L. Casella et al.
LC–MS and LC–MS/MS data were obtained by using an LCQ DECA
ion-trap mass spectrometer equipped with ESI ion source and controlled
by Xcalibur 1.3 software (Thermo-Finnigan, San Jose, CA). ESI experi-
ments were carried out in positive-ion mode under the following constant
instrumental conditions: source voltage 4.5 kV, capillary voltage 15 V, ca-
pillary temperature 2508C, and tube lens voltage 15 V. The system was
run in automated LC–MS/MS mode and by using a Surveyor HPLC
system (Thermo Finnigan, San Jose, CA, USA) equipped with a Simme-
try300 C18 column (3.5 mm, 2.1100 mm, Waters, Milford, MA). The elu-
tion was performed with a 0–55% linear gradient over 65 min with 0.1%
trifluoroacetic acid (TFA) in water as solvent A and 0.1% TFA in aceto-
nitrile as solvent B. MS/MS spectra obtained by CID were performed
with an isolation width of 3 Th (m/z). The activation amplitude was
around 35% of the ejection RF amplitude that corresponds to 1.58 V.
efficient of the nitrophenols at 450 nm obtained from their absorbance
spectra (in phosphate buffer at pH 7.5):[54] for 3-nitrotyramine e450 =2300,
for 3-(4-hydroxy-3-nitrophenyl)propionic acid e450 =3350, and for 3-nitro-
l-tyrosine e450 =3100mꢀ1 cmꢀ1. The kinetic parameters were obtained
from fitting the plots of experimental rates at different substrate/nitrite
concentrations to the appropriate equations.
For each substrate, the rate dependence on the various reactant concen-
trations was studied through three series of steps: 1) finding a suitable
[H2O2]maximizing the rate but avoiding unwanted excess of the oxidant,
and then using this [H2O2]2) to study the dependence of the rate versus
[substrate], and 3) to study the dependence of the rate versus [NO2ꢀ] , by
following the iterative procedure described previously in detail.[11] The
protein concentration (HMb or m’-HMb) was kept at 1 mm in all the reac-
tions, while the concentrations of the other reactants used in the kinetic
studies were as follows:
For the analysis of protein fragments derived from m’-HMb, the mass
spectrometer was set such that one full MS scan was followed by a zoom-
scan and MS/MS scan on the most intense ion from the MS spectrum.
The acquired MS/MS spectra were automatically searched against a pro-
tein database for human proteins (human.fasta) by using the SEQUEST
algorithm to identify the modified residues. This algorithm has been in-
corporated into the Bioworks 3.0 software (ThermoFinnigan, San Jose,
CA). For the analysis of protein fragments of m-HMb, the mass spec-
trometer was set in MS/MS mode for the parent bicharged ions at m/z=
957 (mass of 1912 amu), 995.5 (mass of 1989 amu), and 973 (mass of
1944 amu). To compare the amount of modified heme, the mass spec-
trometer was set in MS/MS mode for the parent ions at 616 and 661 amu
For the phenol nitration catalyzed by HMb: 1) optimization of the perox-
ide concentration: for substrate
1
(2.0 mm): [NO2ꢀ]=1.3m, [H2O2]=
0.071–0.71m; for substrate 2 (0.40 mm): [NO2ꢀ]=0.30m, [H2O2]=0.053–
0.36m; for substrate 3 (0.3 mm): [NO2ꢀ]=0.8m, [H2O2]=0.071–0.71m;
2) dependence of the rate on phenol concentration: for substrate 1:
[H2O2]=0.36m, [NO2ꢀ]=1.3m, [phenol]=0.31–3.7 mm; for substrate 2:
[H2O2]=0.36m, [NO2ꢀ]=0.3m, [phenol]=0.062–1.6 mm; for substrate 3:
[H2O2]=0.53m, [NO2ꢀ]=0.8m, [phenol]=0.013–0.71 mm; 3) dependence
of the rate on nitrite concentration: for substrate 1 (3.1 mm): [H2O2]=
0.36m, [NO2ꢀ]=0.075–2.0m; for substrate 2 (0.62 mm): [H2O2]=0.36m,
[NO2ꢀ]=0.062–0.92m; for substrate
[NO2ꢀ]=0.050–1.1m.
3
(0.71 mm): [H2O2]=0.53m,
Two-dimensional and SDS PAGE analysis: Two-dimensional polyacryl-
amide gel electrophoresis was performed by using the immobilized pH
gradient system.[52] The first dimension, isoelectric focusing, was per-
formed on laboratory-made gels, cast on Gel-Bond (Amersham Biosci-
ences) with a 6.5–8.5 linear immobilized pH gradient obtained with
Acrylamido buffer solutions (Fluka), and the separation was run in the
Multiphor II horizontal system (Amersham Biosciences). The protein so-
lutions (HMb and m’-HMb) were diluted 1:2 with a solution containing
8m urea, 4% (w/v) 3-[(3-cholamidopropyl)dimethylammonio]-1-propane-
sulfonate (CHAPS), and 40 mm Tris. After centrifugation, 125 mL of each
sample containing 30 mg protein were loaded. The gel strips were then
equilibrated with SDS and placed on top of vertical 17% gels, before the
second dimension was performed by using a Mini PROTEAN II cell
(BioRad). SDS PAGE (17% gel) was performed by the method of
Laemmli[53] and the gel was stained with Coomassie Blue.
For the phenol nitration catalyzed by m’-HMb: 1) optimization of the per-
oxide concentration: for substrate 1 (2.0 mm): [NO2ꢀ]=1.0m, [H2O2]=
0.071–0.71m; for substrate 2 (0.40 mm): [NO2ꢀ]=0.80m, [H2O2]=0.071–
0.71m; for substrate 3 (0.30 mm): [NO2ꢀ]=0.80m, [H2O2]=0.071–0.71m;
2) dependence of the rate on phenol concentration: for substrate 1:
[H2O2]=0.36m, [NO2ꢀ]=1.0m, [phenol]=0.062–3.1 mm; for substrate 2:
[H2O2]=0.36m, [NO2ꢀ]=0.80m, [phenol]=0.026–1.3 mm; for substrate 3:
[H2O2]=0.36m, [NO2ꢀ]=0.8m, [phenol]=0.031–0.68 mm; 3) dependence
of the rate on nitrite concentration: for substrate 1 (3.1 mm): [H2O2]=
0.36m, [NO2ꢀ]=0.075–1.7m; for substrate 2 (0.5 mm): [H2O2]=0.36m,
[NO2ꢀ]=0.050–1.1m; for substrate 3 (0.68 mm): [H2O2]=0.36m, [NO2ꢀ]=
0.050–0.80m.
Binding of nitrite: Increasing quantities of a concentrated nitrite solution
in 200 mm phosphate buffer (pH 7.5, final concentration of 0.0019–0.53m)
were added to a solution of HMb (3.8 mm, 1600 mL) in the same buffer in
a quartz cuvette with a pathlength of 1 cm thermostated at 25.0ꢂ0.18C;
UV/Vis spectra were recorded after each addition. Blank spectra were
recorded in the same way but in the absence of protein. After subtracting
the corresponding blank from each spectrum, the resulting spectra were
corrected for dilution and then transformed into difference spectra by
subtracting the native protein spectrum. A plot was constructed with the
difference between the absorbance changes at 424 and at 406 nm, the
wavelengths at which the difference spectra exhibit the maximum varia-
tions, versus the ligand concentration. The binding constant, KB, was ob-
Acknowledgements
This work was supported by funds from the Progetto di Ricerca di Inter-
esse Nazionale (PRIN) of the Italian Ministero dellꢁIstruzione dellꢁUni-
versità e della Ricerca (MIUR). The University of Pavia and the Europe-
an COST D21 Action are also gratefully acknowledged for support. We
thank Prof. Monica Galliano and Dr. Monica Campagnoli for useful sup-
port in the electrophoretic characterization of the proteins.
tained by interpolation of the absorbance data with the binding isotherm
[1]E. Antonini, M. Brunori, Hemoglobin and Myoglobin in Their Reac-
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ꢀ
for low-affinity binding of
a
]
single ligand: DA=DA1KB[NO2
represents the total nitrite concentra-
]
/
total
ꢀ
ꢀ
total
(1+KB[NO2
]
total), where [NO2
tion.[11]
Kinetic studies of phenol nitration catalyzed by HMb and m’-HMb: The
kinetic experiments were carried out in 200 mm phosphate buffer
(pH 7.5) by using a quartz cuvette with a pathlength of 1 cm thermostat-
ed at 25.0ꢂ0.18C and equipped with a magnetic stirrer. The initial solu-
tion containing protein (HMb or m’-HMb, 1 mm) and variable substrate
and nitrite concentrations (final volume 1600 mL) was obtained by mixing
solutions of appropriate concentration of the reagents in the buffer. The
reaction was started by addition of the H2O2 solution and was followed
by monitoring the absorbance change at 450 nm during the initial 10–
15 s. The transformation of the rate data from absorbance per second
into [nitrophenol]produced per second was done by using the extinction co-
[3]H. Frauenfelder, B. H. McMahon, R. H. Austin, K. Chu, J. T.
Groves, Proc. Natl. Acad. Sci. USA 2001, 98, 2370–2374.
[4]D. J. Garry, S. B. Kanatous, P. P. A. Mammen, Trends Cardiovasc.
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[5]U. Flçgel, A. Gçdecke, L.-O. Klotz, J. Schrader, FASEB J. 2004, 18,
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756
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