Báo cáo khoa học: Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylase potx

Deamidation of labile asparagine residues in the autoregulatory
sequence of human phenylalanine hydroxylase
Structural and functional implications
Therese Solstad
1
, Raquel N. Carvalho
1
, Ole A. Andersen
2
, Dietmar Waidelich
3
and Torgeir Flatmark
1
1
Department of Biochemistry and Molecular Biology and the Proteomic Unit, University of Bergen, Norway;
2
Department of
Chemistry, University of Tromsø, Norway;
3
Applied Biosystems, Applera Deutschland GmbH, Langen, Germany
Two dimensional electrophoresis has revealed a micro-
heterogeneity in the recombinant human phenylalanine
hydroxylase (hPAH) protomer, that is the result of sponta-
neous nonenzymatic deamidations of labile asparagine
(Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J.
Biochem. 267, 6302–6310]. Using of a computer algorithm,
the relative deamidation rates of all Asn residues in hPAH
have been predicted, and we here verify that Asn32, followed
by a glycine residue, as well as Asn28 and Asn30 in a loop
region of the N-terminal autoregulatory sequence (residues
19–33) of wt-hPAH, are among the susceptible residues.

First, on MALDI-TOF mass spectrometry of the 24 h
expressed enzyme, the E. coli 28-residue peptide, L15–K42
(containing three Asn residues), was recovered with four
monoisotopic mass numbers (i.e., m/z
1
of 3106.455, 3107.470,
3108.474 and 3109.476, of decreasing intensity) that differed
by 1 Da. Secondly, by reverse-phase chromatography,
isoaspartyl (isoAsp) was demonstrated in this 28-residue
peptide by its methylation by protein-
L
-isoaspartic acid
O-methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on
incubation at pH 7.0 and 37 °C of the phosphorylated form
(at Ser16) of this 28-residue peptide, a time-dependent
mobility shift from t
R
 34 min to  31 min (i.e., to a more
hydrophilic position) was observed on reverse-phase chro-
matography, and the recovery of the t
R
 34 min species
decreased with a biphasic time-course with t
0.5
-values of 1.9
and 6.2 days. The fastest rate is compatible with the rate
determined for the sequence-controlled deamidation of
Asn32 (in a pentapeptide without 3D structural interfer-
ence), i.e., a deamidation half-time of  1.5 days in 150 m
M

Tris/HCl, pH 7.0 at 37 °C. Asn32 is located in a cluster of
three Asn residues (Asn28, Asn30 and Asn32) of a loop
structure stabilized by a hydrogen-bond network. Deami-
dation of Asn32 introduces a negative charge and a partial
b-isomerization (isoAsp), which is predicted to result in a
change in the backbone conformation of the loop structure
and a repositioning of the autoregulatory sequence and thus
affect its regulatory properties. The functional implications
of this deamidation was further studied by site-directed
mutagenesis, and the mutant form (Asn32fiAsp) revealed a
1.7-fold increase in the catalytic efficiency, an increased
affinity and positive cooperativity of L-Phe binding as well as
substrate inhibition.
Keywords: phenylalanine hydroxylase; microheterogeneity;
deamidation; asparagine; structure and function.
The irreversible, spontaneous, nonenzymatic deamidation
of asparagine (Asn) residues is a common post-trans-
lational modification known to occur in a large number of
mammalian proteins [1], and it represents an important
source of protein instability at biologically relevant
conditions [2,3]. The deamidation of Asn at neutral pH
has been reported to proceed primarily by a succinimide
mechanism involving the formation of a succinimide
intermediate via nucleophilic attack on the amide carbonyl
of Asn by the nitrogen of the peptide group linking the
Asn to the following residue [4–6]
2
. As hydrolysis of this
intermediate may occur on either side of the imide
nitrogen, the Asp residue produced by the deamidation

reaction will be linked to the subsequent residue by a
normal
3
a-aspartyl (Asp) or by a b-aspartyl (or isoaspartic
acid – isoAsp) bond. In the latter case, the b-carbon is
part of the polypeptide backbone, and the a-carboxyl
group is present as an atypical one carbon carboxylic acid
side-chain available for methylation by isoaspartyl
O-methyltransferase [7]. In general, Asn residues deami-
date faster and more frequently than do glutamine
residues, due to a more energetically favourable formation
of a cyclic intermediate (reviewed in [8,9]). The rate of Asn
deamidation in proteins has been shown to depend
primarily on their nearest (to the Asn [10]) neighbour
amino acid C-terminal, their localization in the 3D
Correspondence to: T. Flatmark, Department of Biochemistry and
Molecular Biology, University of Bergen, A
˚
rstadveien 19,
N-5009 Bergen, Norway. Fax: +47 5558600, Tel.: +47 55586428,
E-mail: torgeir.fl
Abbreviations: hPAH, human phenylalanine hydroxylase; rPAH, rat
phenylalanine hydroxylase; H
4
, biopterin (6R)-
L
-erythro-5,6,7,8-
tetrahydrobiopterin; PIMT, protein-
L
-isoaspartate O-methyltrans-

ferase; MALDI-TOF, matrix-assisted desorption/ionization time of
flight; IPTG, isopropyl-thio-a-
D
-galactoside;
L
-Phe,
L
-phenylalanine;
MBP, maltose binding protein; wt, wild-type.
Enzyme: Phenylalanine 4-monooxygenase or phenylalanine
hydroxylase (EC 1.14.16.1).
(Received 9 October 2002, revised 23 December 2002,
accepted 8 January 2003)
Eur. J. Biochem. 270, 929–938 (2003) Ó FEBS 2003 doi:10.1046/j.1432-1033.2003.03455.x
structure [9,10] as well as on environmental factors such as
pH, temperature and ionic strength [8,11] and including
some specific ion effects [12]. Two dimensional electro-
phoresis of the 50-kDa subunit of purified monkey,
human and recombinant human PAH (hPAH) has
revealed a marked microheterogeneity in which the
individual molecular forms of the protomer have the
same apparent molecular mass ( 50 kDa), but differ in
their pI by about 0.1 pH unit [13]
4
. The microheterogeneity
was proven to be the result of progressive, spontaneous,
nonenzymatic deamidations of labile amide containing
amino acid residues [13]. Based on the specific deamida-
tion rates in a cellular system (expression in E. coli)and
the experimental conditions in vitro required for the

deamidation reactions to occur, the labile amide groups
were concluded to represent Asn residues [13]. Interest-
ingly, a comparison of the catalytic properties of non-
deamidated and highly deamidated enzyme revealed that
the catalytic efficiency (k
cat
/[S]
0.5
)wasalmostthreefold
higher for the tetramer (as isolated by size-exclusion
chromatography) with multiple deamidated protomers
(generated by 24 h expression in E. coli at 28 °C) than for
the essentially nondeamidated form (generated by 2 h
expression) [13]. Therefore, the unambiguous identification
of the Asn residues susceptible to deamidation at biologi-
cally relevant conditions represents a major challenge for the
characterization and understanding of the catalytic, regula-
tory and stability properties of this homotetrameric enzyme
5
.
Using a recently developed computer algorithm [9,10], that
accurately ( 95%) predicts the relative deamidation rates
of Asn residues within a single protein, when its 3D
structure is known, several candidate Asn residues have
been predicted in hPAH and rPAH [14]. Interestingly, based
on this predictive algorithm and the 2D electrophoretic
patterns of wt-hPAH and the truncated form DN(1–102)/
DC(429–452)-hPAH, two of the labile Asn residues have
been located in the catalytic domain structure. In addition,
three residues in the designated N-terminal autoregulatory

sequence (residues 19–33), extending over the active site
pocket as a ÔlidÕ [15], were also predicted to be susceptible to
deamidation. This sequence contains a cluster of three Asn
residues (Asn28, Asn30 and Asn32) as well as the
phosphorylation site for PKA (Ser16) in close proximity,
and we here present experimental data verifying the
computational prediction of Asn32 as the most susceptible
residue to undergo deamidation to Asp/isoAsp.
Materials and methods
Materials
The restriction protease, enterokinase, was delivered by
Invitrogen (the Netherlands). The IsoQuantÒ protein
isoaspartic acid detection kit was purchased from Promega.
The Sigma Chemical Co. delivered TPCK-treated trypsin
and soybean trypsin inhibitor. The catalytic subunit of
cAMP-dependent protein kinase (PKA) was purified to
homogeneity from bovine heart and was a generous gift
from S. O. Døskeland, Department of Anatomy and Cell
Biology, University of Bergen. A synthetic 28-residue
peptide representing the N-terminal tryptic peptide, LSD
FGQETSYIEDNCNQNGAISLIFSLK (L15–K42), was
synthesized by Research Genetics, AL,
6
USA. [c-
32
P]ATP
and S-adenosyl-
L
-[methyl-
3

H]methionine were obtained
from Amersham Pharmacia Biotech, U.K. Other chemicals
were of the highest purity available, and some specific
chemicals are referred to in the text.
Site-specific mutagenesis
The Asn32fiAsp mutation was introduced into the
pMAL-hPAH expression system containing the entero-
kinase cleavage site (D
4
K) (New England Biolabs) using the
QuikChange
TM
site-directed mutagenesis kit (Stratagene).
The following primers (provided by MWG-Biotech AG)
were used for mutagenesis: (forward) 5¢-AAGACAACT
GCAATCAAGATGGTGCCATATCACTGATC-3¢ and
(reverse) 5¢-GATCAGTGATATGGCACCATCTTGATT
GCAGTTGTCT
T-3¢ (the mismatched nucleotides are
shown in boldtype). The authenticity of the mutagenesis
was verified by DNA sequencing in an ABI Prism
TM
377
DNA Sequencer (Perkin Elmer) using the oligonucleotides
malE, 13B [16] and A
674
[17] and the Big Dye
TM
Terminator
Ready Reaction Mix (Perkin Elmer Applied Biosystems).

The analysis of the electropherograms was carried out
with the programs
CHROMAS
1.6 (Technelysium Pty, Ltd)
and
CLUSTAL X
(1.8). The DNA was introduced into E. coli
TB1 cells by electroporation using a Gene PulserÒ II
(Bio-Rad).
Expression and purification of recombinant hPAH
The pMAL expression system was used for the production
of the wild-type fusion protein MBP-(D
4
K)
ek
-hPAH [18]
with maltose binding protein as the fusion partner. Cells
were grown at 37 °C, and expression was induced at 15 °C
or 28 °C by the addition of 1 m
M
isopropyl thio-b-
D
-galactoside (IPTG); the cells were harvested after 2 h or
24 h of induction. The fusion protein was cleaved by
enterokinase for 5 h at 4 °C using 4 U protease per mg
fusion protein, and the tetrameric forms were isolated to
homogeneity by size-exclusion chromatography [18].
Protein measurements
Purified enzyme was measured by the absorbance at
280 nm, using the absorption coefficient A

280
(1 mgÆmL
)1
cm
)1
) ¼ 1.63 for the fusion protein MBP-(D
4
K)
ek
-hPAH
and 1.0 for the isolated hPAH protein [18].
Phosphorylation of hPAH
The enzyme was phosphorylated by PKA as described
previously [19]. The standard reaction mixture contained
15 m
M
Na/Hepes (pH 7.0), 0.1 m
M
ethylene glycol bis-
(a-amino ether)-N,N,N¢,N¢-tetraacetic acid, 0.03 m
M
EDTA, 1 m
M
dithiothreitol, 10 m
M
MgAc
2
,[c-
32
P]ATP,

60 l
M
ATP, 100 n
M
of the catalytic subunit of PKA and
20 l
M
of hPAH; 30 °C for 30 min.
Trypsination of hPAH
Tryptic proteolysis of hPAH was performed in 20 m
M
Na/Hepes buffer, pH 7.0 at 30 °C for 2 h at a trypsin to
930 T. Solstad et al. (Eur. J. Biochem. 270) Ó FEBS 2003
substrate ratio of 1 : 10 (by mass). Soybean trypsin inhibitor
was added at the end with a protease to inhibitor ratio of
1 : 1.5 (by mass) for the analyses of peptides by reverse-
phase chromatography.
Methylation of tryptic peptides
Therepairenzymeprotein-
L
-isoaspartate O-methyltrans-
ferase (PIMT; EC 2.1.1.77) catalyses the methylation of the
a-carboxyl in isoAsp residues with S-adenosyl-
L
-methionine
as the methyl donor. The products of this reaction are the
formation of peptide/protein
L
-isoaspartartyl methyl ester
and S-adenosyl-

L
-homocysteine. The reaction was per-
formed as described in the manual for the IsoQuantÒ
protein isoaspartic acid detection kit with S-adenosyl-
L
-[methyl-
3
H]methionine as the methyl donor.
Reverse-phase chromatography
Reverse-phase chromatography of the tryptic peptides was
performed using a ConstaMetric Gradient System (Labor-
atory Data Control) and a 4.6 mm · 10 cm Hypersil
ODS C18 column (Hewlett Packard, USA) fitted with a
2-cm guard column of the same material. Solvent A was
50 m
M
ammonium acetate (pH 8.0) and solvent B, 50 m
M
ammonium acetate in 70% (v/v) acetonitrile (pH 8.0), and a
linear gradient of 10–50% solvent B was used at a flow rate
of 1 mLÆmin
)1
for 60 min. Samples were collected every
15 s and the elution pattern of
32
P-labelled and
3
H-labelled
peptides was analysed and resolved into individual compo-
nents, assuming a Gaussian distribution of each peptide,

using the
PEAKFIT
software program (SPSS Inc., IL, USA);
the ÔAutoFit-peak II-ResidualsÕ was used with the confid-
ence level set at ‡ 95%.
2D electrophoresis
Isoelectric focusing (IEF) was performed as described [13].
SDS/PAGE was performed at 200 V for 3–4 h on 10%
(w/v) polyacrylamide gels [20]. The gels were stained by
0.5% (w/v) Coomassie Brilliant Blue R250 (Bio-Rad) in
30% (v/v) ethanol and 10% (v/v) acetic acid. The apparatus
used for IEF and electrophoresis (EPS 3500XL power
supply, Protean Xi 2D Cell and Tube cell) were from
Bio-Rad. Finally, the 2D gels were dried on a slab gel dryer
(Bio-Rad model 443) and scanned on a Hewlett Packard
Scan Jet 4C/T.
Mass spectrometry
Matrix-assisted desorption/ionization time of flight
(MALDI-TOF) spectra and tandem (MS/MS) mass spec-
trometry of target peptides were acquired on a 4700
Proteomic Analyser (Applied Biosystems) in the reflectron
positive-ion mode, and the spectra were mass calibrated
externally. The tryptic peptides were diluted (1 : 100 or
1 : 50) in 25% (v/v) acetonitrile and 0.1% trifluoroacetic
acid with a-cyano-4-hydroxycinnamic acid (Aldrich) as the
matrix. Samples were spotted on the sample plate and
allowed to crystallize at room temperature. The instrument
was supplied with a software tool that uses a scanning
algorithm to isotopically deconvolute the mass spectra; for
theoretical consideration see [21]. The deconvolution

method is particularly useful to detect labile Asn residues
in peptides as deamidation of Asn to Asp/isoAsp increases
the monoisotopic mass ([M + H]
+
) of the peptide by only
1Da.
Assay of hPAH activity
The hPAH activity was assayed as described [18], the
catalase concentration was 0.1 lgÆlL
)1
and the enzyme was
activated by prior incubation (5 min) with
L
-Phe. The
enzyme source was the isolated tetrameric forms and the
reaction time was 1 min 0.5% (w/v) BSA was included in
the reaction mixture to stabilize the diluted, purified
enzyme. The steady-state kinetic data were analysed by
nonlinear regression analysis using
SIGMA PLOT
(Jandel
Scientific Software) and the modified Hill equation of
LiCata and Allewell [22] for cooperative substrate binding
as well as substrate inhibition [13,23].
Results
Expression, purification and 2D electrophoresis
of recombinant hPAH
The expression of wild-type hPAH and its Asn32fiAsp
mutant form in the E. coli pMAL-system resulted in the
expected high yields of the recombinant fusion protein MBP-

(D
4
K)
ek
-hPAH [18] using an IPTG induction period of
2–24 h at 28 °C or 24 h at 15 °C. After cleavage of the
affinity purified fusion proteins with the restriction protease
enterokinase, the tetrameric forms were isolated by size-
exclusion chromatography. Whereas the wild-type protomer
gave a single band on 1D SDS/PAGE, this was not the case
when subjected to 2D electrophoresis. As described previ-
ously [13,24], recombinant wt-hPAH expressed as MBP-
(D
4
K)
ek
-hPAH fusion protein for 24 h at 28 °C revealed
multiple ( 5) molecular forms of the protomer (Fig. 1) that
differed in their isoelectric point by about 0.1 pH unit, but
shared the same apparent molecular mass ( 50 kDa).
Labile asparagine residues in the regulatory domain
Based on the microheterogeneity of the protomer in a
double truncated form of hPAH (DN(1–102)/DC(428–452)-
Fig. 1. 2D-electrophoresis pattern of full-length wt-hPAH obtained as a
fusion protein after 24 h of induction in E. coli at 28 °C. Approximately
30 lg of enterokinase cleaved fusion protein MBP-(D
4
K)
ek
-hPAH

was subjected to 2D electrophoresis and stained with Commassie
Brilliant Blue. The multiple molecular forms of the protomer (denoted
hPAH I-IV [13]) differed in pI by  0.1 pH unit, but shared the same
apparent molecular mass of  50 kDa.
Ó FEBS 2003 Deamidation of labile asparagine residues (Eur. J. Biochem. 270) 931
hPAH), expressed in E. coli, it has been concluded that at
least two of the labile Asn residues are located in the
catalytic domain of the protomer [13]. Furthermore, on
the basis of a nearest neighbour amino acid analysis of all
the Asn residues in wt-hPAH and taking into account the
contribution of the 3D structure (PDB accession numbers,
1PAH and 1PHZ) to the instability of Asn residues [10],
three residues in the N-terminal regulatory domain are
predicted to deamidate nonenzymatically at biologically
relevant conditions ([14] and Table 1). Notably, Asn32 in
hPAH and rPAH (and in addition, Asn8 in rPAH) is thus
predicted to be a very labile residue with a theoretical
deamidation coefficient (C
D
) of 0.5 and a theoretical first-
order half-time of  1.5 days in 150 m
M
Tris/HCl, pH 7.5
at 37 °C ([14] and Table 1). Asn32 is located in a small
cluster of Asn residues, including Asn28 and Asn30, that
have predicted higher deamidation coefficients (7.9 and 5.0)
and longer deamidation half-times (54 and 60 days). From
Fig.2itisseenthatthisclusterofAsnresiduesisinaloop
structure and that Asn30 Od1 is stabilized by a hydrogen
bond to Gln134 Ne2. The conformation of the loop

structure is further stabilized by hydrogen bonds as shown
in Fig. 2. As can be seen from Table 1, none of the other
Asn residues in the N-terminal regulatory domain are
predicted to contribute to the microheterogeneity of the
wild-type protomer. Asn58, which is located at the end of an
a-helix (Ra1) [15], is particularly unlikely to undergo
nonenzymatic deamidation [25].
Table 1. Asn residues in the N-terminal domain, their nearest neighbour amino acids, secondary structure position and their theoretical half-times for
nonenzymatic deamidation/deamidation coefficients. N.D., not determined.
Asn residue Sequence Secondary structure position
First-order deamidation
half-times (t
0.5
)
a
(days)
Deamidation
coefficient (C
D
)
b
Asn8 ENP N.D. >500 N.D.
Asn28 DNC Loop 54.1 7.9
Asn30 CNQ Loop 60 5.0
Asn32 QNG Loop 1.45 0.5
Asn58 END End of Ra1 helix 32 8.4
Asn61 VNL b-Turn between Ra1 and Ra2 291 130
Asn93 TNI Middle of Ra2 helix 271 >500
a
The values were obtained from the estimated half-times of penta-peptides containing the sequence GlyXxxAsnYyyGly [1].

b
The values
were predicted by the computer algorithm developed by Robinson and Robinson [10] based on the crystal structure data obtained for the
truncated dimeric rat PAH (PDF id. code, 1PHZ) containing the regulatory and catalytic domains [15].
Fig. 2. Stereo picture of the three Asn residues in the N-terminal autoregulatory sequence of rPAH. Figure based on the crystal structure of the ligand-
free, phosphorylated dimeric DC(428–452)-rPAH (PDB id. code, 1PHZ), which contains both the regulatory and the catalytic domains (residues
1–427). The N-terminal autoregulatory sequence is highly homologous in rPAH and hPAH, including the conserved Asn residues at positions 28,
30 and 32 [14]. The Asn residues and the surrounding residues are shown by ball-and-stick representation. The figure was produced using
MOLSCRIPT [38].
932 T. Solstad et al. (Eur. J. Biochem. 270) Ó FEBS 2003
Mass spectrometry
To identify the labile Asn residues in the N-terminal
autoregulatory sequence, tryptic peptides of wt-hPAH
(Fig. 3) were analysed by MALDI-TOF using a scanning
algorithm to isotopically deconvolute the mass spectra. The
theoretical isotopic distribution was calculated on the basis
of the elemental composition (C135 H209 N34 O48 S1) for
the peptide L15–K42 (Fig. 4A,D). This acidic and hydro-
phobic 28-residue tryptic peptide (containing Asn28, Asn30
and the predicted most labile residue, Asn32) revealed an
isotopic mass spectrum identical to the theoretical spectrum,
and on deconvolution, a single monoisotopic mass peak
([M + H]
+
)ofm/z 3106.514 Da when obtained from
wt-hPAH isolated after 2 h at 28 °C of induction with
IPTG (Fig. 4B,C). Tandem (MS/MS) mass spectrometry of
this peptide revealed a fragmentation pattern which iden-
tified Asn residues in positions 28, 30 and 32. By contrast,
the same tryptic peptide obtained from wt-hPAH isolated

after 24 h induction at 28 °C, revealed three additional
monoisotopic mass peaks (m/z 3107.470, 3108.474 and
3109.476) of decreasing intensity on deconvolution of the
mass spectrum (Fig. 4E,F)
7
. This increase of 1 Da for each
of the additional peaks corresponds to the increase in mass
as expected from deamidation of 1, 2 or 3 Asn residues,
respectively. The apparent intensity ratio of 3106.455 to
S (3107.470, 3108.474 and 3109.476) was  4:3andmay
give an estimate of the residual amount of nondeamidated
peptide (m/z 3106.455); note, however, the lower S/N ratio
of the spectra in Fig. 4E than in 4B that has an effect on the
accuracy of the deconvoluted spectrum.
Lability of the Asn residues in the autoregulatory
sequence
The 28-residue tryptic peptide, L15–K42 with the cluster of
Asn residues also contains the phosphorylation site (Ser16)
which is a preferred substrate for PKA [26].
32
P-labelled
tetrameric hPAH (obtained after 24 h of induction at 15 °C
Fig. 3. Tryptic peptides of wt-hPAH containing Asn28, Asn30 and
Asn32. The alternative cleavage sites for trypsin are indicated by
arrows, which may contribute to the heterogeneity of phosphopeptides
after reverse-phase chromatography (Fig. 5).
Fig. 4. MALDI-TOF mass spectra of the N-terminal 28-residue tryptic peptide L15–K42 obtained from wt-hPAH isolated after 2 and 24 h of induction
at 28 °CinE. coli. Panels A and D represent the theoretical isotopic mass spectrum of the 28-residue peptide L15–K42 (elemental composition
C135 H209 N3 O48 S1). Panels B and E represent the mass spectra of this peptide obtained from the 2 h and 24 h expressed wt-hPAH at 28 °C,
respectively, and panels C and F represent the corresponding deconvoluted monoisotopic mass spectra ([M + H]

+
). Note that the S/N ratio is
slightly better in the isotopic mass spectrum of B than in E.
17
Ó FEBS 2003 Deamidation of labile asparagine residues (Eur. J. Biochem. 270) 933
in E. coli), that had been fully phosphorylated by PKA, was
digested with trypsin and subjected to reverse-phase chro-
matography that resolved one major (t
R
 34 min) and
some minor phosphopeptides (Fig. 5, inset). The minor
components represent peptides generated by alternative
tryptic cleavage (see Fig. 3) and/or the presence of a mixture
of peptides with either
8
Asn, Asp and isoAsp at position 32
(and eventually at positions 28 and/or 30). In order to study
further the stability of the three Asn residues, the phospho-
peptides were incubated at 37 °C and pH 7 (15 m
M
Na/
Hepes containing 1 m
M
dithiothreitol), and at timed
intervals, aliquots were subjected to reverse-phase chroma-
tography. The main phosphopeptide (with t
R
 34 min)
revealed a time-dependent mobility shift to a more hydro-
philic position with t

R
 31 min. By making corrections for
the decay of
32
P-radioactivity and any loss of peptide, the
amount of phosphopeptide with t
R
 34 min was found to
decrease with a biphasic time-course and with calculated
half-times of 1.9 days (r ¼ 0.98) and 6.2 days (r ¼ 0.92),
assuming pseudo first-order kinetics for the deamidation
[1,13,27].
Demonstration of isoaspartate in tryptic peptides
of wt-hPAH
Theenzymeprotein-
L
-isoaspartate O-methyltransferase
(PIMT) specifically methylates isoAsp residues in peptides
and a broad range of proteins [7] at substoichiometric levels
[28,29,30].Thus,PIMTcanbeusedtoidentifyisoAsp
formed due to nonenzymatic deamidation or spontaneous
isomerization of Asp [30]. In order to detect the presence of
isoAsp residues in hPAH, the wt-hPAH (obtained after 24 h
induction with IPTG at 28 °C) was digested with trypsin,
and the peptides methylated by PIMT with S-adenosyl-
L
-[methyl-
3
H]methionine as the methyl donor and analysed
by reverse-phase chromatography. The

3
H-labelled peptides
were resolved into several components with retention times
in the range of 20–60 min (Fig. 6A), with major peaks at
t
R
 28 min, t
R
 34 min, t
R
 36 min and t
R
 51 min.
Amajor
3
H-labelled peptide was eluted at the end of the
gradient, this was also the case for the synthetic 28-residue
peptide L15–K42 (Fig. 6B). In the latter case, multiple,
closely spaced, but nonresolved peaks of
3
H-radioactivity
were observed and indeed expected from the MALDI-TOF
mass spectrum of the peptide as isolated (Fig. 6B, inset),
including the full-length form with a monoisotopic m/z of
3106.396 (theoretical monoisotopic m/z of 3106.467); such
a heterogeneity was expected on the synthesis of this
28-residue peptide and possibly also as a result of partial
deamidation to Asp/isoAsp during the synthesis procedure.
However, the pattern of nonresolved methylated peptides
eluted between 50 and 60 min (Fig. 6B) demonstrated the

presence of isoAsp residues that increased markedly upon its
incubation in 150 m
M
Tris/HCl buffer, pH 7.5 at 37 °C; i.e.,
at the standard incubation conditions previously selected for
deamidation of model peptides [1].
In order to demonstrate that the phosphopeptides of
wt-hPAH (Fig. 5) also contained isoAsp, the
32
P-labelled
tryptic peptides of wt-hPAH were incubated for 1 week at
37 °C, pH 7.5 and then subjected to methylation by PIMT
and reverse-phase chromatography. The elution pattern of
the tryptic peptides revealed distinctly different profiles for
32
P (phosphopeptides) and
3
H (methylated peptides), but
with some major overlapping peaks at t
R
 29 min,
 36 min and  39 min. In addition, several minor over-
lapping peaks were also observed, thus proving that the
presence of one or more isoAsp residues in the N-terminal
tryptic peptide of wt-hPAH are generated because of
nonenzymatic dedamidation in vitro.
Steady-state kinetic analysis of tetrameric wt-hPAH
and its Asn32fiAsp mutant form
The progressive deamidation events observed on 24 h
expression of hPAH in E. coli have been shown to alter

the catalytic properties of the tetrameric form when isolated
by size-exclusion chromatography [13]. Partially deamida-
ted enzyme (24 h induction at 28 °CinE. coli) revealed a
3-fold higher catalytic efficiency (k
cat
/[S]
0.5
), resulting from a
higher V
max
and an increased affinity for the substrate
L
-Phe, a lower affinity for its pterin cofactor and a
Fig. 5. Time-course for the spontaneous deamidation of the major
tryptic phosphopeptide of wt-hPAH containing the residues Asn28,
Asn30 and Asn32. Full-length wt-hPAH expressed for 24 h at 28 °C
was phosphorylated by PKA and subjected to digestion with trypsin.
(Inset) The elution pattern of the phosphopeptides separated by
reverse-phase chromatography on a Hypersil C18 column; the column
was equilibrated with 50 m
M
ammonium acetate (pH 8.0) and the
peptides eluted with a linear gradient of 10–50% (v/v) of 50 m
M
ammonium acetate in 70% (v/v) acetonitrile (pH 8.0) at a flow-rate of
1mLÆmin
)1
. Detection of the
32
P-radioactivity revealed a heteroge-

neity of the phosphopeptides that may be related to alternative cleavage
sites for trypsin (see Fig. 4) and partial deamidation(s) of AsnfiAsp
and AsnfiisoAsp; main peak at t
R
 34 min. (Main figure) The
phosphopeptides were further incubated in phosphorylation medium
at pH 7.0 and 37 °C, and at timed intervals, aliquots ( 150 lgpep-
tide) were subjected to reverse-phase chromatography. Fractions
(250 lL) were collected every 15 s followed by scintillation counting
and analysis of the data by the
PEAKFIT
software program. Each data
point represents the average value obtained in three separate experi-
ments, and the two lines were calculated by linear regression analysis
with the correlation coefficients r
1
¼ 0.98 and r
2
¼ 0.92. The time-
course for the remaining
32
P-radioactivity in the t
R
 34 min peak (log
d.p.m. t
R
 34 min) was thus resolved into two deamidation half-times
of 1.9 and 6.2 days, assuming pseudo first-order kinetics.
934 T. Solstad et al. (Eur. J. Biochem. 270) Ó FEBS 2003
pronounced substrate (

L
-Phe) inhibition when compared to
the nondeamidated tetramer (2 h induction at 28 °C).
Steady-state kinetic analysis of the Asn32fiAsp mutant
form (2 h induction at 28 °C), demonstrated kinetic
properties that where comparable qualitatively to those
observed for highly deamidated wt-hPAH with a 1.7-fold
increase in its catalytic efficiency, a 34% decrease in the
[S]
0.5
-value for
L
-Phe, increased cooperativity on
L
-Phe
binding and substrate inhibition (Fig. 7, Table 2).
Discussion
The observed microheterogeneity of recombinant wt-hPAH
on isoelectric focusing and 2D electrophoresis (Fig. 1) has
been demonstrated to be the result of spontaneous non-
enzymatic deamidation of labile amide containing amino
acid residues and has implications both for the catalytic
efficiency and stability properties of the enzyme [13]. Based
on the rate of the multiple deamidation reactions, their pH
and temperature dependence, the labile amide residues were
concluded to be Asn, and at least two of them were found to
be present in the double truncated form DN(1–102)/
DC(428–452)-hPAH including the catalytic core domain
of the enzyme [13].
Deamidation of Asn residues can occur by several

alternative mechanisms, but in proteins and peptides the
most common is a nonenzymatic deamidation via the
b-aspartyl shift mechanism (see Introduction), that proceeds
with a high frequency in proteins at neutral to basic pH [31].
Asn, followed by Gly, Ser, Thr or Lys residues are most
commonly subjected to deamidation [9,31], particularly
when the Asn residue is located in a flexible segment of the
protein [32]. Under physiological conditions (with respect to
temperature, pH and ion composition) the ratio of Asp to
isoAspisreportedtobe 1 : 2 for Asn–Gly or Asn–Ser
sequences [33], and ratios of  1 : 3 have been reported in
model pentapeptides [6,34], however, conformational con-
straints in the protein may have an effect on this ratio.
Labile Asn residue(s) in the N-terminal regulatory
domain of wt-hPAH
On the basis of nearest neighbour analyses of the Asn
residue in wt-hPAH and the recently solved 3D crystal
structures of rPAH and hPAH, a computer algorithm has
predicted that the most labile Asn residue in rPAH/hPAH is
Asn32, together with Asn8 in rPAH ([14] and Table 1). Its
nearest neighbour amino acid (Gly33), in a loop structure,
favours the deamidation of Asn32 with the formation of
Asp and isoAsp at a ratio of  1 : 2 [33]. MALDI-TOF
mass spectrometry analyses have confirmed this prediction.
Thus, the 28-residue tryptic peptide {residues 15–42 with a
theoretical monoisotopic ([M + H]
+
) m/z of 3106.467, see
Fig. 4A or D} obtained from wt-hPAH isolated after 24 h
induction at 28 °C revealed on deconvolution of the mass

spectrum four monoisotopic peaks (Fig. 4F) at m/z values
of decreasing intensity (3106.455, 3107.474, 3108.474 and
3109.476; Fig. 4F)
9
.Thesem/z values correspond to that
expected for nondeamidated (m/z 3106.455), mono-deami-
dated (+ 1 Da), double-deamidated (+ 2 Da) and triple-
deamidated (+ 3 Da) forms of the peptide. This conclusion
is further supported by the existence of only one monoiso-
topic peak (i.e., at m/z 3106.514) for the peptide obtained
from the 2 h expressed enzyme (Fig. 4C). That this peptide
represents the nondeamidated form, with Asn residues at
positions 28, 30 and 32, was confirmed by the fragmentation
pattern obtained by tandem (MS/MS) mass spectrometry.
Thus, the MALDI-TOF spectra in Figs 4E, F are compa-
tible with a progressive deamidation of the Asn residues at
positions 28, 30 and 32. However, attempts to further
confirm this conclusion by the MS/MS fragmentation
pattern of the selected precursor ion were not successful. As
Fig. 6. Reverse-phase chromatography of
3
H-labelled methylated tryptic
peptides of wt-hPAH and the synthetic N-terminal peptide, L15–K42.
(A) The pattern of
3
H-labelled methylated tryptic peptides obtained
from wt-hPAH isolated after induction for 24 h at 28 °C. Peptides
from  2.5 mg of enzyme were subjected to methylation and reverse-
phase chromatography as described in the legend to Fig. 5. Fractions
(250 lL) were collected every 15 s and the

3
H-radioactivity was
counted. (B) Approximately 100 lg of the 28-residue synthetic peptide
(L15–K42 of hPAH) was subjected to methylation by protein iso-
aspartyl methyltransferase and then to reverse-phase chromatography.
The bottom trace (thin line) represents the radioactivity profile of the
peptide as isolated and the upper trace (thick line) the profile obtained
after its incubation for 7 days at 37 °C in 150 m
M
Tris/HCl, pH 7.5.
(Inset) The MALDI-TOF mass spectrum of the synthetic peptide
isolated with a main component of m/z 3106.396 (theoretical m/z-value
for the peptide is 3106.467) and several minor components, including
peptides with nonreleased blocking groups (in the high-molecular-
mass region).
Ó FEBS 2003 Deamidation of labile asparagine residues (Eur. J. Biochem. 270) 935
a further approach to study the multiple deamidations in
this 28-residue tryptic peptide, the wt-hPAH was labelled
with
32
P-phosphate (at Ser16) and the phosphopeptides
separated by reverse-phase chromatography (Fig. 6, inset).
When the phosphopeptides were further incubated at 37 °C
and pH 7.0 (15 m
M
Na/Hepes), a half-time of 1.9 days
(Fig. 6) was estimated for the nonenzymatic deamidation of
the major phosphopeptide (as estimated by its time-
dependent change in retention time from t
R

 34 min to a
more hydrophilic position (with t
R
 31 min). This is close
to the half-time estimated for an Asn in a pentapeptide
containing the identical nearest neighbour amino acids
xQNGx as in hPAH, i.e.,  1.5 days when incubated at
37 °C and 150 m
M
Tris buffer, pH 7.5 [1]
10
. As there is no
other Asn–Gly sequence in the human enzyme, our data
(Fig. 6) support the conclusion that Asn32 is the most labile
Asn residue in hPAH. The longer t
0.5
–value (6.2 days)
calculated from the second slope in Fig. 6 most likely
reflects the deamidation of Asn28/Asn30 which are both
predicted to be more stable than Asn32 (Table 1), notably
Asn30 which is stabilized by a hydrogen bond to Gln134
(Fig. 2). The deamidations of these Asn residues were
further substantiated by the chromatography
11
of peptides
containing
32
P-labelled S16 and
3
H-labelled (methylated)

isoAsp of wt-hPAH on reverse-phase chromatography and
the demonstration of isoAsp in a synthetic peptide contain-
ing both the full-length species, L15–K42 – of the expected
monoisotopic mass 3106.467 – and a number of lower
molecular mass peptides, recovered as a mixture of peptides
on reverse-phase chromatography.
Deamidation of Asn32 during isoelectric focusing
and 2D electrophoresis
The rapid rate of deamidation of Asn32 in wt-hPAH
observed in vitro in the present study (Fig. 6) explains why
we have not been able to obtain a single component on
isoelectric focusing and 2D electrophoresis of the 2 h
(28 °C) expressed enzyme [13] as expected from its
MALDI-TOF mass spectrum. Thus, no microheterogeneity
was observed for the Asn containing peptides on MALDI-
TOF and tandem (MS/MS) mass spectrometry of tryptic
peptide obtained from wt-hPAH (2 h induction at 28 °C),
in particular not for the sequence L15–K42 (containing the
Fig. 7. Effect of L-Phe (A and C) and H
4
biopterin (B and D) concentration on the
catalytic activity of recombinant wt-hPAH
and hPAH(Asn32fiAsp) obtained after 2 h
of induction in E. coli at 28 °C. Assay
conditions and nonlinear regression ana-
lysis are described in the Methods section.
In each graph, both the experimental
(closed circle) and fitted (open circle) data
are shown. The kinetic constants obtained
are presented in Table 2.

Table 2. Steady-state kinetic parameters for recombinant wt-hPAH and hPAH(Asn32fiAsp). Wt-hPAH was obtained after 2 h and 24 h of
induction with IPTG in E. coli at 28 °C. The Asn32fiAsp mutant form was obtained after 2 h at 28 °C. The PAH activity was assayed and the
apparent kinetic constants were calculated by nonlinear regression analysis as described in the Materials and methods section. The substrate
concentrations were 1 m
ML
-Phe (H
4
biopterin variable) and 75 l
M
H
4
biopterin (
L
-Phe variable). Values are shown as means ± SEM, n ¼ 3.
18
Enzyme
tetramer
L
-Phe H
4
biopterin
V
max
a
(nmolÆmin
)1
Æmg
)1
)
½S

0:5
a
(l
M
)
k
cat
/[S]
0.5
(l
M
Æmin
)1
) h
Substrate
inhibition
V
max
(nmolÆmin
)1
Æmg
)1
)
K
m
b
(l
M
)
Wt (2 h) 3484 ± 162 238 ± 18 0.72 1.5 ± 0.1 ‚ 5325 ± 137 31 ± 3

Wt (24 h) 4946 ± 281 135 ± 11 1.83 1.9 ± 0.1 + 6392 ± 281 40 ± 5
N32D 3736 ± 470 159 ± 30 1.20 2.2 ± 0.1 + 4725 ± 133 34 ± 2
a
The kinetic parameters were calculated from a modified Hill equation as described in the Materials and methods section.
b
The kinetic
parameters were calculated from the Michaelis–Menton equation.
936 T. Solstad et al. (Eur. J. Biochem. 270) Ó FEBS 2003
predicted most labile residue Asn32; Fig. 4B,C). hPAH
requires  20 h to reach the equilibrium position in the pH
gradient at  20 °C, i.e., conditions that favour deamida-
tion of at least Asn32 and, therefore, represents a major
contributor to the observed microheterogeneity of hPAH
isolated after 2 h of induction with IPTG in E. coli [13].
Thus, the double spot seen, ) e.g., for the most basic
component of the protomers on 2D electrophoresis
(denoted hPAH I [13]) for the 24 h enzyme – (Fig. 1) is
most likely explained by a minor partial deamidation of
Asn32 during isoelectric focusing for 20 h (8
M
urea,
 20 °C) and represents deamidated protomers where
Asp/isoAsp have not yet reached the equilibrium position
in the pH gradient.
12
Structural and functional implications of Asn32
deamidation
In the reported crystal structure of DC(429–452)-rPAH
(PDB id. code, 1PHZ) [15], Asn32 is located in the loop
structure including residues D27–G33 (Fig. 2), preceding

the first b-sheet (Rb1) of the regulatory domain [15], and is
stabilized by several hydrogen bonds, including a hydrogen
bond between Asn30 Od1 and Gln134 Ne2(seeFig.2).
Consequently, the deamidation of Asn32 is likely to affect
the higher order structure of the NH
2
terminus in several
ways. First, on deamidation of Asn32fiAsp/isoAsp, the
resulting charge shift will lead to a repulsive electrostatic
interaction between the negatively charged carboxyl groups
of Asp/isoAsp32 and Asp84. Moreover, the presence of
isoAsp at position 32 in one of the generated isoforms will
also change the backbone conformation by adding an
extra carbon (methylene group) to the polypeptide chain
[35]. Interestingly, in the reported crystal structure of
rPAH, the sequence around Asn32 revealed high displace-
mentfactorsofupto105A
˚
2
[15] reflecting poor electron
density. High displacement factors are a consequence of
dynamic disorder (vibrations of the atoms) in the crystal as
well as static disorder caused by discrepancies between the
different unit cells in the crystal. Combining the crystal
structure information with the results of this study, we
conclude that the recombinant enzyme used in the crystal-
lographic study of rPAH (PDB id. code, 1PHZ) most likely
contained a mixture of isomeric dimer forms with either Asn,
Asp and isoAsp at position 32 in the protomers. Thus, the
conserved residue Asn32 is expected to be deamidated to the

same extent in hPAH as in rPAH, as its nearest neighbour
amino acids and the loop structure are the same in the two
proteins.
The perturbation of the overall conformation of the loop
structure as a result of deamidation of Asn32 to Asp/isoAsp
have immediate implications for the function of the
homotetrameric enzyme as they occur in a conformationally
sensitive part of the protein. Thus, the loop structure
including Asn32 is part of the designated autoregulatory
sequence (residues 19–33) [15] extending like a ÔlidÕ over the
active site pocket and thus may control the access of
substrate and pterin cofactor to this site [15,36]. Phosphory-
lation of hPAH at Ser16 by PKA results in a 1.4-fold
increase in the basal activity and a 1.7-fold increase in
catalytic efficiency [37]. Molecular modelling based on the
crystal structure of the recombinant rat enzyme has revealed
that phosphorylation induces a local conformational change
that is in agreement with the observed increased accessibility
of the substrate to the active site [37]. The functional effect
of deamidation of Asn32fiAsp/isoAsp is rather similar and
can be explained by a related mechanism. Thus, the
substitution of Asn32fiAsp by site-directed mutagenesis
results in a 1.7-fold increase in its catalytic efficiency, a 34%
decrease in the [S]
0.5
-value for
L
-Phe, an increased Hill
coefficient of substrate binding as well as substrate inhibi-
tion (Fig. 7, Table 2).

13
These changes in kinetic properties
are all characteristics observed because of multiple deami-
dations of wt-hPAH on 24 h expression of the recombinant
enzyme in E. coli [13]. It should be noted, however, that
the main-chain loop conformation may be slightly differ-
ent in the Asn32fiAsp/isoAsp deamidated form and the
Asn32fiAsp mutant form, which may account for the
quantitative differences observed between the kinetic pro-
perties of the two events. That Asn32 has a regulatory
function in hPAH is further supported by experiments
demonstrating that both deamidation of Asn32 and muta-
tion of Asn32fiAspareaccompaniedbya 20% increase
in the initial rate of phosphorylation at Ser16 by PKA [39].
Thus, it appears that phosphorylation of Ser16 and
deamidation of Asn32 act synergistically in the regulation
of hPAH.
Acknowledgements
This work was supported by grants from the Research Council (NFR),
the Norwegian Council on Cardiovascular Diseases, Rebergs legat,
L. Meltzers Høyskolefond, the Novo Nordisk Foundation, the
European Commission and the Fundac¸ a
˜
oparaaCieˆ ncia e Tecnologia,
Portugal (SFRH/BD/1100/2000). We thank Ali Sepulveda Mun
˜
oz for
expert technical assistance in preparing the recombinant hPAH fusion
proteins.
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