| 1. CLONING AND TRANSFORMATION |
|
1.1 |
|
What are the differences among the various pMAL vectors? |
|
1.2 |
|
What strain(s) do you recommend as hosts for the pMAL vectors? |
|
1.3 |
|
Can I clone into pMAL vectors just as I would into pUC vectors, i.e.
plating my transformants on Xgal/IPTG plates and picking colonies that are white? |
|
1.4 |
|
What is the transformation efficiency of the pMAL vectors? |
|
1.5 |
|
What primers should I use to sequence the ends of my insert after
I clone it into a pMAL vector? |
|
1.6 |
|
What is the transformation efficiency of the lon mutant strains PR745
and ER2508 ? |
|
1.7 |
|
What are some of the possible explanations for an inability to clone
an insert into a pMAL vector? |
|
1.8 |
|
How can I obtain the sequences of the pMAL vectors? |
|
1.9 |
|
Which strand of DNA is packaged when cells carrying the pMAL vectors
are superinfected with an M13 helper phage such as M13KO7 (NEB cat #315)? |
|
1.10 |
|
Why am I having trouble cleaving a pMAL-2 vector with the XmnI isoschizomer
Asp700 I? |
| 2. EXPRESSION |
|
2.1 |
|
When we analyze our fusion protein expression by Western using the
anti-MBP serum, only a small fraction of the protein is full-length, and most of it migrates close
to the unfused MBP. |
|
2.2 |
|
My fusion protein is insoluble; is there anything I can do to get
it expressed as soluble protein? |
|
2.3 |
|
When I run my uninduced and induced crude extracts on SDS-PAGE side
by side, I don't see an induced band. Why? |
|
2.4 |
|
I've cloned my insert, but after SDS-PAGE the only induced band present
is the size of MBP2*. |
|
2.5 |
|
What are the possible effects of export (secretion, using a pMAL-p2
vector) on solubility/stability of the fusion? |
|
2.6 |
|
What is the minimum size of a fragment that can be cloned intopMAL
and expressed with the MBP? Can short peptide sequences (about 10 amino acids) be added onto MBP? |
|
2.7 |
|
Is the N-terminus the only place where a signal sequence leads to
export of the protein - is it possible that a protein fused to MBP could contain a fortuitous signal
sequence? |
| 3. AFFINITY PURIFICATION |
|
3.1 |
|
Much of my fusion protein flows through the amylose column. Is there
anything I can do to improve my fusion's affinity for the amylose column? |
|
3.2 |
|
How many times can I use the amylose column? |
|
3.3 |
|
What is known about binding in the presence of non-ionic detergents? |
|
3.4 |
|
Can I substitute a different buffer and/or salt concentration in the
column buffer? |
|
3.5 |
|
I see my intact fusion protein by SDS-PAGE when I run cells boiled
in sample buffer, but when I check the crude extract the fusion is degraded. |
|
3.6 |
|
Can I perform a batch purification using the amylose resin? |
|
3.7 |
|
Can MBP fusions be purified in the presence of denaturants like urea
or guanidine-HCl? |
|
3.8 |
|
Is the amylose resin damaged by storage at -20°? When our kit
arrived, it was placed at -20°, but I see that the recommended storage temperature for the
amylose resin is 4°. |
| 4. FACTOR Xa CLEAVAGE |
|
4.1 |
|
Factor Xa seems to be cleaving my protein at several sites, even though
the protein does not contain any IEGR sequences. |
|
4.2 |
|
Are there any control substrates for factor Xa? |
|
4.3 |
|
How can factor Xa be inactivated? |
|
4.4 |
|
How can factor Xa be removed from the reaction mix after cleavage? |
|
4.5 |
|
My protein cleaves very poorly with factor Xa. Is there anything I
can do to improve cleavage? |
|
4.6 |
|
What is the molecular weight and pI of Factor Xa ? |
|
4.7 |
|
Is there any thrombin in NEB's factor Xa preparation? |
|
4.8 |
|
What is maximum concentration of glycerol that factor Xa can withstand
during cleavage? |
|
4.9 |
|
How is the rate of factor Xa affected by urea, guanidine hydrochloride
and SDS? |
|
4.10 |
|
Can MBP fusions be digested with factor Xa while bound to the amylose
resin? |
| 5. SEPARATION OF FUSION PROTEIN DOMAIN
AND STORAGE |
|
5.1 |
|
In order to re-bind MBP to the column, the maltose must be removed.
Can this be done by dialysis? |
|
5.2 |
|
How should I store my protein after it is purified? |
|
5.3 |
|
Is there any way of avoiding degradation of protein during storage
at 4°?. |
| 6. MBP INFORMATION |
|
6.1 |
|
What is MBP2*? Is it different from wild-type MBP produced from E.
coli? |
|
6.2 |
|
Has the crystal structure of the maltose binding protein been determined? |
|
6.3 |
|
How much of MBP is dispensable for binding? |
|
6.4 |
|
What is the Kd , pI and extinction coefficient for MBP2*? |
|
6.5 |
|
What is the origin of the MBP region of the pMAL vectors? |
|
6.6 |
|
Is MBP a monomer or a dimer? |
| 7. MISCELLANEOUS |
|
7.1 |
|
What is the full reference for the pMAL chapter in "Current Protocols
in Molecular Biology"? |
|
7.2 |
|
Protein Fusion and Purification Strain List |
1. CLONING AND TRANSFORMATION |
|
| 1.1 What are the differences among the various pMAL vectors? |
| |
The pMAL-c, -cRI and -p are the earliest versions of the pMAL vectors. pMAL-c and pMAL-p have
a StuI site in the polylinker for cloning blunt-ended fragments. Because the second half of the
StuI site codes for proline, if you clone an EcoRI fragment into pMAL-c or pMAL-p, the factor
Xa site reads IEGRP, and RP won't cut with factor Xa. pMAL-cRI was designed as a short-term solution
to fix this problem, by changing the polylinker to code for IEGRI upstream of the EcoRI
site. The pMAL-c2 and pMAL-p2 vectors are the next generation of pMAL vectors. These vectors avoid
the problem with factor Xa cleavege by using an XmnI site instead of StuI. They also have
a spacer between malE and the factor Xa site which allows some fusions to bind more tightly
to the amylose resin, and an M13 origin for making single stranded DNA. The third generation of
pMAL vectors is distinguished by the addition of vectors that substitute an enterokinase or Genenase
I site for the factor Xa site. These vectors are called pMAL-c2E and pMAL-p2E (enterokinase), and
pMAL-c2G and pMAL-p2G (Genenase). The factor Xa versions are now called pMAL-c2X and pMAL-p2X for
consistency. This third generation of vectors have a few minor modifications outside the polylinker
as well. The NdeI site in the pBR322 origin was destroyed by filling in, and an NdeI site at the
ATG of malE was added by site directed mutagenesis. This allows a malE fusion to
be cut out in order to subclone it, for example into a eukaryotic vector. The NcoI site
in malE was destroyed, as was the AvaI site in the M13 orgin, making the AvaI
site upstream of the factor Xa site unique. In all vectors, the "-c" designation refers
to cytoplasmic expression, i.e. the signal sequence that directs MBP to the periplasmic space has
been deleted. Vectors that are designated "-p" refer to periplasmic expression, and these
contain the wild-type malE signal sequence.
top |
|
| 1.2 What strain(s) do you recommend as hosts for the pMAL vectors? |
| |
The strain we have used most frequently is TB1, #E4122S, which is JM83 hsdR-. There is nothing
special about it with respect to the pMAL system, but it has given the best all-around results
when considering plasmid stability, expression and purification. We have used a number of other
strains successfully for certain proteins. We also use other strains in response to particular
problem (for example, see 2.1). One can start with TB1, or one can use whatever competent cells
are readily available and then try TB1 or another strain if a problem with expression or purification
develops.
top |
|
| 1.3 Can I clone into pMAL vectors just as I would into pUC vectors, i.e. plating
my transformants on Xgal/IPTG plates and picking colonies that are white? |
| |
No. Even though the b-galactosidase a fragment is the same on the pUC and pMAL vectors, the
tac promoter on the pMAL vectors is much stronger than the lac promoter on the pUC vectors. If
cells bearing a pMAL vector are induced with IPTG, the cells eventually die. The blue-to-white
screen is done by replica plating (or picking and stabbing) onto a master amp plate and an amp
Xgal plate containing 0.1 mM IPTG.
top |
|
| 1.4 What is the transformation efficiency of the pMAL vectors? |
| |
The pMAL vectors transform about 1/10th as well as pUC and pBR overall. High amp concentration
(>100ug/ml) can cause lower efficiencies as well.
top |
|
| 1.5 What primers should I use to sequence the ends of my insert after I clone
it into a pMAL vector? |
| |
Use the malE primer (cat. #S1237S) on the 5´ side of the insert. If you want to sequence
the 3´ junction, the pUC/M13 primers that bind to the lacZ-a region (e.g. #S1224S) will work.
top |
|
| 1.6 What is the transformation efficiency of the lon mutant strains PR745 and
ER2508 ? |
| |
This strain has a lower transformation efficiency than its parent, PR700. Testing them side
by side, PR700 gave about 5 x 10ex6/ug, and PR745 gave ~5 x 10ex5/ug, using cells made competent
by the rubidium chloride method. Since the only difference
between the strains is the mini-Tn10 in lon, presumably lon-related sickness is the problem, and
other protease-deficient strains may be effected as well.
top |
|
| 1.7 What are some of the possible explanations for an inability to clone an insert
into a pMAL vector? |
| |
The most common explanation for this is technical difficulties with the subcloning. The next
most common explanation is that expression of the fusion is toxic to E. coli. The tac promoter
induction ratio on the pMAL plasmids is about 1:50, so if the induced level of the fusion is 40%
of the total cellular protein, the uninduced level works out to 0.8%. This amount of a protein
can be toxic, either because of its function (e.g. a protease) or because of its general properties
(e.g. very hydrophobic).
top |
|
| 1.8 How can I obtain the sequences of the pMAL vectors? |
|
pMAL sequences and documents
The sequences are also available by anonymous ftp from vent.neb.com, by Email from
, and by fax.
top |
|
| 1.9 Which strand of DNA is packaged when cells carrying the pMAL vectors are
superinfected with an M13 helper phage such as M13KO7 (NEB cat #315)? |
| |
The strand corresponding to the antisense strand of the malE gene is packaged. This is
the strand that is complementary to the polylinker sequence shown in the 1998/99 catalog on p.
236. The malE primer (#S1237S) hybridizes to the strand that is packaged by the helper phage.
top |
|
| 1.10 Why am I having trouble cleaving a pMAL-2 vector with the XmnI isoschizomer
Asp700 I? |
|
Asp700 I has site preferences, and the XmnI
site in the pMAL-2 polylinker happens to be one that
Asp700 I cleaves poorly.
top |
| |
2. EXPRESSION |
|
| 2.1 When we analyze our fusion protein expression by Western using the anti-MBP
serum, only a small fraction of the protein is full-length, and most of it migrates close to
the unfused MBP. |
|
It is likely that the fusion protein is degraded, leaving a stable MBP-sized breakdown product.
This case is a good candidates for using protease deficient hosts. A list of strains we
have available, free with an order or for the price of shipping, can be obtained from NEB. For
cytoplasmic expression, the most protease deficient strain is CAG629 (#E4125S) - it is also, however,
the most difficult to work with. ER2508 (#E4127S) and CAG597 (#E4123S) are good alternatives. For
periplasmic expression, the most protease deficient strain is CAG597 (#E4123S); KS1000 (#E4128S)
and UT5600 (#E4129S) might be worth trying as well. The CAG strains are difficult to transform,
and often require electroporation to introduce the fusion plasmid.
top |
|
| 2.2 My fusion protein is insoluble; is there anything I can do to get it expressed
as soluble protein? |
|
Expressing at a lower temperature is the first thing to try. One can go as low as 15°, by
moving a water bath into the cold room. Of course, the cells grow very slowly at these temperatures,
so grow the culture at 37° and shift to the low temperature when adding IPTG. One also has
to increase the time of induction to compensate for the slower growth - a rule of thumb is 2x for
every 7°.
Some other references for discussion of solubility problems are:
one of the original papers describing how expression at lower temps produces soluble protein:
Bishai, Rappuoli &Murphy (1987) J. Bact. 169, 5140-5151
same for an exported protein: Tagaki et al. (1988) Bio/technology 6, 948-950 a method for growing
the cells under osmotic stress, which can also help produce soluble protein: Blackwell and Horgan
(1991) FEBS Letters 295:10-12
review on methods to make correctly-folded protein in E. coli: Georgiou and Valax (1996) Current
Opinion in Biotechnology 7, 190-7.
reviews on insolubility: Schein (1989) Bio/technology 7, 1141-1149 Schein (1990) Bio/technology
8, 308-317 Wilkinson & Harrison (1991) Bio/technology 9, 443-448 Kiefhaber et al. (1991)
Bio/techno logy 9, 825-829
reviews on refolding: Zardeneta G; Horowitz PM (1994) Anal Biochem 223(1),1-6 Chaudhuri JB (1994)
Ann N Y Acad Sci 721,374-85 Gilbert HF (1994) Curr Opin Biotechnol 5(5),534-9 Schein CH (1991)Curr
Opin Biotechnol 2(5):746-50 Kelley RF & Winkler ME (1990) Genet Eng (N Y) 12,1-19 Marston & Hartley
(1990) Methods in Enzymology 182, 264-282
extracting from membrane with Sarkosyl: S. Frankel et al. (February, 1991) PNAS, vol.88 pp.
1192-6.
top
|
|
| 2.3 When I run my uninduced and induced crude extracts on SDS-PAGE side by side,
I don't see an induced band. Why? |
|
There are a couple of possible explanations. Inserts cloned in a pMAL-p2 vector have about a
4- to 8-fold reduced level of expression when compared to the same insert in a pMAL-c2 vector.
This often reduces the amount of expression to the point where there is no visible induced band.
In addition, some foreign genes are poorly expressed in E. coli, even when fused to a highly expressed
carrier gene. Possible explanations are message instability or problems with translation - sometimes
it is due to the presence of multiple rare codons in the gene of interest, and in these cases overexpression
of the corresponding tRNA can help (Schenk et al., 1995, BioTechniques 19, 196-200). Even in cases
where a band is not visible, one can get yields up to 5 or 6 mg/liter of culture.
top |
|
| 2.4 I've cloned my insert, but after SDS-PAGE the only induced band present is
the size of MBP2*. |
|
There are two likely explanations for this result. 1) If the protein of interest is in the wrong
translational reading frame, an MBP2*-sized band will be produced by translational termination
at the first in-frame stop codon. 2) If the protein of interest is very unstable, an MBP2*-sized
breakdown product is usually produced (MBP is a very stable protein). The best way to distinguish
between these possibilities is to run a Western blot using anti-MBP antiserum (#E8030S). If proteolysis
is occurring, at least a small amount of full-length fusion can almost always be detected. DNA
sequencing of the fusion junction using the malE primer (#S1237S) will confirm a reading
frame problem. If the problem is proteolysis, you might want to try one of the protease deficient strains (#E4123S - #E4129S) listed on page 227 of the 2000 New England Biolabs Catalog.
top |
|
| 2.5 What are the possible effects of export (secretion, using a pMAL-p2 vector)
on solubility/stability of the fusion? |
|
Initiating export through the cytoplasmic membrane puts a fusion protein on a different folding
pathway - the solubility or stability of a protein is determined by whether this folding pathway
leads to a different 3-dimensional structure for the protein. Some proteins, like MBP itself, can
fold properly either in the cytoplasm or when exported to the periplasm. However, the normal folding
pathway for some proteins is incompatible with passage through the membrane, so the fusion protein
gets stuck in the membrane and cannot fold properly; this can lead to degradation (Gentz et al,
1988, J. Bact. 170, 2212-20). Other proteins, especially ones that have multiple disulfide-bonds,
only fold properly when exported (the E. coli cytoplasm is a reducing environment, and the proteins
that catalyze disulfide bond formation are present in the periplasm)(Bardwell et al., 1991, Cell
67, 581-9). When this class of protein is expressed in the cytoplasm, it may fold improperly and
become degraded or insoluble.
top |
|
| 2.6 What is the minimum size of a fragment that can be cloned into pMAL and expressed
with the MBP? Can short peptide sequences (about 10 amino acids) be added onto MBP? |
|
You can use the MBP system to express short peptides, and we've heard from several customers
that have done it successfully. However, for every 40 mg of MBP (42.5 kDa) one gets about 1 mg
of a 10 amino acid peptide (1.1 kDa).
top |
|
| 2.7 Is the N-terminus the only place where a signal sequence leads to export
of the protein - is it possible that a protein fused to MBP could contain a fortuitous signal
sequence? |
|
It probably would be possible to have some internal region that acts as a signal sequence. It's
also possible that hydrophobic regions in the protein lead to association with the membrane, which
in turn leads to limited cell lysis during preparation of the periplasmic fraction. Neither one
is very common, but perhaps the latter is seen more often.
top |
| |
3. AFFINITY PURIFICATION |
|
| 3.1 Much of my fusion protein flows through the amylose column. Is there anything
I can do to improve my fusion's affinity for the amylose column? |
|
An MBP fusion protein might not stick to the amylose column because of a low intrinsic affinity
or the presence of some factor in the extract that interferes with binding. Factors in the crude
extract that can interfere with binding include non-ionic detergents and cellular components that
are released during alternative methods of lysis such as lysozyme/sonication or multiple passes
through a French press. In addition, cells grown in LB and similar media have substantial amounts
of an amylase that interferes with binding, presumably by either cutting the fusion off the column
or by releasing maltose that elutes the fusion from the column. By including glucose in the media,
expression of this amylase is repressed and the problem is alleviated. A low intrinsic affinity
could be caused by an interaction between the protein of interest and MBP that either blocks or
distorts the maltose-binding site. Although this may be inherent in the protein of interest, sometimes
the problem can be alleviated by shortening or lengthening the polypeptide that is fused to MBP.
top |
|
| 3.2 How many times can I use the amylose column? |
|
The most important variable in determining the useful life of the amylose resin is the amount
of time it is in contact with trace amounts of amylase present in the crude extract (cr.. 3.1).
Under normal conditions (crude extract from 1 liter of cells grown in LB+0.2% glucose, 15 ml column),
the column looses 1-3% of its initial binding capacity each time it is used. If the yield of fusion
protein under these conditions is 40 mg. This means that after 3 to 5 runs there would be a decrease
in the yield. In practice, we often use a column 8 or 10 times before we notice a significant drop
in the yield.
Regeneration: The packed resin may be regenerated by the following wash sequence: Water 3 - column volumes, 0.1% SDS - 3 column
volumes, Water - 1 column volume, Column Buffer - 5 column volumes.
top |
|
| 3.3 What is known about binding in the presence of non-ionic detergents? |
|
What we know is this: 1) some fusion proteins do not bind efficiently (<5% binding) in the
presence of 0.2% Triton X100 or 0.25% Tween 20, while other fusions are unaffected, and 2) for
a fusion that does not bind in 0.25% Tween 20, diluting the Tween to 0.05% restores about 80% of
the binding. We have reports from researchers that purification in the presence of NP40 works,
but because of (1) above we don't know how general this is.
top |
|
| 3.4 Can I substitute a different buffer and/or salt concentration in the column
buffer? |
|
Yes, we have tried HEPES, MOPS, and phosphate buffers instead of Tris-Cl in the column buffer,
at pH's from 7.0 to 7.4 with identical results. NaCl or KCl concentrations of 25 mM to 1 M are
also compatible with the affinity purification.
top |
|
| 3.5 I see my intact fusion protein by SDS-PAGE when I run cells boiled in sample
buffer, but when I check the crude extract the fusion is degraded. |
|
There are several possible explanations for this. For fusions expressed in the cytoplasm, in
many cases most of the degradation happens during harvestand lysis. In this case, harvesting promptly
and lysing the cells quickly may help. In other cases, degradation occurs when the fusion protein
is exposed to periplasmic or outer membrane proteases (Silber et al., 1992 PNAS USA 89:295-299;
Grodberg & Dunn, 1988 J. Bacteriol 170:1245-1253; Sugimura & Higashi, 1988 J. Bacteriol
170:3650-3654).The best strategy in either case is to use a host which is deficient in the offending
protease(s) (c.f. 2.1, strains).
top |
|
| 3.6 Can I perform a batch purification using the amylose resin? |
|
Yes, batch purification works well, although it is difficult to wash all the non-specific proteins
away as effectively as in a column due to the included volume in the resin. The resin can withstand
centrifugation at up to 6000 x g. A good compromise is to load the resin in a batch mode, by incubating
with shaking for 2 h to overnight, then pour it in a column to wash and elute. Dilution of the
crude extract is not as critical for loading the column by the batch method.
top |
|
| 3.7 Can MBP fusions be purified in the presence of denaturants like urea or guanidine-HCl? |
|
No, MBP's affinity to amylose and maltose depends on hydrogen bonds, that in turn are positioned
by the three-dimensional structure of the protein. Agents that interfere with hydrogen bonds or
the structure of the protein interfere with binding as well.
top |
|
| 3.8 Is the amylose resin damaged by storage at -20°? When our kit arrived,
it was placed at -20°, but I see that the recommended storage temperature for the amylose
resin is 4°. |
|
The resin will freeze at -20°, but the performance of the resin is not degraded from one
freeze/thaw cycle.
top |
| |
4. FACTOR Xa CLEAVAGE |
|
| 4.1 Factor Xa seems to be cleaving my protein at several sites, even though the
protein does not contain any IEGR sequences. |
|
The specificity of factor Xa reported in our catalog is as referenced in Nagai and Thogersen
(1987) Meth. Enz. 153, 461-481. The basis for this specificity is that the natural factor Xa sites
in prothrombin are IEGR (or sometimes IDGR), and many examples of fusions with IEGR are cut specifically.
However, proteins can be cleaved at other basic residues, depending on the context (e.g. Nagai
et al., 1985, PNAS 82,7252-5; Quinlan et al., 1989, J Cell Sci 93, 71-83; Eaton et al., 1986, Biochem
25, 505-12; Wearne, 1990, FEBS Lett 263, 23-6). A number of the secondary sites (but not all) that
have been sequenced show cleavage following gly-arg. We have also seen a correlation between proteins
that are unstable in E. coli and cleavage at secondary sites with factor Xa, suggesting that these
proteins are in a partially unfolded state. We've tried altering the reaction conditions to increase
the specificity, but with no success. It is possibly, however, that adding a cofactor or a substrate
analog could change the conformation of the protein enough to block secondary sites (see 4.5 below).
We sell pMAL vectors encoding Genenase I sites (pMAL-c2G, #N8068 and pMAL-p2G,
#N8069) and enterokinase sites (pMAL-c2E, #N8066 and pMAL-p2E,
#N8067) as alternatives.
top |
|
| 4.2 Are there any control substrates for factor Xa? |
|
The Protein Fusion and Purification System comes with an MBP-paramyosin-delSal fusion as a positive
control for factor Xa cleavage. It can be obtained separately as #E8051S. Sigma also sells a colorimetric
substrate, N-benzoyl-ile-glu-gly-arg-p-nitroanilide (cat # B 7020).
top |
|
| 4.3 How can factor Xa be inactivated? |
|
The best way is 2 uM dansyl-glu-gly-arg-chloromethyl ketone. This compound irreversibly inactivates
the enzyme. We get it from Calbiochem, #251700, but there may be other suppliers. We add to a final
concentration of 2 uM, then incubate at least 1 min. at room temperature. It reacts with the active
site histidine, so it could conceivably react with other sites on the protein of interest, but
this is unlikely at the low concentration used. The protease inhibitor chymostatin (60 ug/ml) also
works.
top |
|
| 4.4 How can factor Xa be removed from the reaction mix after cleavage? |
|
Factor Xa can be removed by passing the reaction mix over a small benzamidine-agarose column
(e.g. Amersham #17-5143-01). When 50 µg of factor Xa is passed over a 0.5 ml column, less
than 0.2% of the activity flows through
top |
|
| 4.5 My protein cleaves very poorly with factor Xa. Is there anything I can do
to improve cleavage? |
|
We presume that, in these cases, the fusion protein folds so that the factor Xa site is inaccessible.
In theory anything that perturbs the structure might uncover the site. We've tried increasing the
temperature, changing buffers and salt conditions, and adding detergents. The only thing that worked
was low concentrations of SDS (0.01 to 0.05%; see Ellinger et al., 1991, Virol. 180, 811- 3). Another
researcher found that calcium worked - his protein of interest was a calcium binding protein, supporting
the idea that anything that might change the conformation even slightly (e.g., a cofactor or substrate
analog) could have a dramatic effect.
top |
|
| 4.6 What is the molecular weight and pI of Factor Xa ? |
|
The molecular weight of factor Xa is 42,400 Da. It consists of two disulfide-linked chains,
26,700 and 15,700. On our SDS-PAGE gels they run as 30 kDa and 20 kDa. The calculated pI of factor
Xa is 5.09.
top |
|
| 4.7 Is there any thrombin in NEB's factor Xa preparation? |
|
We cannot detect any thrombin in our prep, but our level of sensitivity is not exquisite - we
look on an overloaded gel, so we probably would see anything over 1%. The activity of factor Xa
on thrombin substrates masks any signal in a proteolytic assay for thrombin (both enzymes cleave
after arginine).
top |
|
| 4.8 What is maximum concentration of glycerol that factor Xa can withstand during
cleavage? |
|
We have tested factor Xa cleavage in up to 20% glycerol, where it still cleaves at about half
the normal rate.
top |
|
| 4.9 How is the rate of factor Xa affected by urea, guanidine hydrochloride and
SDS? |
|
The activity of factor Xa on the chromogenic substrate Bz-IEGR-pNA in the presence of these
denaturants is as follows:
Urea: In 0.25 M urea, factor Xa cleaves at about 33% its normal rate; at 0.5 M, 25% its normal
rate, in 1 M urea, about 10% its normal rate, while in 2 M urea no cleavage is detected.
Guanidine: In 0.25 M guanidine hydrochloride it cleaves at about 15% its normal rate, and in
0.5 M it cleaves at about 5% the normal rate.
SDS: Factor Xa is unaffected by concentrations of SDS below 0.005%. At 0.01% it cleaves at about
half its normal rate, and at 0.03% at about one-third normal. At 0.1% and above no cleavage is
detected.
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| 4.10 Can MBP fusions be digested with factor Xa while bound to the amylose resin? |
|
Cutting a bound fusion with factor Xa has been done, by us and in Rawlings and Kaslow, 1992,
J Biol Chem 267(6)3976-82. It has two problems that make it less than ideal. First, it takes a
lot more factor Xa. With the fusion immobilized, it takes 5% for 24-48h to get decent cleavage.
The second problem is that during the incubation, a little of the MBP always seems to fall off
the column. This may be because there are trace amounts of amylase bound to the column too, and
the amylase liberates enough maltose over time to elute some of the MBP.
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5. SEPARATION OF FUSION PROTEIN DOMAINS
AND STORAGE |
|
| 5.1 In order to re-bind MBP to the column, the maltose must be removed. Can this
be done by dialysis? |
|
Dialysis does not work very well to remove maltose from maltose-binding protein. This is a general
phenomenon of binding protein/ligand interactions - after the free ligand is gone, ligand that
is released from the binding site usually finds another binding site before it encounters the dialysis
membrane (Silhavy et al., 1975, PNAS 72, 2120-4). We have determined empirically that binding the
fusion to a chromatography resin and then washing away the maltose is much more effective. Another
approach is to dialyze vs. buffer in which the protein looses affinity for the ligand (e.g., 2
M urea or pH 4) - this latter approach is not a general one, since some proteins might not be stable
in a denaturant or at low pH. We still prefer standard chromatography (e.g. DEAE) as the separation
step, since it can separate the factor Xa and MBP from the protein of interest. In case
MBP co-elutes with the protein of interest, we include a large volume washing step to remove the
maltose before starting the salt gradient. This way, the mixture can be run over an amylose column
afterward if necessary.
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| 5.2 How should I store my protein after it is purified? |
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Most proteins can be stored for at least a few days at 4° without denaturing. For longer
term storage, one can either freeze at -70° or dialyze into 50% glycerol and store at -20°.
When storing at -70°, aliquot the protein so only the portion to be used must be thawed - repeated
freeze/thaw cycles denature many proteins. Freezing at -20°without glycerol may be OK if the
freezer is not frost-free - the temperature in frost-free freezers cycles enough to cause
problems if glycerol is not present.
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| 5.3 Is there any way of avoiding degradation of protein during storage at 4°?. |
|
Instability of fusion proteins during storage is not generally a problem, but when it is it
has always been traced to contaminating E. coli proteases. Try washing the column more before eluting
with maltose.
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6. MBP INFORMATION |
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| 6.1 What is MBP2*? Is it different from wild-type MBP produced from E. coli? |
|
MBP2* is the protein produced from a pMAL-c2 vector that has a stop codon linker (NEB #S1061S)
cloned into the XmnI site. It differs from wild-type MBP by the addition of a methionine
at the amino terminus (as do all fusions made in pMAL-c2), the deletion of the last four residues
of wild-type MBP, and the addition of the residues encoded by the polylinker.
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| 6.2 Has the crystal structure of the maltose binding protein been determined? |
|
The references for the crystal structure of MBP are Spurlino et al. (1991), J Biol Chem 266(8)5202-19,
and Sharff et al. (1992), Biochem 31, 10657-10663.
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| 6.3 How much of MBP is dispensable for binding? |
|
The exact region of MBP necessary for binding has not been determined, but the structure indicates
that most of the protein is necessary. From the structure, it looks like few if any residues could
be deleted at the C-terminus (other than the polylinker residues, of course). It is possible that
some of the N-terminus could be deleted, but so far this has not been tested.
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| 6.4 What is the Kd , pI and extinction coefficient for MBP2*? |
|
The Kd of MBP for maltose is 3.5 uM; for maltotriose, 0.16 uM (Miller et al., 1983, J Biol Chem
258(22)13665-72.
The extinction coefficient and pI of MBP2* (calculated by computer) are 1.5 (0.1%, 1 cm path)
and 4.92, respectively.
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| 6.5 What is the origin of the MBP region of the pMAL vectors? |
|
The malE gene in the pMAL vectors was derived from the HinfI fragment of the E.
coli malB region. The HinfI fragment lacks the last four amino acids of wild-type malE,
and of course additional amino acids are added as encoded by the polylinker.
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| 6.6 Is MBP a monomer or a dimer? |
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MBP is a monomer. There is one published report that MBP can dimerize in 10 mM Tris-HCl (Richarme,
1982, Biochem. Biophys. Res. Comm. 105, 476-81) but we have not been able to reproduce this result
with MBP2*. Gel filtration chromatography in both column buffer and 10 mM Tris-HCl gives a single
peak of about 40 kDa.
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7. MISCELLANEOUS |
|
| 7.1 What is the full reference for the pMAL chapter in "Current Protocols
in Molecular Biology"? |
|
Riggs, P. 1992. Expression and purification of maltose-binding protein fusions. In Current
Protocols in Molecular Biology (F.A. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman,
J.A. Smith, and K. Struhl, eds.) pp. 16.6.1-16.6.14, Greene Publishing and Wiley- Interscience,
New York.
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| 7.2 Protein Fusion and Purification Strain List |
|
| #E4122S |
TB1 |
ara del(lac proAB) rpsL (phi80 lacZdelM15) hsdR
=JM83 hsdR |
|
|
|
| #E4121S |
ER2507 |
del(malB) zjb::Tn5 del(lac)U169 hsdS20 ara14 galK2 rpsL20 xyl5 mtl1 supE44
leuB6fhuA
= RR1 del(malB) del(lac)U169 pro+ fhuA
The malE gene is included in the malB deletion, so this strain does not make any
MBP from the chromosome. It does not have the lacZdelM15 allele, so it cannot be
used for a-complementation (no blue-to-white screen on Xgal). This strain can be
transformed with high efficiency, similar to RR1 and HB101.
|
|
|
|
| Protease deficient strains: |
| |
|
|
| #E4127S |
ER2508 |
Ion::Tn10del16del17 del(malB) zjb::Tn5 del(lac)U169 hsdS20 ara14 galK2 rpsL20
xyl5 mtl1 supE44 leuB6 fhuA
= RR1 lon del(malB) del(lac)U169 pro+ fhuA
The malE gene is included in the malB deletion, so this strain does not make any
MBP from the chromosome. This strain can be transformed with fairly high efficiency, about
10x down from RR1 and HB101
|
|
|
|
| #E4124S |
CAG626 |
lon lacZam trpam phoam supCts malam rps
CAG626 is ECOk r+m+, so your plasmid has to be modified (i.e., come from an m+ strain
such as TB1, JM83, JM107, etc.) in order to get transformants; the transformation frequency
is about 100x down from other common strains used for recombinant DNA work, so it helps
to use electroporation. (from C. Gross; Baker et al., 1984, PNAS 81, 6779-83) |
|
|
|
| #E4123S |
CAG597 |
rpoHam165 zhg::Tn10 lacZam trpam phoam supCts malam rpsL
rpoHam = htpRam, codes for the heat-shock sigma factor; this strain has a temperature-sensitive
amber supressor (supCts), and should be maintained at 30°C. When you induce your expression
system (e.g. when you add IPTG), shift the cells to 37o or 42°. CAG597 is ECOk r+m+,
so your plasmid has to be modified (i.e., come from an m+ strain such as TB1, JM83, JM107,
etc.) in order to get transformants; the transformation frequency is about 100x down from
other common strains used for recombinant DNA work, so it helps to use electroporation.
(from C. Gross; Baker et al., 1984, PNAS 81, 6779-83) |
|
|
|
| #E4125S |
CAG629 |
lon rpoHam165 zhg::Tn10 lacZam trpam phoam supCts malam rps
rpoHam =htpRam, codes for the heat-shock sigma factor; this strain has a temperature-sensitive
amber supressor (supCts), and should be maintained at 30°C. When you induce
your expression system (e.g. when you add IPTG), shift the cells to 37° or 42°C.
CAG629 is ECOk r+m+, so your plasmid has to be modified (i.e., come from an m+ strain such
as TB1, JM83, JM107, etc.) in order to get transformants; the transformation frequency
is about 100x down from other common strains used for recombinant DNA work, so it helps
to use electroporation. (from C. Gross; Baker et al., 1984, PNAS 81, 6779-83) |
|
|
|
| #E4126S |
PR1031 |
thr::Tn10 dnaJ259 leu fhuA2 lacZ90(oc) lacY glnV44 thi
This strain, an F- derivative of CAG748, has a mutation in the dnaJ gene, which codes
for a "chaperonin." This defect has been shown to stabilize certain mutant proteins
expressed in E. coli, e.g. the lacZ90 ochre fragment and mutants of lambda repressor. (dnaJ
mutant with linked Tn10; from C. Gross via K. Silber; Straus et al. (1988) Genes Dev. 2:897-904;
see also Reidhaar-Olson et al. (1990) Biochemistry 29:7563-7571). |
|
|
|
| E4128S |
KS1000 |
ara del(lac-pro) nalA argIam rif thi1 del(tsp)::kan eda-51::Tn10 /F' lacIq
lac+ pro+
This strain is defective in a periplasmic protease, which can cleave proteins that are
overexpressed in the cytoplasm when the cells are lysed to make a crude extract. (tsp=tail
specific protease, periplasmic protease cleaves the "tail" of a lambda repressor
mutant); from K. Silber; Silber et al. (1992) PNAS USA 89:295-9) |
|
|
|
| E4129S |
UT5600 |
ara14 leuB6 azi6 lacY1 proC14 tsx67 del(ompT-fepC)266 entA403 trpE38 rfbD1
rpsL109 xyl5 mtl1 thi1
This strain is deficient in an outer-membrane protease that cleaves between sequential
basic amino acids (e.g. arg-arg). It can cleave proteins that are overexpressed in the
cytoplasm when the cells are lysed to make a crude extract. (CGSC7092; from B. Bachmann;
Elish et al. (1988) J. Gen. Microbiol. 134: 1355-1364; Grodberg & Dunn (1988) J. Bacteriol
170:1245-1253; Sugimura & Higashi (1988) J. Bacteriol 170:3650-3654). |
|