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Contents
1. Introduction
2. Recombinant protein expression in E.coli
2.1 Promotors and fusion partners
2.2 Codon bias, disulfide bond formation and E.coli strains
2.3 Cell-free expression
3. Preparation and solubilization of inclusion bodies
4.
5. Refolding
5.1 Protein concentration during refolding
5.2 The refolding buffer
5.3 Disulfide bond formation
5.4 Refolding methods
5.5 Folding aids
5.6 Folding screens
6. Analysis of refolded protein
7. Conclusion
Figure 1
Table 1
Table 2
Table 3
References
1
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
2
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
in general, ‘fuse’ the protein of interest with formation. This strain may be particularly
another, to circumvent the solubility issue and useful for eukaryotic or intracellular proteins
also aid in purification. The classic GST which typically display alternative codon
fusion system has been implemented usage and require disulfide bond formation,
successfully for a large number of proteins [1- respectively.
4], however more recently, a number of other
alternative options have also been developed 2.3 Cell-free expression
(Table 2 and [5]). One example is the 42 kDa
Cell free expression (also known as ‘in vitro
maltose binding protein (MBP), which has
transcription-translation’) has been an
been used successfully to increase the
invaluable tool for many years. It exploits the
solubility of a range of targets [6-8] and has
E.coli, wheat germ and rabbit reticulocyte
been shown to have little effect during
systems to generate protein and is
crystallization - this is a great advantage, as
increasingly seen as a viable alternative to
fusion tags generally need to be removed to
other expression systems for recalcitrant
aid in crystallography. A similar tag is Nus A
proteins. The technology itself was developed
(Novagen), a 54 kDa protein, which was
some 30 years ago [17], however, more
identified as being the most soluble protein
recently been subject to several significant
out of a pool of almost 4000 E.coli proteins
developments [18,19]. These include the
[9]. As well as assisting in folding, some tags,
‘continuous-flow’ system whereby amino
such as the ~15 amino-acid S-tag (Novagen),
acids and energy sources are supplied into a
for example can be used to detect, quantitate
reaction chamber, while synthesized proteins
and purify soluble protein [10].
and used substrates are removed using an
ultrafiltration membrane [18], and the
2.2 Codon bias, disulfide bond formation
“semicontinuous’ method, involving the use of
and E.coli strains
two chambers separated by a dialysis
Poor expression of a target protein may also membrane [19,20]. Roche also now offers a
be associated with codon bias – that is, in vitro transcription-translation ‘Rapid
codons used infrequently in the prokaryotic Translation System’, which has been
system. The Rosetta (Novagen) and BL21- successful for a number of targets, and can
CodonPlus strains (Stratagene) have the also incorporate molecular chaperones,
advantage of co-expressing plasmids that detergents and other additives to assist in
code for the rare tRNA’s and have been used folding.
with success for a number of proteins [11-13]. Although not as efficient as the E.coli
Moreover, the development of E.coli that system, the cell free system based upon
accommodates disulfide bond formation can wheatgerm has also been used [21-23].
also improve the yields of certain targets. The Being a eukaryotic system, it has been
AD494(DE3) strain (Novagen), which has a explored as an alternative, particularly for the
single mutation in the thioredoxin reductase production of proteins that may not otherwise
gene, has enabled the production of a range express in E.coli. Cell-free protein expression
of proteins [14-16]. The Origami strain has been limited in the past by low efficiency,
(Novagen), however, combines a double membrane clogging and consequent
mutation in both the thioredoxin reductase questionable reproducibility. However, in light
and the glutathione reductase gene, hence of recent advancements in the technology,
providing a more favourable oxidizing continued improvements may encourage
environment within the cytoplasm. more frequent use and in the future it may
Furthermore, the recent Rosetta-Gami strain emerge as an increasingly viable alternative
(Novagen) is a powerful combination of the to the traditional E.coli expression system.
Rosetta and Origami strains, encompassing
rare codon usage and disulfide bond
3
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
4
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
5
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
are instances, however, where refolding into fruitful. If a protein has a hexa-histidine tag, it
low molar concentrations of denaturant (1-2 can be immobilized on a Ni2+ affinity column
M) aids in the solubility of the protein. in its denatured state. By applying buffers
Rapid dilution has been used successfully with a decreasing concentration of
for a range of proteins [43-46], however, the denaturant, either step-wise or by using a
time period used dilution may be detrimental gradient, the protein can be refolded and then
for some proteins, especially if they usually eluted [48,49].
refold over a relatively long time period of Gel filtration is an alternative technique,
minutes to hours. Forcing the protein to adopt whereby the denatured protein is loaded onto
its conformation in a short time frame may the column and refolds as it is passed
increase its chances of misfolding and through with buffer [50,51]. A variation of this
aggregation. Slow dilution is an alternative is to equilibrate the column with a linear
method, as it is a more gentle approach and gradient with decreasing denaturant
dramatically decreases the effective concentrations, such that the protein refolds
concentration of the refolding protein. The gradually [52]. Flow rates required for
‘dropwise’ or ‘pulsed dilution’ method involves successful on-column refolding vary – for
the solubilized inclusion bodies being some proteins, slower flow rates improves
delivered very slowly to the refolding buffer recovery [38], in other cases faster flow rates
(using a pump) and has been successfully are better [53].
used for some proteins [36,47]. On-column refolding methods have also
been improved by immobilizing common
Dialysis ‘foldases’ onto the column matrix and
exploiting them as a folding ‘platform’. This
In this method, the concentrated denatured
has been demonstrated successfully with
protein is dialyzed against a refolding buffer,
GroEL [54,55]and DsbA/DsbC [56]. One
such that the concentration of denaturant
associated concern with on-column refolding
decreases with buffer exchange. This slow
is the clogging of filters by aggregated
removal of denaturant allows refolding to
protein, however, carefully filtering or
occur. Unfortunately, the slow removal of
centrifuging samples prior to loading onto the
denaturant often results in the formation and
column, and sensible choice of column matrix
exposure of long lived intermediate species
can minimize these problems.
over a time period and hence there may be
an increased propensity for the protein to
Other refolding techniques
aggregate. A variation of one-step dialysis,
where protein is dialyzed against refolding Whilst a majority of proteins can be refolded
buffer containing no denaturant, is the use of by classic dilution, dialysis or on-column
a series of refolding buffers with decreasing techniques, the potential development of
denaturant concentrations. By dialyzing in a other refolding techniques is constantly being
step-wise fashion (usually 1-3 progressive explored by researchers. One recent foray
lower denaturant concentrations), this allows has been the use of reverse micelles, in
an equilibrium to be established. Once again, which the protein is trapped in a water-
whilst refolding is more controlled in this sodium bis-2-ethylhexyl sulfosuccinate-
environment, long-live intermediate species isooctane reverse micellar system [57]. This
can still be problematic. was shown to result in the successful
recovery of monomeric protein where other
On-column refolding techniques had failed. Variation in the size of
the micelles enabled manipulation of the
On-column refolding has been applied to
degree of oligomerisation of the protein.
several proteins with success and offers an
alternative where other methods may not be
6
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
7
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
6. CONCLUSION
Handling inclusion bodies can be a time-
consuming and often frustrating trial-and
error process. Whilst fundamental principles
underpin the process, there are no clear rules
which apply to all proteins, and an approach
suitable for one protein maybe equally
inappropriate for another. Despite this,
working with inclusion bodies can be
beneficial, especially when it is impossible to
express reasonable quantities of soluble
protein. As more proteins are successfully
refolded, trends and patterns may become
clearer. This will aid the progression and
further development of biotechnological tools.
8
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
Figure 1: A schematic outline of the procedure for purification and refolding of proteins
from inclusion bodies
`
Cell Lysis
(eg.sonication, French press)
Centrifugation
Refolding
Dialysis On-column refolding Dilution
(direct or step) (linear or step-wise gradient) (step or drop-wise)
Post-refolding Analysis
Eg. Activity assay Circular Dichroism
Non-denaturing PAGE Size Exclusion Chromatography
Light-scattering Ultracentrifugation
9
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
Table 2: Examples of fusion partners and tags which facilitate solubility and tracking
protein expression
10
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
Table 3: Examples of buffer additives which may be used to facilitate protein refolding
CHAPS 30 mM Detergent
EDTA 20 mM Chelator
Glycerol 10-50% Stabilizer
Guanidine HCl 0.1-1 M Chaotroph
L-arginine 0.4-0.5M Stabilizer
Lauroylsarcosine (sarkosyl) Up to 4 M Detergent
Lauryl maltoside 0.3 mM Detergent
MgCl2/CaCl2 2-10 mM Cation
NaCl/Ammonium sulfate 0.2-0.5 M Salt
Non-detergent sulfobetaine (NDSB) 256/201 Up to 1M Solubilizer
PEG 3350 Up to 0.05% (w/v) Osmolyte
SDS 0.1 % Detergent
Sodium citrate/sulfate 0.2-0.5 M Salt
Sucrose/glucose 0.4 M Stabilizer
TMAO 1-3 M Osmolyte
Tris 0.4-1 M Buffer
Triton X-100 0.1-1 % Detergent
Tween – 80 0.01 % Detergent
Urea 0.1-2 M Chaotroph
11
Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.
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