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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

A PRACTICAL GUIDE TO PROTEIN EXPRESSION AND REFOLDING


FROM INCLUSION BODIES

Lisa D. Cabrita, Michelle K.M. Chow and Stephen P. Bottomley

This is an edited version of:


“Protein Expression and Refolding – a practical guide to getting the most out of inclusion
bodies”, Cabrita and Bottomley, 2004, Biotechnology Annual Review, 10:31-50.

If referring to anything in this document, please cite the above paper.

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

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

1. INTRODUCTION 2. RECOMBINANT PROTEIN EXPRESSION


IN E.COLI
One of most significant aspects of biomedical
and scientific research in the post-genomic The expression of recombinant proteins
era is the ability to rapidly express and purify within E.coli is affected by several factors.
a target protein. With an immense amount of These include, but are not limited to: plasmid
sequence data available, all over the world, copy number, mRNA stability, upstream
structural genomic projects are being elements, temperature and codon usage. The
undertaken in which a vast array of proteins expression of an uncharacterized protein
are expressed, purified and structurally often depends largely on a combination of
characterised. In addition to these high- these and other factors, and success in
throughput approaches, both academic and protein expression is often difficult to predict.
industrial laboratories are expressing proteins However, over the years numerous advances
of interest for structural, functional and have been made to improve both expression
therapeutic investigations. The general and solubility. This has been made possible
course for this process involves rapid cloning through the development of novel tags, fusion
of target genes, followed by recombinant partners, and vector systems, such that the
expression of the protein, usually in the host choices for recombinant expression in E.coli
E.coli. are continually expanding.
Currently, E.coli remains the dominant
expression host for recombinant proteins, 2.1 Promoters and fusion partners
due to its advantages such as ease of
In regulating protein expression, the choice of
handling, cost effectiveness and high
promoter and/or vector system is important,
success rates. However, it does have some
as one system may be more suited to a given
disadvantages, for example, the inability to
target protein than another. Several
perform many post-translational modifications
promoters are available (Table 1) - probably
and frequent deposition of the expressed
the most well-known variety is the T7-derived
protein product into insoluble inclusion
promoter, as found in the pET vectors
bodies. Inclusion body formation is often an
(Novagen). These IPTG-inducible promoters
undesired event, and a number of
have in the past been associated with “leaky”,
approaches can be utilized to obtain soluble
or premature, expression prior to induction,
protein. On the other hand, inclusion body
which is problematic for proteins which are
formation does not necessarily have to be a
toxic to cells. However, this issue has been
dead-end process. Sometimes harvesting of
addressed with co-transformed plasmids
proteins from inclusion bodies can prove to
pLysS and pLysE which can act as strong
be very fruitful and may present a valid option
repressors. Aside from this issue, the T7 is a
for successful purification (Figure 1). In
strong promoter which enables high level
recent years, there has been an increase in
expression of target proteins. Overexpression
products and protocols which are generally
can also lead to the formation of intracellular
applicable to the inclusion body issue. New
inclusion bodies, sometimes in far greater
strains of E.coli and fusion partners are
excess than the soluble protein. This
available, which offer a range of options to
insoluble-soluble ratio can sometimes be
minimize, or maximize, inclusion body
adjusted by altering the expression time,
formation. Furthermore, a more rational
induction temperature and/or IPTG levels.
approach to protein refolding has been
The T7-based vectors have previously
established, which allows the user to
included affinity tags to facilitate the detection
determine very quickly whether refolding from
and purification of proteins, although they are
inclusion bodies is a viable option.
also now often designed to include other
features. Of interest are ‘fusion partners’ that

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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

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

3. PREPARATION AND SOLUBILIZATION need for disulfide bond reduction is


OF INCLUSION BODIES highlighted by a pivotal study which
Inclusion bodies are dense amorphous demonstrated that these bonds persist in high
aggregates of misfolded protein. They are denaturant concentrations in the absence of
generally formed if a protein has a high reducing agents [33]. Usually solubilization
propensity to misfold and aggregate, or if the can be performed in any buffer that is
cellular protein production machinery is compatible with the protein of interested, for
overwhelmed and unable to operate example Tris, Hepes or phosphate. Generally
efficiently. The formation of inclusion bodies a neutral pH (7-8) is suitable for
can sometimes be especially advantageous, solubilization.
especially if the protein is toxic to the cell, or Upon solubilization of inclusion bodies,
susceptible to proteolytic attack. ample incubation time should be allowed for
Inclusion bodies are easily identifiable, complete unfolding to occur. Incubation at
with a morphology similar to strings or either room temperature or 30°C for 1-4
clusters [24], and their isolation from other hours is generally sufficient, whilst some
cellular components can be easily achieved. studies have opted for 16-24 hours at 4°C.
Inclusion bodies are contained within the Sometimes inclusion bodies may be difficult
insoluble fraction yielded from cell lysis and to solubilize and therefore some agitation or
subsequent centrifugation, and it is generally increased temperature may be required.
accepted that they may be composed of 40- Sometimes inclusion bodies are purified
90% target protein. Successful renaturation further by column chromatography such as
depends on the purity of inclusion bodies, as ion exchange, size exclusion or metal affinity
proteinaceous contaminants can decrease conducted under denaturing conditions [34-
the efficiency of renaturation, presumably as 36]. This has been seen to enrich the
such contaminants can promote co- proportion of monodispered protein which
aggregation [25]. Inclusion bodies are can increase the yield of the refolded target
therefore best washed and centrifuged a protein [37]. More recently, it has been shown
several times in buffer containing detergents that inclusion bodies could be directly purified
such as Triton X-100 (0.1-4% (v/v)), sodium by gel filtration only using a macroporous
deoxycholate (2% (w/v)), sarkosyl, or even medium (eg. 4% agarose) coupled with a
low concentrations (0.5-1 M) of denaturants French press to reduce cell debris [38].
such as guanidine hydrochloride (GdnHCl) or
urea. Such additives remove cellular
contaminants that adsorb onto the 4. REFOLDING
hydrophobic inclusion bodies. The renaturation process aims to effectively
Following washing, inclusion bodies are remove the denaturant and thiol reagents and
then solubilized, usually with 4-6 M GdnHCl allow the protein to refold. The refolding
or 8 M urea. GdnHCl is a stronger process is a competing reaction with
denaturant, while during prolonged misfolding and aggregation events and its
incubations at alkaline pH urea can suffer success depends on a number of factors.
from the formation of isocyanate ions which Studies have shown that for many proteins,
can modify amino acid side chains [26,27]. especially those larger than 150 amino acids,
Aside from denaturants, other unfolding folding involves the formation of an
alternatives include detergents such as intermediate species, often resembling a
sarkosyl [28,29], SDS [30] and alkaline pH ‘molten globule’. The molten globule
[31,32]. It is important that during unfolding ensemble can represents a branch point in
any disulfide bonds present are also reduced the folding pathway where it may also lead to
– this is usually achieved with β- misfolding and aggregation, as this species
mercaptoethanol or DTT (5-100 mM). The contains some secondary structure, but little

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

tertiary structure and hydrophobic patches 4.3 Disulfide bond formation


normally buried within the protein are
A redox system during renaturation is
exposed to solvent [39]. Under appropriate
required for the correct formation of proteins
conditions these regions can promote
with native disulfide bonds. The combination
aberrant interactions that may lead to
of reduced and oxidized forms of redox
aggregation. Therefore it is important to
agents are generally used in molar ratios
minimize the aggregation reaction. Several
from 1:1 up to 10:1. Glutathione
variables play important roles in this process,
(GSH/GSSG) is a common reagent, however,
including final concentration of the protein to
other alternatives may include a combination
be refolded, the components of the refolding
of cysteine and cystine, or DTT/oxidized
buffer and the method of refolding.
glutathione. While molecular oxygen in the air
is suitable and sufficient to promote disulfide
4.1 Protein concentration during refolding
bond formation, a redox system accelerates
The amount of protein refolded will impact the the shuffling of disulfide bonds. Trace
yield of protein obtained. Folding competes amounts of metal ions and slightly alkaline
with aggregation, and therefore it is generally pH (8-9) may also be included to catalyze the
accepted that refolding at low protein redox reaction. EDTA can be beneficial to
concentrations (10-100µg/ml) is the most minimize the effects of oxygen oxidizing
successful approach. There have been thiols. The time required for disulfide bond
situations where proteins have been refolded shuffling varies between proteins, anywhere
in high concentrations of up to 5 mg/ml [40- from 2 hours to 150 hours. 16-48 hours is
42], albeit in low concentrations of common for efficient disulfide shuffling,
denaturant, however, generally speaking, the however, the exact time must be determined
lower the final protein concentration during empirically.
refolding, the greater the efficiency of the
process. 4.4 Refolding methods
Several different methods can be used to
4.2 The refolding buffer refold proteins. These include dialysis,
Components of a refolding buffer vary widely, dilution and column chromatography
depending on the protein of interest. techniques. The method selected depends on
Parameters such as pH, ionic strength, redox the propensity of the protein to aggregate and
conditions and the presence of ligands can all the kinetics of refolding. The temperature at
influence the outcome of refolding. Most which refolding is performed may vary,
commonly Tris or Hepes-based buffers at although generally, in order minimize
neutral pH with 50-500 mM NaCl are used, aggregation, 4°C is best.
however again this depends on the target
protein. Numerous additives can also be Dilution
included, with varying success with numerous
Refolding by dilution can be described as
targets. These include detergents, polar
‘rapid’ or ‘slow’. In rapid dilution, the
additives, weak chaotrophs, osmolytes and
denatured protein is delivered to the refolding
cations (Table 3). Such additives may either
buffer such that in a very short time period,
act as stabilizers (which stabilize the native
the concentrations of both the protein and
state or solubilize intermediate forms), or
denaturant decrease rapidly. For example, if
promote correct folding by preventing
the protein was denatured in 8 M urea and
aggregation. If the target protein is prone to
diluted 10-fold into buffer, the final
proteolysis, a common approach is to include
concentration of denaturant is 0.08 M. The
proteinase inhibitors (eg. PMSF, aprotinin,
aim of dilution is to remove the denaturant, so
leupeptin) in the refolding buffer.
its final concentration should be low. There

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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

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

4.5 Folding aids yields. It was found that while procathepsin


folded best in the presence of detergent,
Several molecular chaperones can be
arginine and a redox system, cathepsin
included either in vivo or in vitro to aid folding.
required only glycerol and the redox couple.
The most well known E.coli chaperones
This illustrates the powerful nature of the
include GroEL-GroES, DnaK-DnaJ-GrpE
factorial screen and also demonstrates how
(Hsp70) and also ClpA/ClpB (Hsp100) which
seemingly similar proteins may have very
have been used successfully in refolding
different requirements for refolding.
studies [58-61]. Whilst molecular chaperones
promote correct folding, foldases can
accelerate the process. The three known 5. ANALYSIS OF REFOLDED PROTEIN
types of foldases are 1) peptidyl prolyl
Once refolding is completed, it is necessary
cis/trans isomerases (PPI’s), which arrange
to determine whether the process has yielded
prolines into their correct orientation [62], 2)
folded or aggregated protein, and also
disulfide oxidoreductase (DsbA) and disulfide
whether disulfide bonds (if any) have formed
isomerase (DsbC), which are found in E.coli
correctly. Perhaps the simplest way to assess
and promote disulfide bonds [63,64] and 3)
the quality of the protein is by using a known
protein disulfide isomerase (PDI), a
activity assay. While this is possible for some
eukaryotic protein which catalyses oxidation
proteins, a number of targets will have no
and isomeration [65].
known function or structure, especially
considering the growing level of high
4.6 Folding screens
throughput production of proteins from
As finding the right conditions to refold a different genomes. Therefore, it is important
protein can be a time-consuming process, to develop other techniques to analyse the
several commercial screens are available to nature of the protein.
focus on potential conditions that return the Such techniques commonly include size-
best yield of monomeric protein. One such kit exclusion chromatography and non-
is Hampton Research’s FoldIt screen, which denaturing PAGE, as well as circular
employs a variety of additives, redox dichroism (CD) which reports on secondary
conditions and pH. Similar kits are also structure. Distinct features of a typical CD
available through Novagen and Sigma- scan report on the presence of α-helical, β-
Aldrich. These kits are the result of sparse sheet or random coil structure. Proteins will
screens which have proven successful for the generally be a combination of α-helical and β-
refolding of a number of proteins [66-68]. The sheet content, while aggregated material may
commercially prepared kits enable a number produce a spectrum of predominately random
of refolding conditions to be sampled coil. Fluorescence techniques such as
simultaneously on a small scale, the aim dynamic light scattering [70], which
being to find suitable conditions which can be determines the average diameter of particles
up-scaled for batch refolding and purification. in solution and lateral turbidimetry [6] can
An elegant example of using factorial also report the presence of aggregates [71],
screens is demonstrated by a study involving as can ultracentrifugation [72] and electron
procathepsin S and cathepsin S [69]. An microscopy [73].
initial screen used to identify folding Assessing the nature of disulfide bonds
conditions targeted L-arginine and pH as two can be achieved by a number of methods.
key factors. While pH was important for both Perhaps the most straightforward method is
proteins, arginine was more beneficial for the use of reducing and non-reducing gel
procathepsin only. Once these conditions electrophoresis. In the absence of reducing
were established, a second screen based on agent, there should be a defined ‘band shift’,
these findings was performeds to improve accompanied with any additional bands that

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

were record of linked domains. For a single


domain protein, a ‘laddering’ effect is a tell-
tale sign of intermolecular disulfide bond
formation. The use of thiol specific dyes
(eg.DTNB (Ellman’s reagent)) [74], mass
spectrometry [75] and gel electrophoresis
(‘cysteine counting’) [76] are all common
techniques that are also employed.

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.

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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

Pellet (insoluble fraction) retained

Purification of Inclusion Bodies


Resuspension and centrifugation Chromatography (denaturing conditions)
Eg. Triton X-100, high salt, EDTA Eg. Gel Filtration, Ni-NTA

Solubilization of Inclusion Bodies


Example denaturants:
4-6 M GdnHCl 6-8 M Urea 0.5-2% SDS

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

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

Table 1: Examples of promoters often used in E.coli expression

Promotor type Example vector Inducing agent

T7 pET (Novagen) IPTG


T5 pQE (Qiagen) IPTG
trc pTrcHis (Invitrogen) IPTG
tac pMAL (New England Biolabs) IPTG
lac pTrip1Ex2 (Clontech) IPTG
Trp pLEX (Invitrogen) Tryptophan
araB PBAD (Invitrogen) L-arabinose
PL (λ) pKC30 Temperature shift (42°C)
phoA pBKIGF2B-A Phosphate
PLtetO-1 plP-PROTete-6xHN (Clontech) tetracycline

Table 2: Examples of fusion partners and tags which facilitate solubility and tracking
protein expression

Tag Size Location in relation to target


protein

Chloramphenicol acetyltransferase 24 kDa N terminus


Glutathione S-transferase (GST) 26 kDa N terminus
Maltose binding protein (MBP) 40 kDa N or C terminus
NusA 54 kDa N terminus
S-Tag 15 residues N or C terminus, or internal
Thioredoxin 11 kDa N terminus
Ubiquitin 76 residues N terminus
Z-domain (derived from Protein A) 58 residues N Terminus

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

Table 3: Examples of buffer additives which may be used to facilitate protein refolding

Additive Concentration used Effect

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

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Protein Expression and Refolding from Inclusion Bodies, Cabrita et al.

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