Analysis of the effect of potato carboxypeptidase inhibitor
pro-sequence on the folding of the mature protein
Sı
´
lvia Bronsoms, Josep Villanueva, Francesc Canals, Enrique Querol and Francesc X. Aviles
Institut de Biotecnologia i Biomedicina and Departament de Bioquı
´
mica i Biologia Molecular, Universitat Auto
`
noma de Barcelona,
Spain
Protein folding can be modulated in vivo by many factors.
While chaperones act as folding catalysts and show broad
substrate specificity, some pro-peptides specifically facilitate
the folding of the mature protein to which they are bound.
Potato carboxypeptidase inhibitor (PCI), a 39-residue pro-
tein carboxypeptidase inhibitor, is synthesized in vivo as a
precursor protein that includes a 27-residue N-terminal and
a seven-residue C-terminal pro-regions. In this work the
disulfide-coupled folding of mature PCI in vitro has been
compared with that of the same protein extended with either
the N-terminal pro-sequence (ProNtPCI) or both N- and
C-terminal pro-sequences (ProPCI), and also with the
N-terminal pro-sequence in trans (ProNt + PCI). No
significant differences can be observed in the folding kinetics
or efficiencies of all these molecules. In addition, in vivo
folding studies in Escherichia coli have been performed using
wild-type PCI and three PCI mutant forms with and without
the N-terminal pro-sequence, the mutations had been pre-
viously reported to affect folding of the PCI mature form.
The extent to which the Ônative-likeÕ form was secreted to the

molecular chaperonesÕ, and their role in folding has been
demonstrated both in vitro and in vivo [7]. There are not
many examples of the role of the pro-regions in small
disulfide-rich proteins. In these proteins, the folding process
differs from that of larger proteins in that is strongly
constrained by the formation of the disulfide bridges.
Among the most studied proteins of this group we find the
bovine pancreatic trypsin inhibitor (BPTI). Its N-terminal
pro-region contains a cysteine residue which appears to
increase both the yield of properly folded mature BPTI and
therateofthefoldingprocessin vitro [10], providing an
intramolecular thiol-disulfide catalyst. Nevertheless, it did
not appear to have any positive effect under physiological
conditions [11]. Similarly, the pro-region of the guanylyl
cyclase activating peptide (GCAPII) contributes signifi-
cantly to the correct disulfide-coupled folding of the mature
protein and the dimerization of the molecule [12]. In
contrast, the studies performed with x-conotoxins demon-
strated that the mature forms of these molecules contain
sufficient information to direct their folding and correct
disulfide pairing in vitro [13,14]. In all cases, the in vitro
folding of the mature disulfide-rich protein is characterized
by a low efficiency and a slow kinetics. This fact suggests
that these proteins need other factors, apart from their
mature amino acid sequence, in order to fold efficiently and
rapidly into the native form in vivo. The nature of these
factors, whether they are found in their pro-region or in
Correspondence to F. X. Aviles and J. Villanueva, Institut de
Biotecnologia i Biomedicina, Universitat Auto
`

suggest a possible involvement of them in the in vivo folding
of PCI.
Here, using different protein variants, we have investi-
gated the role of both pro-sequences in the in vitro refolding
of PCI, together with studies of the influence of the
N-terminal pro-region on its in vivo expression. Both studies
conclude that the pro-regions do not significantly influence
the folding of PCI.
Experimental procedures
Plasmid constructs and mutagenesis
A plasmid containing a synthetic gene encoding for the
major isoform of PCI (IIa)[20] cloned into pINIII-OmpA3
vector [21], was used as a template to generate the plasmidic
constructions used for the expression of the PCI forms
studied. ProNtPCI was obtained by means of one-step
PCR, subcloned into pGEM-T Vector System (Promega),
restricted with XbaIandEcoRI and ligated into pIN-III-
OmpA3 vector. Similarly, this construction was used as a
template to generate the D3, Y37G and G35P/P36G
ProNtPCI mutant genes, by means of one-step PCR.
Constructs for D3, Y37G and G35P/P36G PCI mutant
genes were achieved by PCR of wild-type mature PCI [22].
ProNtPCI was also cloned into pBAT4 expression vector
[23], derived from the pET plasmids [24], with and without
the leader sequence OmpA. ProPCI was generated from
ProNtPCI by means of one-step PCR and cloned into
pBAT4 vector without the leader sequence OmpA. All
constructs cloned into pINIII vector were transformed into
Escherichia coli strain MC1061 and those cloned into
pBAT4 vector were transformed into E. coli strain

attenuation unit at 550nm, induced by addition of 0.2 m
M
isopropyl thio-b-
D
-galactoside, and cells were harvested by
centrifugation 2.5 h after induction. The cell pellet from a
1 L culture was resuspended in 50 mL 20 m
M
Tris/HCl,
0.5 m
M
EDTA (pH 8.5) and was maintained on ice for
10 min. The solution was sonicated for 10 min on ice at
50 Hz at half power, on a Labsonic-Braun sonicator and
centrifuged at 22 000 g for 25 min. The pellet was resus-
pended in 50 mL 20 m
M
Tris/HCl, 0.5 m
M
EDTA and 2%
Triton X-100 (pH 8.5) and centrifuged at 22 000 g for
25 min. The pellet was resuspended in 10 mL 6
M
guani-
dinium chloride and 30 m
M
dithiothreitol (pH 8.5). After
6 h the sample was centrifuged at 3000 g for 10 min and
the supernatant was dialyzed against 0.1
M

M
dithiothreitol, to a final protein concentration of
46.5 l
M
. After 2 h at 25 °C, the reduced and denatured
proteins were passed through a PD-10 (Pharmacia) column
equilibrated with 0.1
M
Tris/HCl buffer (pH 8.5). The
proteins were eluted in 1.2 mL and split in three parts which
were diluted to a final protein concentration of 14.5 l
M
,
with the 0.1
M
Tris/HCl buffer (pH 8.5), the same buffer
containing 1 m
M
Cys and the same buffer containing 4 m
M
Cys and 2 m
M
Cys-Cys, respectively. In the experiments
where the N-terminal pro-sequence was tested in trans,the
peptide was added to the denatured and reduced PCI in the
dilution buffer, to a final concentration of 14.5 l
M
.Samples
3642 S. Bronsoms et al. (Eur. J. Biochem. 270) Ó FEBS 2003
of all reaction mixtures were collected in a time-course

pH 7.5. To 985 lL of substrate, 5 lL of bovine
carboxypeptidase A (CPA) (Sigma) at 0.02 mgÆmL
)1
were added and the absorbance change at 330 nm was
measured during 2 min; then 10 lLofincreasing
concentrations of PCI or ProNtPCI were added and
the measures were continued for 2 min. The slope of the
first part of the assay corresponded to m
o
and the slope
of the second part to m
i
. The residual enzymatic activity
was calculated (m
o
to m
i
) and plotted as function of the
inhibitor concentration.
Mass spectrometry
Molecular mass was determined by MALDI-TOF mass
spectrometry on a Bruker–Biflex spectrometer. Ionization
wasaccomplishedwitha337-nmpulsednitrogenlaser
and spectra were acquired in the linear positive ion mode,
using a 19 kV acceleration voltage. Samples were pre-
pared mixing equal volumes of the protein solution and a
saturated solution of sinapinic acid, used as a matrix, in
aqueous 30% acetonitrile with 0.1% trifluoroacetic acid
(v/v).
Circular dichroism spectroscopy

Exoproteolysis
Fifteen micrograms lyophilized aliquots of ProNtPCI were
dissolved in 10 lL10m
M
Tris/HCl buffer (pH 8.5) con-
taining 5 lg of leucine aminopeptidase (Sigma). Samples
were collected in a time-course manner, diluted with water
containing 0.1% trifluoroacetic acid (1 : 2) and the pro-
teolyzed products present in the mixture were identified
by MALDI-TOF mass spectrometry.
Nuclear magnetic resonance
NMR spectra were recorded on a Bruker AMX spectro-
meter operating at 500 MHz. Two milligrams of PCI, 2 mg
of the N-terminal pro-sequence peptide and 100 lgof
ProNtPCI were resuspended in 500 lLofNaH
2
PO
4
pH 4.00 containing 10% D
2
O and the spectra were
acquired at 35 °C.
Results
Expression in
E. coli
In order to study experimentally whether PCI pro-regions
influence the folding of mature PCI, two precursor forms of
PCI were obtained by recombinant expression. The first
expression trials of ProNtPCI in E. coli MC1061 using a
pINIIIOmpA3-derived secretion vector led to a low yield of

stage of fast unspecific disulfide formation is followed by
a second stage (rate limiting step) of disulfide reshuffling
which leads to the native form [18]. Such behaviour was
investigated for the different recombinant molecular forms
of this study. The yield of native-like forms achieved after 7 h
of refolding in absence of an external thiol was similar in all
the molecules tested (<5%) (Fig. 1A, left). The RP-HPLC
chromatogram profiles from the 7 h refolding mixture of
Ó FEBS 2003 Folding of PCI precursor form (Eur. J. Biochem. 270) 3643
PCIandPCIplustheProNtintrans were indistinguishable.
Thus, we can assume that the molar ratio among scrambled
and native species is not affected by the addition of the ProNt
segment in trans. The ratio between the native form and the
ensemble of scrambled species remains constant for all tested
forms. Therefore, in the absence of redox agents, neither the
N-terminal nor the C-terminal PCI pro-sequences have an
effect on the final yield of native PCI, indicating that the
overall folding process is similar among all the molecules
tested under these conditions.
It is worth mentioning that the folding of PCI is
accelerated by the presence of external thiols in the folding
mixture [18]. While the addition of Cys accelerates the
second stage of disulfide reshuffling of scrambled forms to
native PCI, the addition of Cys-Cys enhances the first
stage of disulfide formation, which leads to the formation
of scrambled species. We analyzed the refolding process of
all the above mentioned recombinant forms in the
presence of 4 m
M
Cys and 2 m

corresponding ProNtPCI mutant protein and wild-type
ProNtPCI. Twenty-four hours after induction of protein
expression the supernatant was collected, analyzed by
RP-HPLC (Fig. 3) and the species were identified by
Fig. 1. In vitro folding studies of PCI, PCI plus the ProNt in trans, ProNtPCI, and ProPCI in the presence of selected redox agents. Reduced and
denatured proteins were refolded in the absence (no added thiols) (A), or presence (4 m
M
Cys/2 m
M
Cys-Cys) (B) of external thiols. Folding
intermediates were acid-trapped and analyzed by RP-HPLC. Elution positions of native (N) and reduced (R) forms are indicated.
Fig. 2. Refolding efficiencies of PCI, PCI plus the ProNt peptide in
trans,ProNtPCIandProPCI.Reduced and denatured proteins were
refolded in the presence of 4 m
M
Cys/2 m
M
Cys-Cys and acid-trapped
folding intermediates were analyzed by RP-HPLC. The yield of native
form was calculated in each time point from the peak areas in the
corresponding RP-HPLC chromatograms.
3644 S. Bronsoms et al. (Eur. J. Biochem. 270) Ó FEBS 2003
MALDI-TOF mass spectrometry. As previously mentioned,
theN-terminalpro-regionisdegradedintheE. coli
extracellular media when secreted therefore the protein
species found in the culture media were the mature PCI
forms without the pro-region.
The amount of each expressed protein was calculated by
comparison of the corresponding RP-HPLC peak areas
(data not shown). The final yield of each native-like

may be helpful to indicate its folding state, as it shows a
characteristic positive ellipticity band at 228 nm when it is
properly folded and possesses the wild-type Y37 residue
[22]. Thus, this maximum band at 228 nm would also be
expected for ProNtPCI. However, when the CD spectrum
of ProNtPCI was recorded, such a spectral band was not
observed at pHs of either 2.0 or 7.0 (Fig. 4). So, apparently,
the environment of Y37 is affected in the pro form.
Time-course deuteron to proton exchange monitored
by MALDI-TOF MS [27] was also performed for both
proteins. PCI contains 65 labile hydrogens and NMR has
demonstrated that five of them form the slow exchange core
[26]. The results indicate that the hydrogen exchange
kinetics followed by both proteins are similar (Fig. 5). For
each protein a major subpopulation of protons exchange
rapidly (within 2 h) and the equilibrium is reached after
24 h. However, the number of slow exchanging deuterons is
significantly different. While PCI retains five deuterons
protected from exchange when equilibrium is reached,
ProNtPCI retains nine under the same conditions. In
addition, the number of deuterons retained before achieving
Fig. 3. In vivo expression of recombinant forms of wild-type PCI, wild-type ProNtPCI and variants of them with mutations at the C-tail. (A) Schematic
representation of the recombinant proteins produced for this study. Amino acids are in one-letter code. The N-terminal pro-sequence is indicated
with a white box, the mature protein with a light shaded box and the mutated amino acids with a white box. (B) Recombinant proteins were
produced in E. coli MC1061 cells in the expression vector pINIII-OmpA3. The supernatants, after 24 h induction, were analyzed by RP-HPLC.
The quantity of each native and scrambled form was calculated from the peak area of its corresponding RP-HPLC chromatogram. The elution
position of each native or native-like form is indicated (N). In case of G35P/P36G mutants the disulfide pairing is not the same as wild-type PCI [22];
in these cases, S stands for the most stable form.
Ó FEBS 2003 Folding of PCI precursor form (Eur. J. Biochem. 270) 3645
the equilibrium is significantly higher in ProNtPCI than in

NOESY proton NMR spectra of this molecule were also
recorded (data not shown). Comparison of both spectra
indicate the lack of non-sequential interactions and, hence,
the lack of a compact and defined fold. The comparative
analysis of
1
H-NMR spectra of mature PCI and ProNtPCI
indicates that both molecules display a significant dispersion
of resonances at both the low field (amide and aromatic
region) and the high field (methyl region) (Fig. 7B,C),
reflecting a well folded and tight globular structure, as
recently we reported for mature PCI [26]. The ProNtPCI
spectrum displays a noisier appearance than that of PCI due
to the limited amount of protein available to perform the
experiment. However, it can be observed that the pattern of
resonances in both, amide and methyl regions, show
important differences. Such differences could arise from
changes in the structure of the PCI core and/or from the
additional structure adopted by the pro-region and its
interactions with the PCI core.
Discussion
Previous work from our laboratory has demonstrated that
PCI can correctly refold in vitro with kinetics and efficiencies
depending on the redox conditions used [18]. As its rate of
refolding in vitro is extremely slow, other folding helpers, as
molecular chaperones, isomerases or pro-regions are expec-
ted to catalyze its folding in vivo. Both, its N- and C-terminal
pro-regions are removed in vivo before the protein is secreted,
so it is plausible that these extensions might be involved in
the folding process. Such a role could be assigned to the

rich protein, the x-conotoxin [13,14], where the N-terminal
pro-sequence has no effect on the mature protein folding. In
contrast, for this protein, it has been found that the presence
of an additional glycine residue at the C terminus (equi-
valent to the C-terminal pro-sequence) enhances the yield of
properly folded x-conotoxin MVIIA. It is noteworthy that
a somewhat similar glycine residue, placed after the last
cysteine of the T-knot core, is conserved among all the
known members of the squash inhibitor family and in PCI
as well, where it plays an important role on its folding [22].
Unlike the case of conotoxins, in the latter molecules this
glycine cannot be ascribed to the C-terminal pro-sequence,
as it is kept in the protein after maturation.
The in vivo studies presented here show that for PCI and
for the mutant proteins tested the N-terminal pro-sequence
has no effect on the expression level or the final yield of
native form produced. In addition, the ratio between the
scrambled species and the native form that appears in the
cell culture supernatants were similar. Thus, the N-terminal
pro-region does not affect the in vivo folding of the mature
PCI in E. coli either. However, it could be argued that in its
biological environment, in potato, the pro-region of PCI
could play a role in the in vivo folding, interacting with other
cellular factors. A slightly different behaviour has been
described for another small disulfide-rich protein, BPTI, in
which the N-terminal pro-region has not been found to play
a substantial role in its disulfide bond formation or
rearrangement within microsomes [11], even though it
seems to have a slight positive effect on its folding rate
in vitro [10].

N-terminal pro-sequence and 100 lg of ProNtPCI were dissolved in 500 lLof20m
M
NaH
2
PO
4
at pH 4.00, containing 10% D
2
O and the spectra
were recorded at 35 °C in a 500-MHz spectrometer. Insets show expanded high and low field areas of the spectra of the proteins. The strong
resonances at around 1.9, 2.1 and 8.6 p.p.m., visualized in the spectrum C, are attributed to organic molecule contaminants.
3648 S. Bronsoms et al. (Eur. J. Biochem. 270) Ó FEBS 2003
center of ProNtPCI pro-region gives us information about
the possible boundaries of secondary structure elements. As
we have shown recently [28], such a behaviour is found to be
generated by the initial residues of stable regular secondary
structure elements in globular proteins, when these ones are
trimmed by exoproteases.
In depth NMR analysis (i.e. n-dimensional) of ProNtPCI
has not been performed due to the small amount of material
available. However, the comparison of monodimensional
1
H-NMR spectra indicates that ProNtPCI has a well-
defined three-dimensional globular structure and that
displays some extra interactions in addition to those
belonging to the mature native PCI. At this respect, are
noteworthy the changes observed at very low field (amide
region) between the spectra of both proteins, and parti-
cularly the resonance visualized at about 11.8 p.p.m. for
ProNtPCI, not present for wild-type PCI.

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