       400       410       420


 



       430       440       450       460       470       480


365019
YFNTLSRQHLALLLLEPDDQKRINLVNTFSHYITGALTQVPPGGKDGLRPDGTAWRHEGN



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
YFNTLSRQHLALLLLEPDDQKRINLVNTFSHYITGALTQVPPGGKDGLRPDGTAWRHEGN



       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
FNGGAFGIHRWQDKMVTLKAYNTNVWSSEIYNKDNRYGRYQSHGVAQIVSNGSQLSQGYQ



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
FNGGAFGIHRWQDKMVTLKAYNTNVWSSEIYNKDNRYGRYQSHGVAQIVSNGSQLSQGYQ



       610       620       630       640       650       660


 



       670       680       690       700       710       720


365019
QEGWDWNRMPGATTIHLPLKDLDSPKPHTLMQRGERGFSGTSSLEGQYGMMAFDLIYPAN



::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::


—
QEGWDWNRMQGATTIHLPLKDLDSPKPHTLMQRGERGFSGTSSLEGQYGMMAFDLIYPAN



       670       680       690       700       710       720


 



       730       740       750       760       770       780


365019
LERFDPNFTAKKSVLPADNHLIFIGSNINSSDKNKNVETTLFQHAITPTLNTLWINGQKI



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
LERFDPNFTAKKSVLAADNHLIFIGSNINSSDKNKNVETTLFQHAITPTLNTLWINGQKI



       730       740       750       760       770       780


 



       790       800       810       820       830       840


365019
ENMPYQTTLQQGDWLIDSNGNGYLITQAEKVNVSRQHQVSAENKNRQPTEGNFSSAWIDH



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
ENMPYQTTLQQGDWLIDSNGNGYLITQAEKVNVSRQHQVSAENKNRQPTEGNFSSAWIDH



       790       800       810       820       830       840


 



       850       860       870       880       890       900


365019
STRPKDASYEYMVFLDATPEKMGEMAQKFRENNGLYQVLRKDKDVHIILDKLSNVTGYAF



::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


—
STRPKDASYEYMVFLDATPEKMGEMAQKFRENNGLYQVLRKDKDVHIILDKLSNVTGYAF



       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






REFERENCES


    1. Fethiere 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 Y S, Linhardt R J, 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 R O, Yamagata S, Miura Y, Harada T and Yamagata T. (1995) Anal Biochem. 225:333-40.
    5. Yamagata T, Saito H, Habuchi O and Suzuki S. (1968) J Biol. Chem. 243:1536-42.


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

1. A composition comprising:
a mutant proteoglycan degrading polypeptide, said mutant proteoglycan degrading polypeptide being a deletion mutant of chondroitinase ABC Type I (SEQ ID NO: 1) truncated by a deletion of about 1 to about 120 amino acids from the N-terminus of said chondroitinase ABC Type I, wherein said deletion mutant retains its proteoglycan degrading activity, wherein the mutant proteoglycan degrading polypeptide is selected from SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4.

2. The composition of claim 1 wherein the mutant proteoglycan degrading polypeptide degrades a proteoglycan in a tissue of the central nervous system.

3. The composition of claim 1 further including cells.

4. The composition of claim 1 and a pharmaceutically acceptable excipient.

5. The composition of claim 1 further including molecules which block the action of neurite growth inhibitors, molecules which promote neurite adhesion, diagnostic molecules or a combination of these.

6. A purified chondroitinase mutant polypeptide that degrades a proteoglycan comprising a deletion mutant of chondroitinase ABC Type I (SEQ ID NO: 1) truncated by a deletion of about 1 to about 120 amino acids from the N-terminus of said chondroitinase ABC Type I, wherein said mutant proteoglycan degrading polypeptide is selected from SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO:4.

7. A purified chondroitinase mutant polypeptide that degrades a proteoglycan comprising a deletion mutant of chondroitinase ABC Type I (SEQ ID NO: 1) truncated by a deletion of about 1 to about 275 amino acids from the C-terminus of chondroitinase ABC Type I, wherein said mutant proteoglycan degrading polypeptide is SEQ ID NO: 4.

8. A composition comprising:
a mutant proteoglycan degrading polypeptide, said mutant proteoglycan degrading polypeptide being a deletion mutant of chondroitinase ABC Type I SEQ ID NO:1 truncated by a deletion of about 1 to about 275 amino acids from the C-terminus of said chondroitinase ABC Type I, wherein said mutant retains its proteoglycan degrading activity, wherein the mutant proteoglycan degrading polypeptide is SEQ ID NO: 4.

9. The composition of claim 8, wherein the mutant proteoglycan degrading polypeptide degrades a proteoglycan in a tissue of the central nervous system.

10. The composition of claim 8 further including cells.

11. The composition of claim 8 and a pharmaceutically acceptable excipient.

12. The composition of claim 8 further including molecules which block the action of neurite growth inhibitors, molecules which promote neurite adhesion, diagnostic molecules or a combination of these.