# Patent

## Title
Method for purifying protein

## Abstract

The present invention provides a method for purifying a protein, includes the step of: contacting a fusion protein of a first protein and a second protein with a bivalent cation-containing solution, the fusion protein being adsorbed to a silicon oxide-containing substance, the first protein being capable of binding to the silicon oxide-containing substance in a solution containing 0.1M sodium chloride. With this arrangement, it is possible to easily produce large quantity of proteins which are high in purity without sacrificing activity of the proteins.

## Background
This Nonprovisional application claims priority under 35 U.S.C. §119(a) on Patent Application No. 2008-198819 filed in Japan on Jul. 31, 2008, the entire contents of which are hereby incorporated by reference.
TECHNICAL FIELD
The present invention relates to a method for purifying a protein. More specifically, the present invention relates to an affinity purification method using molecules which can be adsorbed to a silicon oxide-containing substance.
BACKGROUND ART
A protein is one of main substances constituting an organism, and has been widely used as a medical product, a medical material or the like. Conventionally, a protein to be used has been obtained by various methods (e.g. purification of a protein from a natural material). In recent years, a method for forcibly expressing a target protein in various kinds of cells has been used, and such protein has been used in various ways. However, such a conventional method undesirably requires complicated steps to purify a desired protein from a cell. Further, a great amount of protein is required in some applications. However, such a classical method unfortunately cannot produce a large amount of protein.
Various methods have been developed which allow easy purification of proteins which are forcibly expressed in various kinds of cells. Examples of such methods include a method in which a fusion protein having a tag of various kinds attached thereto are forcibly expressed in various kinds of cells, respectively, and then the fusion proteins are purified by adsorption between the tag and a carrier having affinity with the tag. Until now, various kinds of tags have been developed. Examples of such tags include a GST protein, an HA tag, a Flag tag, a Myc tag, and a His tag.
Citation List
Patent Literature 1
WO2007/055288 Pamphlet (Publication Date: May 18, 2007)
Non-Patent Literature 1
Taniguchi, K. et al., The Si-tag for immobilizing proteins on a silica surface. Biotechnol. Bioeng. 96: 1023-1029 (2007)
Non-Patent Literature 2
Fuchs, S. M. and Raines, R. T. Polyarginine as a multifunctional fusion tag. Protein. Sci. 14: 1538-1544 (2005)
Currently, functional analysis of various kinds of proteins is in progress, and such tags are used in examining interaction between plural proteins. Since the analysis needs to be conducted from many different perspectives, wider variety of tags used for protein purification are better.
SUMMARY OF INVENTION
The present invention was attained in view of the above problems, and an object of the present invention is to find tags available for protein purification and to provide a novel method for purifying a protein.
The inventors of the present invention have studied on a technique for causing proteins to be adsorbed onto a surface of a silicon oxide-based board, and have found that there exist proteins each of which specifically binds to a silicon oxide-containing substance (see Patent Literature 1 and Non-Patent Literature 1, for example). Further, it is reported that a protein having nine arginine residues (polyarginine tags) attached thereto can be directly adsorbed to a surface of glass or a silica resin without losing an enzymatic activity thereof (see Non-Patent Literature 2, for example). These techniques have an advantage of capable of causing a protein to be tightly adsorbed onto a board. However, these techniques require use of strong acid or strong base in order to dissociate the protein from the silicon oxide-containing substance so that the board can be reused. The protein thus dissociated could not be reused. This means that these techniques cannot be used as a protein collecting technique.
Based on a unique viewpoint, the inventors of the present invention has examined whether a protein which is adsorbed to a silicon oxide-containing substance can be dissociated from the silicon oxide-containing substance with the use of a cation solution or an anion solution. However, even a NaCl solution, which is often used in column chromatography, having the highest concentration could not dissociate a protein from a silicon oxide-containing substance to which the protein is adsorbed. However, as a result of diligent studies based on their unique viewpoint, the inventors of the present invention found that a protein adsorbed to a silicon oxide-containing substance can be dissociated from the silicon oxide-containing substance with the use of a bivalent cation-containing solution. Based on this finding, the present invention was attained.
A method for purifying a protein of the present invention, includes the step of: contacting a fusion protein of a first protein and a second protein with a bivalent cation-containing solution, the fusion protein being adsorbed to a silicon oxide-containing substance, the first protein being capable of binding to the silicon oxide-containing substance in a solution containing 0.1M sodium chloride.
It is preferable that the method for purifying a protein of the present invention, further includes the step of: adsorbing the fusion protein to the silicon oxide-containing substance.
It is preferable that the method for purifying a protein of the present invention, further includes the step of: expressing the fusion protein in a transformant.
It is preferable that the method for purifying a protein of the present invention, further includes the step of: causing second DNA encoding the second protein to be linked in-frame with first DNA encoding the first protein.
In the method for purifying a protein of the present invention, it is preferable that the bivalent cation-containing solution is a MgCl2 solution, a CaCl2 solution or a NiCl2 solution.
In the method for purifying a protein of the present invention, it is preferable that the bivalent cation-containing solution is 0.2M or more in bivalent cation concentration.
In the method for purifying a protein of the present invention, it is preferable that the first protein is a polypeptide selected from: (a) polypeptide with the amino acid sequence represented by SEQ ID NO: 1, and (b) polypeptide with an amino acid sequence in which one or several amino acids are substituted, deleted, inserted, and/or added in the amino acid sequence represented by SEQ ID NO: 1.
In the method for purifying a protein of the present invention, it is preferable that the first protein is a polypeptide selected from: (c) polypeptide with the amino acid sequence represented by SEQ ID NO: 45, 47 or 49, and (d) polypeptide with the amino acid sequence in which one or several amino acids are substituted, deleted, inserted, and/or added in an amino acid sequence represented by SEQ ID NO: 45, 47 or 49.
A method for purifying a protein of the present invention, includes the step of: contacting a protein adsorbed to a silicon oxide-containing substance with a bivalent cation-containing solution, the protein being capable of binding to the silicon oxide-containing substance in a solution containing 0.1M sodium chloride.
In the method for purifying a protein of the present invention, it is preferable that the protein has a second protein fused therewith.
A kit for protein purification of the present invention, includes an expression vector having first DNA encoding a first protein, and an insertion site in which second DNA encoding a second protein is linked in-frame with the first DNA, the first protein being capable of binding to a silicon oxide-containing substance in a solution containing 0.1M sodium chloride.
It is preferable that the kit for protein purification of the present invention, further includes silica particles or a silica board.
It is preferable that the kit for protein purification of the present invention, further includes a bivalent cation-containing solution.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1
FIG. 1 is an electrophoretogram showing how tightly a silica binding tag and a silica binding tag fusion protein A bind to silica.
FIG. 2
FIG. 2 is an electrophoretogram showing how tightly a modified silica binding tag binds to silica.
FIG. 3
FIG. 3 is an electrophoretogram of silica binding tags purified with a silica packed column.
FIG. 4
FIG. 4 is an electrophoretogram of silica binding tags dissociated from silica particles with the use of various kinds of elution solutions.
FIG. 5
FIG. 5 is an electrophoretogram of silica binding tags dissociated from silica particles with a MgCl2 solution of various concentrations.
FIG. 6
FIG. 6 is an electrophoretogram of silica binding tags dissociated from silica particles with the use of various kinds of bivalent cations.
FIG. 7
FIG. 7 is an electrophoretogram for comparison between (i) purification efficiency obtained in a case where a silica binding tag fusion protein A was purified with the use of a His tag and (ii) purification efficiency obtained in a case where a silica binding tag fusion protein A was purified with the use of a silica binding tag.



DESCRIPTION OF EMBODIMENTS
The inventors of the present invention have found proteins each of which specifically binds to a silicon oxide-containing substance (see Patent Literature 1). Another protein (second protein) can be immobilized, via such a protein (first protein), on a surface of a silicon oxide-containing substance without being altered in structure and function. This time, the inventors of the present invention found a method for dissociating a protein from the silicon oxide-containing substance without damaging the structure and function of the second protein.
The term “first protein”, i. e., “protein which specifically binds to a silicon oxide-containing substance” used herein refers to any “protein capable of binding to a silicon oxide-containing substance in a solution containing 0.1M sodium chloride”. Further, such a protein can be derived from any organism such as bacteria, yeast, plant, or animal. For convenience of explanation, the first protein is referred to also as “SBP” (abbreviation of silicon material binding protein).
The term “silicon oxide-containing substance” used herein refers to any substance which includes oxygen (O) and silicon (S). Since elements other than oxygen and silicon are not limited to specific ones, the “silicon oxide-containing substance” may be “a substance constituted only by oxygen and silicon” or may be “a substance constituted by oxygen, silicon, and other elements”. The “silicon oxide-containing substance” may be, for example, silicon dioxide (silica), glass, asbestos, quartz, crystal, silica sand, amphibole, pyroxene, mica, talc, or feldspar. The “silicon oxide-containing substance” includes an organic silicon oxide-containing substance (e.g. silicone).
The first protein used in the present invention can be any protein capable of binding to a silicon oxide-containing substance in a solution containing 0.1M sodium chloride. For example, the first protein can be obtained by adding a silicon oxide-containing substance to a protein solution (i.e. a solution containing at least one type of protein), collecting the silicon oxide-containing substance, washing the silicon oxide-containing substance in a solution containing 0.1M sodium chloride, and then isolating the protein binding to the silicon oxide-containing substance even after the washing.
A protein solution to be used can be, for example, a cell lysate, random peptide library derived from phage library, or synthesized peptide library, but is not limited to these. The protein solution can contain substances other than a protein. The protein solution may be prepared by a known method that is appropriately selected according to a material as used. For example, the cell lysate can be prepared by a method of physically disrupting cells by means of a homogenizer, ultrasonic waves, or the like, a method of disrupting cells by using an enzyme or a surface activating agent, a method of disrupting cells by a combined use of enzyme or a surface activating agent, and a physical method, or other methods.
The silicon oxide-containing substance to be added is not limited to a specific one. For example, the inventors of the present invention added 10 mg silicon powder or 5 mg asbestos (chrysotile) to a 1 ml cell lysate derived from bacteria (see Patent Literature 1). Further, the inventors of the present invention added 5 mg asbestos (chrysotile) to a 0.6 ml cell lysate derived from a mouse lung (see Patent Literature 1).
After the addition of the silicon oxide-containing substance to the protein solution, it is preferable to sufficiently mix a mixture solution of the protein and the silicon oxide-containing substance. Conditions under which the mixture solution is mixed are not limited to specific ones. For example, the mixture solution is mixed by inversion at 4° C. for 15 to 30 minutes.
The silicon oxide-containing substance can be collected by subjecting the mixture solution to centrifugation at such revolutions that allow only the silicon oxide-containing substance to precipitate, and then removing a supernatant from the mixture solution. Alternatively, the silicon oxide-containing substance can be collected by filtering the mixture solution through a filter having an appropriate pore size. However, a method for collecting the silicon oxide-containing substance is not limited to these. The collection of the silicon oxide-containing substance makes it possible to remove proteins which do not bind to the silicon oxide-containing substance.
The silicon oxide-containing substance is washed in order to remove proteins which non-specifically bind to the silicon oxide-containing substance. For example, the silicon oxide-containing substance can be washed by a method of adding a solution containing 0.1M sodium chloride to the silicon oxide-containing substance thus collected, sufficiently mixing the solution thus obtained by a method such as pipetting, and then subjecting the solution to centrifugation or filtering the solution as in the above case. Repeating this operation several times enhances a washing effect. Further, in a case where the protein solution is prepared with the use of the solution containing 0.1M sodium chloride used for washing, the washing effect (effect of removing non-specific binding) can be enhanced.
A washing solution which contains 0.1M sodium chloride can be any solution which contains 0.1M sodium chloride, and therefore is not limited to a specific one. However, the washing solution is preferably a buffer solution whose pH is around neutral. Note that the term “solution containing 0.1M sodium chloride” is intended to exclude a sodium chloride concentration of below 0.1M at which many proteins non-specifically bind to the silicon oxide-containing substance. A solution containing at least 0.1M sodium chloride is included in the “solution containing 0.1M sodium chloride”.
The first protein used in the present invention can be any protein capable of binding to a silicon oxide-containing substance in a solution containing 0.1M sodium chloride. However, in a case where a sodium chloride concentration in the solution is high, it is possible to obtain a protein which more specifically binds to a silicon oxide-containing substance. For example, in order to obtain a protein which specifically binds to silica, it is preferable to use a solution containing 0.2M sodium chloride, it is more preferable to use a solution containing 0.5M sodium chloride, and it is further more preferable to use a solution containing 1M sodium chloride. For example, in order to obtain a protein which specifically binds to asbestos, it is preferable to use a solution containing 0.2M sodium chloride, and it is more preferable to use a solution containing 0.3M sodium chloride. Further, it is possible to obtain a protein which exhibits high binding specificity by adding a surface activating agent to the washing solution.
In order to obtain a bacteria-derived protein which specifically binds to silica, the inventors of the present invention used, as a washing buffer solution, 25 mM Tris-HCl buffer solution (pH 7.5) containing 1M sodium chloride and 0.5% polyoxyethylene sorbitan monolaurate (Product Name: Tween 20 (registered trademark)). Further, in order to obtain a bacteria-derived protein which specifically binds to asbestos, the inventors of the present invention used, as a washing buffering solution, 25 mM Tris-HCl buffer solution (pH 7.5) containing 0.1M sodium chloride and 0.5% polyoxyethylene sorbitan monolaurate (Product Name: Tween 20 (registered trademark)) (see Examples).
A method for isolating a protein specifically binding to a silicon oxide-containing substance from the silicon oxide-containing substance can be, for example, a method of using a surface activating agent such as dodecyl sodium salfate, a method of lowering pH, or a method of increasing a sodium chloride concentration in the solution (increasing a sodium chloride concentration to a concentration of approximately 2M), but is not limited to these. The inventors of the present invention used a solution containing 1% dodecyl sodium salfate and 2% mercaptoethanol (see Examples).
The first protein thus obtained can be identified by a known method. For example, a protein isolated from a silicon oxide-containing substance as above is separated by polyacrylamide gel electrophoresis, and is transferred on a polyvinylidene fluoride (PVDF) film. The film is stained with coomassie brilliant blue, and then a band of a target protein is cut out. A triptic digest of the band thus cut out is analyzed with the use of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOFMS), and the target protein can be identified by peptide mass fingerprint analysis. As a result, it is possible to obtain an amino acid sequence of the target protein from a known protein database. Moreover, for example, it is possible to determine an amino acid sequence with the use of an automatic peptide sequencer.
Determination of an amino acid sequence makes it possible to obtain a base sequence of a gene encoding the target protein from a known gene database, for example. Moreover, a DNA fragment encoding the target protein is cloned with a primer or a probe designed on the basis of the amino acid sequence of the target protein. Thus, it is possible to determine a base sequence with the use of a DNA sequencer.
The first protein which can be suitably used in the present invention can be a protein having the amino acid sequence represented by SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 41, or 43. The inventors of the present invention identified each of these proteins as the first protein. The inventors of the present invention found out for the first time that each of these proteins, which are all known proteins, is capable of specifically binding to a silicon-oxide containing substance.
Among these eighteen proteins, a protein having the amino acid sequence represented by SEQ ID NO: 1, 3, 5, 7, 9, or 11 is a protein identified by the inventors of the present invention as a protein which specifically binds to silica, and a protein having the amino acid sequence represented by SEQ ID NO: 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 41 or 43 is a protein identified by the inventors of the present invention as a protein which specifically binds to asbestos.
Further, a protein which (i) has the amino acid sequence having deletion, substitution, or addition of one or several amino acids in the amino acid sequence represented by SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 41, or 43 and (ii) is capable of binding to a silicon oxide-containing substance in a solution containing 0.1M sodium chloride can be suitably used in the present invention. The meaning of the wording “deletion, substitution, or addition of one or several amino acids” is described later.
The first protein used in the present invention can be produced by subjecting a cell serving as a supply source of the first protein to incubation which is followed by isolating and purifying processes. Further, the first protein can be produced by establishing a recombinant expression vector by a known genetic engineering method and by incorporating the recombinant expression vector into a suitable host cell so that it is expressed as a recombinant protein.
The present invention is described below with reference to an embodiment in which silica is used as a silicon oxide-containing substance and a ribosomal protein L2 is used as the first protein (a protein which specifically binds to a silicon oxide-containing substance). A person skilled in the art will easily understand that the present invention is not limited to this embodiment. All of the academic literatures and patent literatures mentioned in this specification are hereby incorporated by reference.
A protein purifying method of the present embodiment includes the step of dissociating a fusion protein of a ribosomal protein L2 and a second protein from silica with the use of a bivalent cation-containing solution. That is, according to the protein purifying method of the present embodiment, the ribosomal protein L2 is specifically dissociated from silica with the use of a bivalent cation in order to purify a target fusion protein.
The ribosomal protein L2 is a protein that was found by the inventors of the present invention to specifically bind to silica (silicon dioxide, SiO2). The term “protein” used herein is interchangeable with “polypeptide” or “peptide”. The term “protein” includes a fragment of a protein. Further, the term “protein” includes a fusion protein. The term “fusion protein” is a protein in which fragments or whole of two or more heteroproteins are fused.
The ribosomal protein L2 may be derived from any organism such as bacteria, yeast, plant, or animal, or may be artificially synthesized. Specifically, the ribosomal protein L2 may be selected from:
(a) polypeptide having the amino acid sequence represented by SEQ ID NO: 1, and
(b) polypeptide having the amino acid sequence in which one or several amino acids are substituted, deleted, inserted, and/or added in the amino acid sequence represented by SEQ ID NO: 1.
Alternatively, the ribosomal protein L2 may be selected from:
(c) polypeptide having the amino acid sequence represented by SEQ ID NO: 45, 47, or 49;
(d) polypeptide having the amino acid sequence one or several amino acids are substituted, deleted, inserted, and/or added in the amino acid sequence represented by SEQ ID NO: 45, 47 or 49.
Note that the polypeptide having the amino acid sequence represented by SEQ ID NO: 1 corresponds to an entire length of the ribosomal protein L2, and the polypeptide having the amino acid sequence represented by SEQ ID NO: 45 or 47 corresponds to a section of the ribosomal protein L2 which is necessary for adsorption to silica (corresponds to positions 1 through 60 or positions 204 through 273 of the amino acid sequence represented by SEQ ID NO: 1). A protein having the section corresponding to positions 1 through 60 or positions 204 through 273 in the amino acid sequence represented by SEQ ID NO: 1 can continue to be adsorbed to silica. That is, a ribosomal protein L2 which can be used in the present invention is a fragment of polypeptide having the amino acid sequence represented by SEQ ID NO: 1. The fragment is a protein including positions 1 through 60 or positions 204 through 273 in the amino acid sequence represented by SEQ ID NO: 1. Alternatively, the ribosomal protein L2 which can be used in the present invention may be fusion polypeptide of (i) polypeptide including positions 1 through 60 of the amino acid sequence represented by SEQ ID NO: 1 and (ii) polypeptide including positions 204 through 273 of the amino acid sequence represented by SEQ ID NO: 1 (that is, the ribosomal protein L2 may be polypeptide having the amino acid sequence represented by SEQ ID NO. 49). In this specification, the ribosomal protein L2 which can be used in the present invention indicates polypeptide capable of specifically binding to silica, and is referred to also as “silica binding tag”. Further, the wording “binding” can be used instead of “adsorption” of a protein to silica.
The wording “one or several amino acids are substituted, deleted, inserted, and/or added” means that amino acids as many as can be substituted, deleted, inserted, and/or added by a known mutant peptide producing method such as a site-specific mutagenesis (preferably not more than 10, more preferably not more than 7, and further preferably not more than 5). Such a mutant protein is not limited to a protein that is artificially mutated by a known mutant polypeptide producing method, and therefore may be obtained by isolating and purifying a naturally existing protein.
It is well known in the art that some amino acids in an amino acid sequence of a protein can be easily modified without significantly affecting a structure or a function of the protein. It is also known in the art that mutation occurs not only in an artificially modified protein, but also in a naturally existing protein without causing a significant change in structure and function of the protein. The mutation preferably includes substitution, deletion, insertion, and/or addition of amino acid which is conservative or non-conservative. Silent substitution, addition, and deletion are preferable, and conservative substitution is particularly preferable.
Typical examples of conservative substitution include substitution of one of aliphatic amino acids Ala, Val, Leu, and Ile with another amino acid, exchange of hydroxyl residues Ser and Thr, exchange of acidic residues Asp and Glu, substitution between amide residues Asn and Gln, exchange of basic residues Lys and Arg, and substitution between aromatic residues Phe and Tyr.
The term “second protein” used herein mainly refers to a protein to be purified, and is used interchangeably with “target protein”. An arrangement of the second protein is not limited to a specific one, and therefore a desired protein can be used as the second protein.
Next, a method for fusing together a ribosomal protein L2 and a second protein is described.
The method for fusing together a ribosomal protein L2 and a second protein may be any method which enables strong fusion between the ribosomal protein L2 and the second protein, and is therefore not limited to a specific one. The ribosomal protein L2 and the second protein can be fused together in any bonding manners such as covalent bond, hydrophobic bond, ion bond, hydrogen bond, and a combination of these. The covalent bond is preferably used since it can produce stronger fusion between the ribosomal protein L2 and the second protein.
For example, a ribosomal protein L2 and a second protein may be fused together with the use of a cross-linking agent. Such a cross-linking agent is not limited to a specific one, and therefore can be any known cross-linking agent. For example, such a cross-linking agent preferably is dimethyl suberoimidate dihydrochloride (DMS), suberic acid di-N-hydroxysuccinimide ester (DSS), tartaric acid N-hydroxydisuccinimide ester (DST), p-phenylene bismaleimide (pPDM), methyl 4-mercaptobutylimidate hydrochloride (MBI), or methyl 4-azidebenzoimidate hydrochloride (ABI), but is not limited to these. With this arrangement, it is possible to realize strong fusion between a ribosomal protein L2 and a second protein. It is preferable to adopt this arrangement especially in a case where both of ribosomal protein L2 and second protein are easily obtainable proteins. A method for fusing together a ribosomal protein L2 and a second protein with the use of a cross-linking agent can be a known method appropriately selected in accordance with the type of the cross-linking agent.
Alternatively, fusion between a ribosomal protein L2 and a second protein can be carried out by causing both of the ribosomal protein L2 and the second protein to be expressed as a fusion protein with the use of an expression vector. With this arrangement, it is possible to easily produce a fusion protein in which the ribosomal protein L2 and the second protein are fused. As a result, it is possible to easily purify wide variety of proteins in large amount.
An arrangement of the expression vector is not limited to a specific one, provided that it includes a base sequence encoding a fusion protein of a ribosomal protein L2 and a second protein. The expression vector may be any vector which can express a fusion protein in a host. For example, the expression vector can be produced by using plasmid, phage, or cosmid.
The expression vector has a tag sequence encoding a ribosomal protein L2 in a base sequence encoding a fusion protein. The tag sequence may be:
(e) polynucleotide having the base sequence represented by SEQ ID NO: 2, or
(f) polynucleotide which hybridizes the base sequence represented by SEQ ID NO: 2 or a base sequence that is complementary to the base sequence represented by SEQ ID NO: 2 under a stringent condition.
The expression vector has a tag sequence encoding a ribosomal protein L2 in a base sequence encoding a fusion protein. The tag sequence may be:
(g) polynucleotide having the base sequence represented by SEQ ID NO: 46, 48, or 50, or
(h) polynucleotide which hybridizes the base sequence represented by SEQ ID NO: 46, 48, or 50 or a base sequence that is complementary to the base sequence represented by SEQ ID NO: 2 under a stringent condition.
Note that the polynucleotide having the base sequence represented by SEQ ID NO: 2 corresponds to an entire length of the ribosomal protein L2, and the polynucleotide having the base sequence represented by SEQ ID NO: 46 or 48 corresponds to a section of the ribosomal protein L2 which is necessary for adsorption to silica (corresponds to positions 1 through 60 or positions 204 through 273 of the amino acid sequence represented by SEQ ID No: 1). Further, polynucleotide having the base sequence represented by SEQ ID NO: 50 corresponds to fusion polypeptide of (i) the section of the ribosomal protein L2 (positions 1 through 60 of the amino acid sequence represented by SEQ ID NO: 1) and the section of the ribosomal protein L2 (positions 204 through 273 of the amino acid sequence represented by SEQ ID NO: 1).
The wording “stringent condition” means that hybridization will occur only if there is at least 90%, preferably 95%, or most preferably 97% identity between the sequences.
The hybridization can be carried out by a known method such as a method described in “Molecular Cloning: A Laboratory Manual 3rd Edition, J. Sambrook and D. W. Russell, Cold Spring Harbor Laboratory, NY (2001)”. In general, the higher the temperature becomes, or the lower the salt concentration becomes, the higher the stringency becomes (the more difficult the hybridization becomes) so that more homologous polynucleotide can be obtained.
A promoter appropriate for a host is selected and is inserted in an expression vector, and a base sequence encoding a fusion protein is inserted at a downstream of the promoter.
The expression vector preferably contains an expression control region (e.g., promoter, terminator, and/or replication origin) depending on the type of a host to be introduced. For example, a conventional promoter (e.g., trc promoter, tac promoter, lac promoter) is preferably used as a promoter of an expression vector for bacteria. For example, a glyceraldehyde 3-phosphate dehydrogenase promoter or a PH05 promoter is preferably used as a promoter of an expression vector for yeast. For example, an amylase promoter or a trpC promoter is preferably used as a promoter of an expression vector for filamentous fungi. A viral promoter (e.g., SV40 early promoter, SV40 late promoter) is preferably used as a promoter of an expression vector for animal cells.
An expression vector can be produced by a conventional method using restriction enzyme and/or ligase. Moreover, transformation of a host by an expression vector can be carried out by a conventional method.
The expression vector preferably includes at least one selective marker. Such a selective marker is not limited to a specific one. However, in a case where an eukaryotic cell is used as a host, dihydrofolate reductase or neomycin resistant gene is preferably used as such a selective marker. Further, in a case where E. coli or other bacteria is used as a host, tetracycline resistance gene or ampicilin resistant gene is preferably used as such a selective marker.
The selective marker is used to confirm whether the expression vector has been introduced in a host, and whether a fusion protein has been expressed in a host.
Such a host is not limited to a specific one. For example, the following conventionally known cells can be used: bacteria such as Escherichia coli, yeast (budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe)), nematode (Caenorhabditis elegans), oocyte of an African clawed frog (Xenopus laevis), animal cells (e.g., CHO cell, COS cell, NIH3T3 cell, Bowes melanoma).
A method for introducing an expression vector into a host, namely a method for transforming a host is not limited to a specific one. A conventionally known method such as electroporation, calcium phosphate method, liposome method, or DEAE dextran method can be suitably used as such a method.
A ribosomal protein L2 can be fused with a second protein at any position. For example, the ribosomal protein L2 can be fused with an amino acid at the N terminal of the second protein, an amino acid at the C terminal of the second protein, or amino acids between the N terminal and the C terminal. In a case where the aforementioned expression vector is used, the ribosomal protein L2 is preferably fused with the N terminal or C terminal of the second protein. With this arrangement, it is possible to simplify a structure of the expression vector and to easily insert various kinds of base sequences encoding various kinds of second proteins into the expression vector.
The second protein thus fused with the ribosomal protein L2 is firmly adsorbed to silica (silicon dioxide, SiO2). Silica to which a protein is adsorbed is not limited to a specific form. For example, the silica preferably has a particle shape or a board shape. Note that it is unnecessary that the whole of the particle or the board is made of silica, but it is only necessary that at least a part of the particle or the board is made of silica. For example, in a case where a column is formed with the use of particle-shaped silica, it is possible to more easily purify the second protein. Moreover, use of the particle-shaped silica makes it possible to easily obtain a second protein adsorbed to silica by centrifugation. Further, use of board-shaped silica not only makes it possible to purify a protein, but also makes it possible to easily produce various kinds of boards on which proteins are immobilized (e.g. semiconductor substrate in which a silicon substrate is used).
A way in which a fusion protein of a ribosomal protein L2 and a second protein is adsorbed to silica is not limited to a specific one. For example, adsorption of the fusion protein to silica is preferably accomplished by mixing the fusion protein and silica in a solution.
Such a solution is not limited to a specific one, but for example, preferably is a NaCl solution with high concentration. Concentration of NaCl in the solution is not limited to a specific one, but for example, preferably is 0.5M to 5M, more preferably is 0.5M to 2.5M, most preferably is 1M to 2M. Since, according to this arrangement, a fusion protein is fused with silica under extremely high NaCl concentration, it is possible to prevent substances other than the fusion protein from binding to silica. In other words, with this arrangement, it is possible to purify a fusion protein to high purity.
Such a solution preferably contains a surface activating agent. The surface activating agent is not limited to a specific one, but preferably is polyoxyethylene sorbitan monolaurate, dodecyl sodium sulfate, cholic acid, or deoxycholic acid. With this arrangement, it is possible to purify a fusion protein of a ribosomal protein L2 and a second protein to higher purity.
A protein purifying method of the present embodiment includes the step of dissociating a fusion protein of a ribosomal protein L2 and a second protein from silica with the use of a bivalent cation-containing solution.
The bivalent cation-containing solution is not limited to a specific one, but preferably is a MgCl2 solution, a CaCl2 solution, or NiCl2 solution, further preferably is a MgCl2 solution or a CaCl2 solution, and most preferably is a MgCl2 solution, for example. With this arrangement, it is possible to specifically dissociate a fusion protein of a ribosomal protein L2 and a second protein from silica.
Concentration of bivalent cation in the bivalent cation-containing solution is not limited to a specific one, but preferably is 0.2M or more, further preferably is 1M or more, and most preferably is 2M or more, for example. With this arrangement, it is possible to more effectively dissociate a fusion protein of a ribosomal protein L2 and a second protein from silica.
The step of dissociating a fusion protein from silica may be carried out, for example, by centrifugation or a column method. As for the centrifugation, for example, silica to which a fusion protein is adsorbed is dispersed in a bivalent cation-containing solution. Next, the solution in which silica is dispersed is subjected to centrifugation, so that the fusion protein dissociated from silica can be obtained in a supernatant. As for the column method, a column is filled with silica to which a fusion protein is adsorbed. The fusion protein is eluted from the column with the use of a bivalent cation-containing solution.
In this way, a fusion protein dissociated from silica can be easily obtained.
A fusion protein dissociated from silica contains bivalent cation (e.g. MgCl2) in high concentration. In view of this, the protein purifying method of the present embodiment preferably includes the step of removing the bivalent cation in accordance with the intended use. The bivalent cation may be removed by any method. However, for example, the bivalent cation is preferably removed by dialysis. With this arrangement, it is possible to more highly purify a protein.
Moreover, the protein purifying method of the present embodiment preferably includes, before the dissociating step, the step of washing silica so that a fusion protein of a ribosomal protein L2 and a second protein is not dissociated from silica. The step of washing silica is not limited to a specific one. However, for example, the washing of silica is preferably carried out with the use of a highly-concentrated NaCl solution. Concentration of NaCl in the solution is not limited in particular, but preferably is 0.5M to 5M, more preferably is 2M to 5M, and most preferably is 2M. With this arrangement, it is possible to effectively remove substances other than the second protein which is adsorbed to silica. In other words, with this arrangement, it is possible to highly purify a protein.
The solution preferably contains a surface activating agent. The surface activating agent is not limited to a specific one, but preferably is polyoxyethylene sorbitan monolaurate, dodecyl sodium sulfate, cholic acid, or deoxycholic acid. With this arrangement, it is possible to more highly purify a protein.
As described above, the present invention provides a novel protein purifying method.
The present invention makes it possible to highly purify a large amount of proteins capable of binding to silica. As such, the present invention can be applied to a wide variety of field such as manufacture of a protein chip, a nano-biodevice, or a medical product. Since a protein produced by the method of the present invention is capable of binding to silica, the present invention can be applied especially to manufacture of a semiconductor.
EXAMPLES
[1. Construction of Silica Binding Tag Fusion Protein A (SBP-protein A) Expression Vector]
Two types of oligonucleotide primers (primer 1, primer 2) were produced based on a sequence of a protein A gene (spa) derived from Staphylococcus aureus subsp. aureus MW2.







(SEQ ID NO: 33)








Primer 1:
5′-ATCGAATTCTGCGCAACACGATGAAGCTCAAC-3′


 







(SEQ ID NO: 34)








Primer 2:
5′-GTTGAGCTCGTGTTGTTGTCTTCCTCTTTTG-3′






The protein A gene was amplified by a PCR method with the use of the primer 1 and the primer 2 by using chromosomal DNA of Staphylococcus aureus subsp. aureus MW2 as a template. The PCR reaction was performed using KOD Plus DNA polymerase (TOYOBO) according to TOYOBO's protocol. Note that, in the base sequences of the primers, “GAATTC” is an EcoRI recognition site, and “GAGCTC” is a SacI recognition site.
Products obtained by the PCR reaction and expression vector pET21-b (Novagen) were digested with the use of restriction enzymes EcoRI and SacI at 37° C. for two hours. Subsequently, DNA fragments thus amplified and pET21-b were purified by agarose gel electrophoresis. The DNA fragments and pET21-b thus purified were ligated with the use of Ligation High (TOYOBO) at 16° C. for two hours.
The expression vector thus obtained was used to transform Escherichia coli MV1184. From a colony of E. coli thus obtained, an expression vector into which a target DNA fragment was inserted was selected. The expression vector was named as pET-SpA.
Next, two types of oligonucleotide primers (primer 3, primer 4) were produced based on a sequence of a ribosomal protein L2 gene (rp1B) derived from E. coli K12.







(SEQ ID NO: 35)










Primer 3:
5′-GTTGTCGACATGGCAGTTGTTAAATGTAA-3′



 







(SEQ ID NO: 36)










Primer 4:
5′-GTTGCGGCCGCTTTGCTACGGCGACGTACG-3′






The ribosomal protein L2 gene was amplified by a PCR method with the use of the primer 3 and the primer 4 by using chromosomal DNA of E. coli K12 as a template. The PCR reaction was performed using KOD Plus DNA polymerase (TOYOBO) according to TOYOBO's protocol. Note that, in the base sequences of the primers, “GTCGAC” is a SalI recognition site, and “GCGGCCGC” is a NotI recognition site.
Products obtained by the PCR reaction and expression vector pET-SpA were digested with the use of restriction enzymes SalI and NotI at 37° C. for two hours. Subsequently, DNA fragments thus amplified and pET-SpA were purified by agarose gel electrophoresis. The DNA fragments and pET-SpA thus purified were ligated with the use of Ligation High (TOYOBO) at 16° C. for two hours.
The expression vector thus obtained was used to transform E. coli MV1184. From a colony of E. coli thus obtained, an expression vector into which a target DNA fragment was inserted was selected. The expression vector was named as pET-SpA-Sitag.
[2. Construction of Silica Binding Tag (SBP) Expression Vector]
Two types of oligonucleotide primers (primer 3, primer 4) were produced based on a sequence of a ribosomal protein L2 gene (rp1B) derived from E. coli K12.








(SEQ ID NO: 37)









Primer 5:
5′-CATCGAATTCTATGGCAGTTGTTAAATGTAAA-3′


 







(SEQ ID NO: 38)








Primer 6:
5′-AGTTGAGCTCGTTTTGCTACGGCGACGTACGA-3′






The ribosomal protein L2 gene was amplified by a PCR method with the use of the primer 5 and the primer 6 by using chromosomal DNA of E. coli K12 as a template. The PCR reaction was performed using KOD Plus DNA polymerase (TOYOBO) according to TOYOBO's protocol. Note that, in the base sequences of the primers, “GAATTC” is a EcoRI recognition site, and “GAGCTC” is a SacI recognition site.
Products obtained by the PCR reaction and expression vector pET21-b (Novagen) were digested with the use of restriction enzymes EcoRI and SacI at 37° C. for two hours. Subsequently, DNA fragments thus amplified and pET21-b were purified by agarose gel electrophoresis. The DNA fragments and pET21-b thus purified were ligated with the use of Ligation High (TOYOBO) at 16° C. for two hours.
The expression vector thus obtained was used to transform E. coli MV1184. From a colony of E. coli thus obtained, an expression vector into which a target DNA fragment was inserted was selected. The expression vector was named as pET-L2N.
[3. Construction of Modified Silica Binding Tag (1-60) Expression Vector]
Two types of oligonucleotide primers (primer 7, primer 8) were produced based on a sequence of a ribosomal protein L2 gene (rp1B) derived from E. coli K12.







(SEQ ID NO: 39)








Primer 7:
5′-AGTAATGCTAGCGCAGTTGTTAAATGTAAACCG-3′


 







(SEQ ID NO: 40)








Primer 8:
5′-ACAATCTCGAGTTACTGCTTGTGGCC-3′






A region of the ribosomal protein L2 gene which corresponds to 60 residues of the N terminal was amplified by a PCR method with the use of the primer 7 and the primer 8 by using chromosomal DNA of E. coli K12 as a template. The region is polynucleotide represented by SEQ ID NO: 46. The polynucleotide encodes polypeptide represented by SEQ ID NO: 45. The PCR reaction was performed using KOD Plus DNA polymerase (TOYOBO) according to TOYOBO's protocol. Note that, in the base sequences of the primers, “GCTAGC” is a NheI recognition site, and “CTCGAG” is a XhoI recognition site.
Products obtained by the PCR reaction and expression vector pET21-b (Novagen) were digested with the use of restriction enzymes NheI and XhoI at 37° C. for two hours. Subsequently, DNA fragments thus amplified and pET21-b were purified by agarose gel electrophoresis. The DNA fragments and pET21-b thus purified were ligated with the use of Ligation High (TOYOBO) at 16° C. for two hours.
The expression vector thus obtained was used to transform E. coli JM109. From a colony of E. coli thus obtained, an expression vector into which a target DNA fragment was inserted was selected. The expression vector was named as pET-L2 (1-60).
[4. Purification of Silica Binding Tag, Modified Silica Binding Tag, and Silica Binding Tag Fusion Protein A Using Silica]
The pET-L2N, pET-L2 (1-60), pET-SpA-Sitag were used to produce a silica binding tag, a modified silica binding tag, and a silica binding tag fusion protein A, respectively. Each of these proteins were purified with the use of silica particles. The following description deals with this process.
First, E. coli to which the vectors were introduced was incubated at 37° C. Note that the introduction of the vectors to the E. coli was carried out by a known method. When OD600 reached 0.6, IPTG was added so that the final concentration became 0.5 mM. Four hours after the addition of IPTG, the E. coli was collected by centrifugation.
The E. coli was suspended in a disrupting solution (2M: NaCl, 0.5% (v/v): surface activating agent (Tween 20), 25 mM: Tris-HCl (pH 8.0)). Subsequently, the E. coli was disrupted by an ultrasonic treatment.
After the disruption of the E. coli, the disrupting solution was subjected to centrifugation (24000×g, 15 minutes) so that a supernatant was collected. Note that the supernatant is referred to as “bacteria extraction solution (CE)” in FIG. 1. Note also that “M” in FIG. 1 indicates a molecular-weight marker.
Silica particles (silicon dioxide fine powder ca. 0.8 μm, SOEKAWA CHEMICAL Co., Ltd.) were added to the supernatant. The resulting solution was mixed at 4° C. for 30 minutes.
After the mixing, the silica particles were collected by centrifugation (3000×g, 5 minutes). Note that a supernatant obtained by this centrifugation is referred to as “silica unbound fraction (UB)” in FIG. 1. The silica particles thus collected were washed twice with the disrupting solution.
The silica particles thus washed were suspended in a 100 mM Tris-HCl buffer solution containing 2M MgCl2. The resulting solution was stirred at 4° C. for 10 minutes. Thus, proteins binding to silica were dissociated from silica. After the stirring, the silica particles were precipitated by centrifugation (3000×g, 5 minutes). Subsequently, a supernatant obtained by this centrifugation was collected. Note that the supernatant is referred to as “elution protein fraction (P)” in FIG. 1.
FIG. 1 is an electrophoretogram showing how strongly each of a silica binding tag and a silica binding tag fusion protein A binds to silica.
As shown in FIG. 1, it has been revealed that a silica binding tag is dissociated from silica with the use of 2M MgCl2. It has also been revealed that the elution protein fraction (P) contains a silica binding tag (SBP) or a silica binding tag fusion protein (SBP-protein A) with high purity of approximately 90%.
Moreover, removal of MgCl2 in the elution protein fraction (P) by dialysis caused a silica binding protein or a fusion protein contained in the elution protein fraction (P) to bind to silica again. That is, it has been revealed that a degree of binding between a silica binding tag and silica can be reversibly adjusted by adjusting concentration of MgCl2.
FIG. 2 is an electrophoretogram showing how strongly a modified silica binding tag binds to silica. Note that the lane 1 indicates a modified silica binding tag in the bacteria extraction solution (CE), the lane 2 indicates a modified silica binding tag in the silica unbound fraction (UB), and the lane 3 indicates a modified silica binding tag in the elution protein fraction (P).
It is preferable that a size of a tag used for purifying a protein is as small as possible. As shown in FIG. 2, a size of a modified silica binding tag is approximately 60 amino acids, and is therefore very small as compared to an original silica binding tag. However, it has been revealed that the modified silica binding tag can be suitably used as a tag used for purifying a protein since the modified silica binding tag is purified to high purity (approximately 90%) as shown in FIG. 2.
[5. Purification of Silica Binding Tag Using Silica Packed Column]
Silica particles (diameter: 0.1 μm, approximately 800 mg, QUARTRON SP-03B, FUSO CHEMICAL CO., LTD.) were packed in a commercially available empty column (Tricorn 5/20; GE Healthcare). Thus, a silica packed column was obtained. The silica packed column was sufficiently washed with the use of Milli-Q water and a washing solution (25 mM Tris-HCl (pH 8.0), 0.5M NaCl, 0.5% Tween 20). Subsequently, an extract of E. coli (0.45 g wet cells of E. coli) in which a silica binding tag was expressed was added to the silica packed column at a flow rate of 0.5 mL/min.
The silica packed column was washed with a 5 mL washing solution. Subsequently, a 100 mM Tris-HCl (pH 8.0) buffer solution containing 2M MgCl2 was added to the silica packed column so that the silica binding tag was eluted. FIG. 3 is an electrophoretogram of a silica binding tag purified with the silica packed column.
As shown in FIG. 3, a silica binding tag could be purified to high purity (approximately 90%).
[6. Conditions under which Silica Binding Tag is Dissociated]
A study was conducted as to conditions under which a silica binding tag was dissociated from silica particles.
First, a 10 μg silica binding tag purified by column chromatography and 10 mg silica particles were added to a 1 mL buffer solution (25 mM Tris-HCl (pH 8.0), 2M NaCl, 0.5% (v/v) Tween 20). The resulting solution was mixed at 4° C. for 30 minutes.
Subsequently, silica particles to which the silica binding tag bound were collected by centrifugation (12000×g, 1 minute, 4° C.). The silica particles thus collected were washed twice with the use of the buffer solution. Various kinds of elution solutions were added to the silica particles thus washed. The resulting solution was mixed for 5 minutes. Subsequently, a supernatant was removed by centrifugation.
To the remaining silica particles, a 30 μl sample buffer for SDS-PAGE was added. The resulting solution was heated at 100° C. for 5 minutes. Thus, the silica binding tag remaining on the silica particles was dissociated in the sample buffer. Subsequently, the sample buffer in which the silica binding tag was dissociated was subjected to SDS-PAGE (12.5%).
FIG. 4 shows the result of the SDS-PAGE. In FIG. 4, the lane 1 indicates a silica binding tag binding to silica particles in a case where an elution solution was not used (negative control), the lane 2 indicates a silica binding tag remaining on silica particles in a case where a 5M NaCl solution was used as an elution solution, the lane 3 indicates a silica binding tag remaining on silica particles in a case where a 100 mM Tris-HCl (pH 8.0) buffer solution containing 2M MgCl2 was used as an elution solution, the lane 4 indicates a silica binding tag remaining on silica particles in a case where a CHAPS-NaOH (pH12) buffer solution was used as an elution solution, the lane 5 indicates a silica binding tag remaining on silica particles in a case where a 1N NaOH solution was used as an elution solution, the lane 6 indicates a silica binding tag remaining on silica particles in a case where a CH3COOH—NaOH (pH 4.26) was used as an elution solution, the lane 7 indicates a silica binding tag remaining on silica particles in a case where a 1N HCl solution was used as an elution solution, and the lane 8 indicates a purified silica binding tag which was used in this experiment.
As shown in FIG. 4, it was proved that a silica binding tag is dissociated from silica particles in a case where an acid solution such as a 1N HCl solution or an alkali solution such as a 1N NaOH solution is used as an elution solution (see the lane 5 or lane 7, for example). However, such a condition causes protein denaturation. Consequently, it is impossible to purify a protein without losing the activity of the protein. It is necessary to dissociate a silica binding tag under a neutral condition in order to dissociate a protein having a silica binding tag from silica particles without losing the activity of the protein. In view of this, a study was conducted as to whether or not it is possible to dissociate a silica binding tag by using various kinds of ions.
It was impossible to dissociate a silica binding tag from silica particles in a case where a high concentration NaCl solution, which has been conventionally used as an elution liquid, was used as an elution solution. It was impossible to dissociate a silica binding tag from silica particles even with a NaCl solution whose concentration was increased to 5M (see the lane 2).
In contrast, it was proved that it is possible to dissociate a silica binding tag from silica particles in a case where a 100 mM Tris-HCl (pH 8.0) buffer solution containing 2M MgCl2 is used as an elution solution (see the lane 3).
[7. Concentration of MgCl2 in Elution Solution]
Escherichia coli to which pET-L2N was introduced was incubated in 2×YT medium. When OD600 reached 0.6, IPTG was added so that the final concentration became 0.5 mM.
Four hours after the addition of IPTG, the incubated E. coli was collected by centrifugation (6000×g, 15 minutes, 4° C.). The E. coli thus collected was suspended in a buffer solution (25 mM Tris-HCl (pH 8.0)), and was then disrupted by an ultrasonic treatment.
The resulting solution was subjected to centrifugation (40000×g, 20 minutes, 4° C.) to obtain a supernatant. The supernatant was determined as a bacteria disrupted solution. 500 μL of the bacteria disrupted solution and 10 mg silica particles were added to a 1 mL buffer solution (25 mM Tris-HCl (pH8.0), 2M NaCl, 0.5% (v/v) Tween 20). The resulting solution was mixed at 4° C. for 30 minutes.
Subsequently, silica particles to which a silica binding tag bound were collected by centrifugation (12000×g, 1 minute, 4° C.). The silica particles thus collected were washed twice with the use of the buffer solution. Various kinds of elution solutions were added to the silica particles thus washed. The resulting solution was mixed for 5 minutes. Subsequently, a supernatant and a pellet of the silica particles were separately collected by centrifugation.
A sample buffer was added to a part of the supernatant and the silica particles. The samples were subjected to SDS-PAGE (12.5%).
The remaining supernatant was mixed with silica particles again so that a silica binding tag bound to the silica particles. Subsequently, second elution was carried out by the same method as above. This is to confirm whether a degree of purification was improved by carrying out purification steps twice.
FIG. 5 shows the result of the SDS-PAGE. In FIG. 5, the lane 1 indicates a silica binding tag contained in an E. coli disrupted solution, each of the lanes 2 to 5 indicates a silica binding tag obtained in a case where a 100 mM Tris-HCl (pH 8.0) buffer solution containing 1M MgCl2 was used as an elution solution, and each of the lanes 6 to 9 indicates a silica binding tag obtained in a case where a 100 mM Tris-HCl (pH 8.0) buffer solution containing 2M MgCl2 was used as an elution solution. More specifically, each of the lanes 2 and 6 indicates a silica binding tag contained in the first elution fraction (supernatant), and each of the lanes 3 and 7 indicates a silica binding tag remaining on silica particles after the first elution. Further, each of the lanes 4 and 8 indicates a silica binding tag contained in the second elution fraction (supernatant), and each of the lanes 5 and 9 indicates a silica binding tag remaining on silica particles after the second elution.
As shown in FIG. 5, it was proved that it is possible to dissociate a silica binding tag even by using 1M MgCl2 (see the lane 2). It was proved that, in this case, the silica binding tag partially remains on the silica particles (see the lane 3)
In contrast, it was proved that, in a case where 2M MgCl2 is used, almost all of the silica binding tag can be dissociated from the silica particles (see the lane 6) without remaining on the silica particles (see the lane 7).
It was proved that a silica binding tag can be purified to 90% purity or more with only one purifying operation, thereby making it unnecessary to carry out the purifying operation twice.
[8. Dissociation Effect of Bivalent Cation Other Than Mg2+]
A study was conducted as to whether or not it is possible to dissociate a silica binding tag from silica particles with the use of bivalent cation other than Mg2+. An experiment was carried out in accordance with the method described in [7. Concentration of MgCl2 in Elution Solution]. The inventors of the present invention tried to study dissociation effect of a CaCl2 solution, a NiCl2 solution, a FeCl2 solution, a ZnCl2 solution, and a MnCl2 solution. However, preparation of a 2M FeCl2 solution, a 2M ZnCl2 solution, and a 2M MnCl2 solution in a Tris buffer solution caused a precipitate. Therefore, only dissociation effect of a 2M CaCl2 solution and a 2M NiCl2 solution was studied.
FIG. 6 shows a result of SDS-PAGE. In FIG. 6, the lane 1 indicates a silica binding tag which remained on silica particles in a case where a CaCl2 solution was used as an elution solution, the lane 2 indicates a silica binding tag which remained on silica particles in a case where a NiCl2 solution was used as an elution solution, the lane 3 indicates a silica binding tag contained in an elution solution in a case where a CaCl2 solution was used as the elution solution, and the lane 4 a silica binding tag contained in an elution solution in a case where a NiCl2 solution was used as the elution solution.
As shown in FIG. 6, it has been revealed that a silica binding tag can be dissociated from silica particles with the use of either CaCl2 solution or NiCl2 solution. It has been also revealed that each of CaCl2 solution and NiCl2 solution is inferior to a MgCl2 solution in dissociation effect (elution effect) of a silica binding tag.
[9. Affinity Purifying Method Using Silica Binding Tag and Comparison with Affinity Purifying Method Using His Tag]
E. coli into which an expression vector pET-SpA-Si tag was introduced was incubated at 37° C. Note that the expression vector was introduced into the E. coli by a known method.
When OD600 reached 0.6, IPTG was added to the incubation solution so that the final concentration became 0.5 mM. Four hours after the addition of IPTG, the E. coli was collected by centrifugation.
A silica binding tag fusion protein A expressed in the E. coli had two kinds of tags for purification, i.e., a silica binding tag and a His tag, each of which was fused with a protein A. A comparison was carried out in purification efficiency between the silica binding tag and the His tag by carrying out purification using the silica binding tag and purification using the His tag.
E. coli was suspended in a disrupting solution (25 mM Tris-HCl (pH 8.0), 2M NaCl, 0.5% (v/v) surface activating agent Tween 20 (registered trademark)). Subsequently, the E. coli was disrupted by an ultrasonic treatment. After the disruption of the E. coli, the disrupting solution was subjected to centrifugation (24000×g, 15 minutes) to obtain a supernatant.
For purification using the His tag, a HisTrap HP 1 mL column (manufactured by GE Healthcare biosciences) was used. Note that the purification was basically carried out in accordance with the GE Healthcare biosciences'protocol. To put it simply, the column was equilibrated with a buffer solution (20 mM sodium phosphate (pH 7.4), 0.5M NaCl, 5 mM imidazole), and then the supernatant obtained by the centrifugation was added to the column. The column was washed with the use of the buffer solution. Subsequently, a target protein was eluted with gradient elution from 5 mM to 500 mM imidazole.
As for purification using the silica binding tag, silica particles (Silicon dioxide fine powder ca. 0.8 μm, SOEKAWA CHEMICAL Co., Ltd.) were added to the supernatant obtained by the centrifugation. The resulting solution was mixed at 4° C. for 30 minutes. After the mixing, the silica particles were collected by centrifugation (3000×g, 5 minutes). The silica particles thus collected were washed with the disrupting solution twice. The silica particles thus washed were suspended in a 100 mM Tris-HCl buffer solution containing 2M MgCl2. The suspension was stirred at 4° C. for 10 minutes. Thus, proteins binding to silica were dissociated from the silica. After the stirring, the silica particles were precipitated by centrifugation (3000×g, 5 minutes). Subsequently, a supernatant was collected.
FIG. 7 shows a result obtained by subjecting proteins purified with the His tag and proteins purified with the silica binding tag to SDS-PAGE (12.5%). In FIG. 7, the lane 1 indicates a purification fraction obtained with the use of a HisTrap column, the lane 2 indicates a HisTrap column unbound fraction, the lane 3 indicates a purification fraction obtained with the use of a silica binding tag, the lane 4 indicates a silica particle unbound fraction, the lane 5 indicates a supernatant of an E. coli disrupted solution which is obtained before purification (supernatant obtained by centrifugation), and the lane M indicates a molecular weight marker.
Analysis using image analysis software Image J revealed that a target protein obtained through purification using the His tag was 93% in purity and 77% in yield (see the lane 1). On the other hand, a protein obtained through purification using the silica binding tag was 85% in purity and 93% in yield (see the lane 3). That is, it was possible to purify a target protein with high purity comparable to that of conventional affinity purification and with high yield.
The embodiments and concrete examples of implementation discussed in the foregoing detailed explanation serve solely to illustrate the technical details of the present invention, which should not be narrowly interpreted within the limits of such embodiments and concrete examples, but rather may be applied in many variations within the spirit of the present invention, provided such variations do not exceed the scope of the patent claims set forth below.

## Claims

1. A method for purifying a protein, comprising the step of:
contacting a fusion protein of a first protein and a second protein with a bivalent cation-containing solution, the fusion protein being adsorbed to the silicon oxide component of a silicon oxide-containing substance, the first protein being capable of binding to the silicon oxide-containing substance in a solution containing 0.1 M sodium chloride, wherein the fusion protein dissociates from the silicon oxide-containing substance after the fusion protein is contacted with the bivalent cation-containing solution.

2. The method for purifying a protein according to claim 1, further comprising the step of:
adsorbing the fusion protein to the silicon oxide-containing substance.

3. The method for purifying a protein according to claim 2, further comprising the step of:
expressing the fusion protein in a transformant.

4. The method for purifying a protein according to claim 3, further comprising the step of:
causing second DNA encoding the second protein to be linked in-frame with first DNA encoding the first protein.

5. The method for purifying a protein according to claim 1, wherein:
the bivalent cation-containing solution is a MgCl2 solution, a CaCl2 solution or a NiCl2 solution.

6. The method for purifying a protein according to claim 1, wherein:
the bivalent cation-containing solution is 0.2M or more in bivalent cation concentration.

7. The method for purifying a protein according to claim 1, wherein:
the first protein is a polypeptide selected from:
(a) polypeptide with the amino acid sequence represented by SEQ ID NO: 1, and
(b) polypeptide with an amino acid sequence in which one or several amino acids are substituted, deleted, inserted, and/ or added in the amino acid sequence represented by SEQ ID NO: 1.

8. The method for purifying a protein according to claim 1, wherein:
the first protein is a polypeptide selected from:
(c) polypeptide with the amino acid sequence represented by SEQ ID NO: 45, 47 or 49, and
(d) polypeptide with an amino acid sequence in which one or several amino acids are substituted, deleted, inserted, and/or added in the amino acid sequence represented by SEQ ID NO: 45, 47 or 49.

9. A method for purifying a protein, comprising the step of:
contacting a protein adsorbed to the silicon oxide component of a silicon oxide-containing substance with a bivalent cation-containing solution,
the protein being capable of binding to the silicon oxide-containing substance in a solution containing 0.1M sodium chloride, wherein the protein dissociates from the silicon oxide-containing substance after the protein is contacted with the bivalent cation-containing solution.