3128 J. Am. Chem. Soc., Vol. 121, No. 13, 1999
Parac et al.
complexes are well suited for the traditional task of sequence
determination and for new challenges, such as preparation of
semisynthetic proteins, structural mapping and functional analy-
sis of protein domains, analysis of protein interactions with other
proteins and with nucleic acids, elucidation of protein folding,
analysis of nonnative states, and development of new drugs.
Because of their small size, transition-metal complexes can be
applied in structural studies that require relatively high “resolu-
tion”, at the level of functional groups and chemical bonds in
proteins.
Experimental Procedures
2 4
Chemicals. The deuterium-containing compounds D O, DClO , and
NaOD and the salts K [PdCl ] and AgClO monoxydrate (99.999%
2 4 4
pure) were obtained from Aldrich Chemical Co. All other chemicals
were of reagent grade. Dipeptide His-Gly and amino acids 1-Me-His
and 3-Me-His were obtained from Sigma Chemical Co. The terminal
amino group in each of these substrates was acetylated by a published
procedure.53 Dipeptides 1-Me-AcHis-Gly and 3-Me-AcHis-Gly were
synthesized from 1-Me-AcHis and 3-Me-AcHis by a standard solid-
state method, and their purity was checked by HPLC; this was done
by the staff of the Protein Facility. The complex [Pd(H
prepared by a published method.
Measurements. Proton NMR spectra of solutions in D
as an internal reference, were recorded with Bruker DRX 400 and
Varian Unity 500 spectrometers. Temperature was kept within (0.5
°C. The pH was measured with Fisher 925 instrument and a Phoenix
Ag/AgCl reference electrode. The pD values were calculated by the
standard formula:54 pD ) pH + 0.41. Ultraviolet-visible spectra were
recorded with a Perkin-Elmer λ-18 spectrophotometer.
2
+
2
O)
4
]
was
Studies in our laboratory showed that palladium(II) complexes
spontaneously bind to the side chains of methionine and histidine
residues and effect hydrolytic cleavage of short peptides with
36
2
O, with DSS
35-51
half-lives that range from several hours to several minutes.
Because palladium(II) complexes are diamagnetic, kinetic
1
experiments are easily done by H NMR spectroscopy. Because
the cleavage reactions occur with turnover,4
3,48,50
the simple
palladium(II) complexes that catalyze them can be considered
primitive artificial peptidases. Our successes in selective cleav-
Study of Hydrolysis. Because all the solutions were made in D
all the aqua ligands actually were D O. For simplicity and consistency
with our previous publications, however, we show aqua ligands as H O.
For the cleavage of peptides with K [PdCl ], 400 µL of a 100 mM
solution of K [PdCl ] in D O, 100 µL of a 100 mM solution of peptide
in D O, 50 µL of a 100 mM solution of DSS in D O, and 150 µL of
D O were mixed in the NMR tube. For the cleavage of peptides with
2
O,
age of cytochrome c,38 myoglobin, and other proteins bode
well for the general applicability of these new reagents in
biochemistry and allied disciplines. Before palladium(II) com-
plexes can become widely accepted, the basis for their selectivity
must be explained in studies with peptides.
51
52
2
2
2
4
2
4
2
2
2
2
2+
[
Pd(H
was mixed with 500 µL of a 100 mM solution of the peptide or the
histidine derivative in D O, in the Eppendorf vial. The pH was adjusted
to 1.0 (i.e., pD to 1.4) with 2.0 M DClO and was measured at the
2 4 2
O) ] , 2.00 mL of a 100 mM solution of this complex in D O
The present study shows, for the first time, that peptide bonds
2
-
can be cleaved with commercially available salts of [PdCl4]
2
anion; no chemical derivatization or modification of this simple
complex is required. Aquation of this complex, however, causes
4
beginning and at the end of each experiment. The difference was always
less than 0.10. Samples were kept at 40 °C for different periods of
time. The reactions were followed by H NMR spectroscopy, and the
spectra were very similar to those that we published before.
2+
a remarkable difference in reactivity; the complex [Pd(H2O)4]
cleaves peptides more rapidly and with different regioselectivity
than its chloro precursor does. We combine experimental
kinetics and theoretical molecular dynamics to study how simple
substitution of ancillary ligands affects hydrolytic cleavage of
peptides by palladium(II) complexes and to determine the
stereochemical basis for the regioselectivity of cleavage.
1
40,43
The
error in integration of the resonances was estimated at (5%. In all the
2
+
experiments with [Pd(H
[PdCl ]
4
2
O)
, the reactions were quenched by adding 400 µL of a 200
mM solution of sodium diethyldithiocarbamate (Naddtc) in D O to 200-
µL aliquots of the reaction mixture. The insoluble [Pd(ddtc) ] was
4
] , and in the early experiments with
2-
2
2
1
(27) Heyduk, E.; Heyduk, T. Biochemistry 1994, 33, 9643.
removed by centrifugation, and H NMR spectra of the clear supernatant
(
28) Ghaim, J. B.; Greiner, D. P.; Meares, C. F.; Gennis, R. B.
were recorded. Free glycine and free acetic acid were identified by
their H NMR chemical shifts and by enhancement of the corresponding
Biochemistry 1995, 34, 11311.
29) Greiner, D. P.; Hughes, K. A.; Gunasekera, A. H.; Meares, C. F.
Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 71.
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O. N.; Ishihama, A.; Meares, C. F. Biochemistry, 1998, 37, 1344.
1
(
resonance upon addition of these compounds to the reaction mixture.
Molecular Dynamics Simulation. To sample the conformational
space of the Pd(II)-peptide complex, we performed a Langevin
molecular dynamics simulation in a vacuum (dielectric constant of 1.0),
over a period of 3.00 ns, with an integration step of 1.00 fs; the energies
were saved after each 10 fs, for further analysis. The system was
coupled to a heat bath at 1000 K, and the friction coefficient â was set
(
(
31) Rana, T. M. AdV. Inorg. Biochem. 1993, 10, 177.
(32) Yashiro, M.; Takarada, T.; Miyama, S.; Komiyama, M. J. Chem.
Soc., Chem. Commun. 1994, 1757.
33) Allen, G.; Campbell, R. O. Int. J. Peptide Protein Res. 1996, 48,
65.
(
2
-
1
55
to 2.0 ps . In addition to the original set of CHARMM parameters,
the improper torsion centered at the C atom of histidine was constrained
to keep this atom trigonal and therefore keep the C -C bond coplanar
(
(
(
(
(
34) Hegg, E. L.; Burstyn, J. N. J. Am. Chem. Soc. 1995, 117, 7015.
35) Burgeson, I. E.; Kosti c´ , N. M. Inorg. Chem. 1991, 30, 4299.
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38) Zhu, L.; Qin, L.; Parac, T. N.; Kosti c´ , N. M. J. Am. Chem. Soc.
γ
â
γ
with the imidazole ring, as it must be. The palladium(II)-ligand torsion
angles were left unconstrained. The parameters that are not included
in the CHARMM set are given in Supporting Information, Table S1.
The bonded energy parameters for the coordinated water were taken
from the SPCE model for water.56 Atomic charges in the palladium(II)
complex were calculated by the extended H u¨ ckel method and are given
in Supporting Information, Table S2. Nonbonded energies for all pairs
of atoms were calculated without any cutoffs. The C-terminus of the
peptide was reasonably assumed to be protonated.
1
994, 116, 5218.
(39) Zhu, L.; Kosti c´ , N. M. Inorg. Chim. Acta 1994, 217, 21.
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(
(
(
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The molecular dynamics trajectory was used to find conformations
with the interatomic distances that are comparable to, or smaller than,
the sum of the van der Waals radii of the two atoms involved. The
1
996, 41, 390.
(
(
45) Chen, X.; Zhu, L.; Kosti c´ , N. M. Chin. Chem. Lett. 1996, 7, 127.
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(
(
(
(
(
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3
83.
52) Milovi c´ , N. M.; Kosti c´ , N. M. Unpublished results.
(