Control of the coordination structure of organometallic palladium complexes in an apo-ferritin cage

Article abstract of DOI:10.1021/ja802463a

We report the preparation of organometallic Pd(allyl) dinuclear complexes in protein cages of apo-Fr by reactions with [Pd(allyl)Cl]₂ (allyl = η³-C₃H₅). One of the dinuclear complexes is converted to a trinuclear complex by replacing a Pd-coordinated His residue to an Ala residue. These results suggest that multinuclear metal complexes with various coordination structures could be prepared by the deletion or introduction of His, Cys, and Glu at appropriate positions on protein surface. Copyright

Full text of DOI:10.1021/ja802463a

Published on Web 07/18/2008
Control of the Coordination Structure of Organometallic Palladium
Complexes in an apo-Ferritin Cage
†
‡
†
⊥
,†,§
Satoshi Abe, Jochen Niemeyer, Mizue Abe, Yusuke Takezawa, Takafumi Ueno,*
|
‡
,⊥
Tatsuo Hikage, Gerhard Erker, and Yoshihito Watanabe*
Department of Chemistry, Graduate School of Science, High Intensity X-ray Diffraction Laboratory, and Research
Center for Materials Science, Nagoya UniVersity, Nagoya 464-8602, Japan, PRESTO, Japan Science and
Technology Agency (JST), Saitama 332-0012, Japan, and Organisch-Chemisches Institut, UniVersit a¨ t M u¨ nster,
Corrensstrasse 40, M u¨ nster 48149, Germany
Received April 4, 2008; E-mail: yoshi@nucc.cc.nagoya-u.ac.jp; taka@mbox.chem.nagoya-u.ac.jp
Metal clusters such as the Mn cluster of photosystem II, FeMoco
of nitrogenase, and iron-sulfur clusters of ferredoxins play essential
1
–4
roles in many biological systems. The coordination geometries
and the functions of these clusters are influenced by amino acid
residues in the active sites. Recently, preparation of non-native
multinuclear metal clusters in the protein scaffolds have been
5–8
reported. Tri- or pentanuclear oxo-clusters of Zr(IV) and Hf(IV)
have been identified within the dityrosyl cluster nucleation motif
6
,7
of ferric-ion-binding protein.
Several types of polynuclear
tungsten oxide clusters are formed in the binding cavity of a Mo/
8
W-storage protein. We have also previously reported the utilization
of the apo-ferritin (apo-Fr) cage for preparing a single Pd nano-
cluster as well as size selective olefin hydrogenation catalyzed by
9
this composite. These results suggest that multinuclear metal
complexes with various coordination structures could be formed
by designing amino acid residues on the protein surface. In this
report, we describe the preparation of various organometallic
multinuclear Pd complexes in the protein cages of apo-Fr and its
II
mutants (Figure 1a) by their reactions with [Pd (allyl)Cl]
2
(allyl
Figure 1. (a) Reaction scheme for the preparation of Pd(allyl) ·apo-Fr; (b)
entire structure of apo-Fr viewed down a 3-fold axis (PDB ID: 1DAT); (c)
close up view of the 3-fold axis channel.
3
)
η -C
3 5
H ), which catalyze organic reactions such as C-C bond
10,11
formation reactions.
More importantly, we have successfully
controlled the coordination structures of these multinuclear Pd
complexes by replacing histidine residues at the binding sites.
II
plasma-optical emission spectrometry (ICP-OES) and bicinchoni-
nate (BCA) analyses of the purified composite indicate that the
number of Pd complexes incorporated in Pd(allyl)·apo-Fr is 103
( 1.
Ferritin (Fr), an iron storage protein composed of 24 subunits,
is a spherical protein assembly which has interior space with 8 nm
1
2,13
in diameter (Figure 1b).
The space has been utilized for the
deposition of metal particles and metal complexes such as FeS,
CdS, CdSe, Pd, Ag, Gd-HPDO3A (gadolinium-[10-(2-hydroxypro-
pyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid]), and
The composite was crystallized by a hanging drop vapor diffusion
method in the presence of cadmium ions, which are essential for
13,20
the crystallization of apo-Fr, as reported previously.
The crystal
9,14–19
hexacyanoferrate(III).
These metal ions are incorporated into
structure of Pd(allyl)·apo-Fr was refined to 1.7 Å resolution as
2
1
the Fr cage through the 3-fold channels located at the intersections
of the three subunits (Figure 1c) and accumulated in the interior
space to form metal nanoparticles by self-assembly or redox
shown in Figure 2a. The root-mean-square deviation (rmsd) of
the CR atoms of Pd(allyl)·apo-Fr from that of apo-Fr is 0.47.
This indicates that the folding of apo-Fr is preserved even in the
presence of the Pd complexes on the interior surface of apo-Fr.
The anomalous difference Fourier maps show that dinuclear
Pd(allyl) complexes are formed at two Pd binding sites per single
Fr subunit. In other words, there are 48 Pd binding areas on the
interior surface of Pd(allyl)·apo-Fr that contribute to the capture
of 96 Pd atoms (Figure 2a-c). The total number of Pd atoms
observed in the crystal structure is almost identical to that of Pd
atoms determined by quantitative analyses by ICP and BCA
methods.
13
9
,14–16,19
reactions.
Recombinant L-chain apo-Fr from horse liver (10 µM, 5 mL in
5
0 mM Tris/HCl (pH8.0), 0.15 M NaCl) was treated with 100 equiv
II
of [Pd (allyl)Cl]
2
(10 mM, 0.5 mL) in acetonitrile and the reaction
mixture (9% acetonitrile aqueous solution) was stirred for 1 h at
5 °C. After dialysis against a 0.15 M NaCl aqueous solution, apo-
2
Fr assembly containing Pd(allyl) complexes (Pd(allyl)·apo-Fr) was
¨
purified by a size exclusion column (AKTA design, Superdex
G-200) to remove unbound Pd complexes. Inductively coupled
The two binding areas are located at the 3-fold axis channel and
at a metal binding domain called as the “accumulation center”
(Figure 2a). Pd1 of wild type apo-Fr (PdW1) and PdW2 located
†
Department of Chemistry, Graduate School of Science, Nagoya University.
‡
13
Universit a¨ t M u¨ nster.
§
PRESTO, Japan Science and Technology Agency (JST).
|
at the 3-fold axis channel have a thiol-bridged dinuclear structure
High Intensity X-ray Diffraction Laboratory, Nagoya University.
⊥
ꢀ
Research Center for Materials Science, Nagoya University.
stabilized by the coordination of N of His114 and the O atom of
1
0512 9 J. AM. CHEM. SOC. 2008, 130, 10512–10514
10.1021/ja802463a CCC: $40.75  2008 American Chemical Society

C O M M U N I C A T I O N S
Figure 2. Crystal structures of Pd(ally)·apo-Frs. The interior structures of (a) Pd(allyl)·apo-Fr, (d) Pd(allyl)·apo-H114AFr, and (g) Pd(allyl)·apo-
H49AFr. Close views of 3-fold channels and accumulation centers of Pd(allyl) · apo-Fr (b and c), Pd(allyl) · apo-H114AFr (e and f), Pd(allyl) · apo-
H49AFr (h and i), respectively. The Pd and Cd atoms are indicated as greenish blue and beige spheres, respectively. The anomalous difference Fourier maps
at 4.0 σ indicate the positions of palladium atoms which are shown in magenta. The selected 2|Fo| - |Fc| electron density maps at 1.0 σ are shown in blue.
γ
γ
ꢀ
a water molecule. PdW1-S Cys126, PdW2-S Cys126, PdW1-N His114
,
Two mutants, apo-C126AFr and apo-C48A/H49AFr, were
prepared to elucidate the effect of the cysteine residues for the
and PdW2-OH2O distances are 2.47, 2.38, 2.14, and 2.34 Å,
respectively (Figure 2b). PdW3 and PdW4 at the accumulation
center are bound to O of Glu45 and N of His49, respectively,
while the thiol-group of Cys48 serves as a bridging ligand between
ligation of the Pd(allyl) complex in apo-Fr. When apo-C126AFr
ꢀ
δ
II
mutant was treated with 100 equiv of [Pd (allyl)Cl]
2
under the same
conditions as apo-Fr, the quantitative analyses show that the number
of Pd atoms in apo-C126AFr (37 ( 4) was smaller than the number
of Pd atoms (103 ( 1) in apo-Fr. This indicates that Pd(allyl)
complexes can be bound to the accumulation center in spite of the
deletion of Cys126. In the case of apo-C48A/H49AFr, the number
of Pd atoms in apo-C48A/H49AFr (54 ( 5) was about half of Pd
atoms in apo-Fr, suggesting that Pd(allyl) complexes are bound to
the binding site at the 3-fold channel. These results indicate that
the cysteine residues are crucial to stabilize the coordination of
Pd(allyl) complexes at these sites.
γ
γ
ꢀ
PdW3 and PdW4 with PdW3-S Cys48, PdW4-S Cys48, PdW3-O Glu45
,
δ
and PdW4-N His49 distances of 2.31, 2.57, 2.30, and 2.17 Å,
respectively (Figure 2c). The distances of PdW1-PdW2 (3.68 Å)
and PdW3-PdW4 (3.12 Å) are too long to directly interact each
2
2,23
3
other.
Moreover, the η -allyl ligands of PdW1, PdW3, and
PdW4 give clear electron density maps near each Pd atom, although
the electron density map of the allyl ligand of PdW2 is slightly
weak (Figure 2b and 2c). In addition, the B-factor of the PdW2
atom is larger (42.19) than the B-factor of the PdW1, PdW3, and
PdW4 atoms (24.80, 19.86, 22.54, respectively).
To alter the coordination structures of Pd(allyl) complexes of
A larger B-factor value of PdW2 indicates that the PdW2(allyl)
complex could be fluctuating or changing locations because the
PdW2 atom is coordinated only by a single Cys residue at position
Pd(allyl)·apo-Fr, two mutants, in which His114 or His49 was
replaced with Ala, were prepared. The mutants, apo-H114AFr and
II
apo-H49AFr, were treated with 100 equiv of [Pd (allyl)Cl]
2
under
1
26. Thus, the PdW2(allyl) complex is not strongly fixed relative
the same conditions used for analyses of apo-Fr. The quantitative
analyses of the composites show that the numbers of Pd atoms
retained in Pd(allyl)·apo-H114AFr and Pd(allyl)·apo-H49AFr
are 78 ( 6 and 99 ( 4, respectively.
ThecrystalstructuresofPd(allyl)·apo-H114AFrandPd(allyl)·apo-
H49AFr show that the numbers of Pd atoms in the cages are 72
to the other three Pd complexes. Each Pd atom (PdW1-PdW4) in
apo-Fr has square-planar geometry with an allyl ligand and amino
acid residues or a water molecule (Figure 2b and 2c). These
structures are similar to those reported for dinuclear Pd allyl
4
,24
complexes.
J. AM. CHEM. SOC. 9 VOL. 130, NO. 32, 2008 10513

C O M M U N I C A T I O N S
2
1
and 96 (Figure 2d and 2g), respectively, which are almost identical
to the values obtained by the quantitative analyses performed using
ICP and BCA methods. Pd(allyl)·apo-H114AFr has thiolato-
bridged trinuclear Pd complexes at the 3-fold channels because the
deletion of His114 causes a 2.4 Å shift of the position of the CR
atom of Cys126 toward the center of the 3-fold channel (Figure
surfaces. Further work on the design of polynuclear metal com-
plexes and catalytic reactions is currently in progress.
Acknowledgment. This work was supported by the Global COE
Program in Chemistry, Nagoya University for S.A., International
Research Training Group (DFG, JSPS) “Complex Functional
Systems” (M u¨ nster and Nagoya), Grant-in-Aid for Scientific
Research (Grant No. 18685019 for T.U.) and on Priority Areas
2
e). The PdA1-PdA1′ distance (3.24 Å) indicates that the
complexes have no direct bonding interaction among the Pd
The coordination geometry of each Pd atom is a typical
square-planar structure with an allyl ligand and two S atoms at
the 3-fold axis channel with a six-membered-ring structure as a
reported Pd trinuclear complex (Figure 2e). The coordination
structures of PdA2 and PdA3 are identical to those of Pd(allyl) ·apo-
Fr (Figure 2f).
(
Grant No. 16033226, Chemistry of Coordination Space for Y.W.)
25,26
atoms.
from Ministry of Education, Culture, Sports, Science and Technol-
ogy, Japan, and PRESTO, Japan Science and Technology Agency
γ
(
JST), and Amano Enzyme Inc.
2
7
Supporting Information Available: Experimental details, X-ray
crystallographic data. This material is available free of charge via the
Internet at http://pubs.acs.org.
The crystal structure of Pd(allyl)·apo-H49AFr shows that the
coordination structure of the dinuclear Pd complex at the accumula-
tion center is altered from that of Pd(allyl)·apo-Fr, although the
structures of PdB1 and PdB2 are the same as that of Pd(allyl)·apo-
Fr (Figure 2h and 2i). PdB3 and PdB4 form a dinuclear structure
even after the deletion of His49 (Figure 2i). However, the distance
between PdB3 and PdB4 is 2.81 Å, which is shorter than that of
both Pd(allyl)·apo-Fr (3.12 Å) and a reported thiolato-carboxylato
References
(
(
1) Loll, B.; Kern, J.; Saenger, W.; Zouni, A.; Biesiadka, J. Nature 2005, 438,
1040–1044.
2) Ferreira, K. N.; Iverson, T. M.; Maghlaoui, K.; Barber, J.; Iwata, S. Science
2
004, 303, 1831–1838.
(3) Einsle, O.; Tezcan, F. A.; Andrade, S. L. A.; Schmid, B.; Yoshida, M.;
Howard, J. B.; Rees, D. C. Science 2002, 297, 1696–1700.
(
4) Redon, R.; Cramer, R.; Bernes, S.; Morales, D.; Torrens, H. Polyhedron
2001, 20, 3119–3125.
2
8
ꢀ
ꢀ
(5) Zeth, K.; Offermann, S.; Essen, L. O.; Oesterhelt, D. Proc. Natl. Acad.
Sci. U.S.A. 2004, 101, 13780–13785.
(6) Zhong, W. Q.; Alexeev, D.; Harvey, I.; Guo, M. L.; Hunter, D. J. B.; Zhu,
H. Z.; Campopiano, D. J.; Sadler, P. J. Angew. Chem., Int. Ed. 2004, 43,
Pd dinuclear complex (3.30 Å) because each O
of the carboxylate moiety of Glu45 is bound to PdB3 and PdB4.
1 2
and O atom
A Suzuki coupling reaction of 4-iodoaniline and phenylboronic
acid to afford 4-phenylaniline was examined to evaluate the catalytic
activities of these composites, since Pd(allyl) complexes are
known to catalyze the Suzuki coupling reaction. The turnover
frequencies (TOF ) [product (mol)] per Pd(allyl)·apo-Frs per
5
914–5918.
(7) Alexeev, D.; Zhu, H. Z.; Guo, M. L.; Zhong, W. Q.; Hunter, D. J. B.;
2
9
Yang, W. P.; Campopiano, D. J.; Sadler, P. J. Nat. Struct. Biol. 2003, 10,
2
97–302.
3
0
(8) Schemberg, J.; Schneider, K.; Demmer, U.; Warkentin, E.; Muller, A.;
Ermler, U. Angew. Chem., Int. Ed. 2007, 46, 2408–2413.
(9) Ueno, T.; Suzuki, M.; Goto, T.; Matsumoto, T.; Nagayama, K.; Watanabe,
1
hour) of the coupling reactions were determined by H NMR based
Y. Angew. Chem., Int. Ed. 2004, 43, 2527–2530.
(
10) Trost, B. M.; Crawley, M. L. Chem. ReV. 2003, 103, 2921–2943.
11) Tsuji, J., Palladium Reagents and Catalysts. In New PerspectiVes for the
21st Century; Wiley: Chichester, U.K., 2004.
on the consumption of 4-iodoaniline and the formation of the
product. The size exclusion column chromatography of the reaction
solution showed that the spherical 24-mer assembly of the
composite is maintained during the reaction. The activity of
Pd(allyl)·apo-Fr (3500 ( 400) is almost identical to that of
Pd(allyl)·apo-H49AFr (3400 ( 300). On the other hand, the
activity of Pd(allyl)·apo-C48A/H49AFr (1900 ( 100) is 1.8-fold
lower than that of Pd(allyl) ·apo-Fr due to deletion of binding sites
at the accumulation center. These results show that each Pd
dinuclear complex at both binding areas has similar activity of
Suzuki coupling. Pd(allyl)·apo-H114AFr (900 ( 50) shows about
(
(
12) Liu, X. F.; Theil, E. C. Acc. Chem. Res. 2005, 38, 167–175.
13) Hempstead, P. D.; Yewdall, S. J.; Fernie, A. R.; Lawson, D. M.; Artymiuk,
P. J.; Rice, D. W.; Ford, G. C.; Harrison, P. M. J. Mol. Biol. 1997, 268,
(
4
24–448.
(
14) Douglas, T.; Dickson, D. P. E.; Betteridge, S.; Charnock, J.; Garner, C. D.;
Mann, S. Science 1995, 269, 54–57.
(
15) Kramer, R. M.; Li, C.; Carter, D. C.; Stone, M. O.; Naik, R. R. J. Am.
Chem. Soc. 2004, 126, 13282–13286.
(16) Yamashita, I.; Hayashi, J.; Hara, M. Chem. Lett. 2004, 33, 1158–1159.
(
17) Aime, S.; Frullano, L.; Crich, S. G. Angew. Chem., Int. Ed. 2002, 41, 1017–
019.
(18) Dominguez-Vera, J. M.; Colacio, E. Inorg. Chem. 2003, 42, 6983–6985.
1
(
19) Uchida, M.; Klem, M. T.; Allen, M.; Suci, P.; Flenniken, M.; Gillitzer, E.;
Varpness, Z.; Liepold, L. O.; Young, M.; Douglas, T. AdV. Mater. 2007,
19, 1025–1042.
20) Granier, T.; Comberton, G.; Gallois, B.; d’Estaintot, B. L.; Dautant, A.;
Crichton, R. R.; Precigoux, G. Proteins 1998, 31, 477–485.
4
-fold lower activity than that of Pd(allyl)·apo-Fr. The lower
(
reactivity of Pd(allyl)·apo-H114AFr suggested that the trinuclear
Pd cluster at the 3-fold channel interferes with the penetration of
substrates or that the geometry of Pd complexes at the 3-fold
channel is different from Pd(allyl) · apo-Fr. Pd(allyl) · apo-
C126AFr (830 ( 70) shows lower activity than the expected value
1750), which is half the TOF of Pd(allyl)·apo-Fr; the reason is
not clear at this moment. Although the catalytic activities per Pd
atoms of Pd(allyl)·apo-Fr are about twice lower than that of
Pd (allyl)Cl] under the same conditions, the catalytic activities
2
(21) Atomic coordinates are deposited in the Protein Data Bank under accession
numbers 2ZG7, 2ZG8, and 2ZG9 for Pd(allyl)· apo-Fr, Pd(allyl)·apo-
H49AFr, and Pd(allyl)· apo-H114AFr, respectively.
(22) Mendia, A.; Cerrada, E.; Arnaiz, F. J.; Laguna, M. Dalton Trans. 2006,
6
09–616.
(
(
23) Ukhin, L. Y.; Dolgopolova, N. A.; Kuzmina, L. G.; Struchkov, Y. T. J.
Organomet. Chem. 1981, 210, 263–272.
(
24) Weckenmann, U.; Mittler, S.; Kramer, S.; Aliganga, A. K. A.; Fischer,
R. A. Chem. Mater. 2004, 16, 621–628.
(25) Basato, M.; Grassi, A.; Valle, G. Organometallics 1995, 14, 4439–4442.
(26) Burrows, A. D.; Mingos, D. M. P. Trans. Metal Chem. 1993, 18, 129–
II
31
[
1
48.
of the Pd(allyl)·apo-Frs could be improved by increasing the
number of Pd(allyl) complexes in apo-Fr by the introduction of
Cys residues on the interior surface of apo-Fr.
(27) Sellmann, D.; Geipel, F.; Heinemann, F. W. Eur. J. Inorg. Chem. 2000,
2
71–279.
(
28) Buey, J.; Coco, S.; Diez, L.; Espinet, P.; Martin-Alvarez, J. M.; Miguel,
J. A.; Garcia-Granda, S.; Tesouro, A.; Ledoux, I.; Zyss, J. Organometallics
1
998, 17, 1750–1755.
In summary, we have demonstrated that a variety of coordination
structures of multinuclear Pd complexes such as dinuclear and
trinuclear complexes are constructed by protein engineering of the
interior surface of apo-Fr. These results suggest that multinuclear
metal complexes with various coordination structures could be
prepared by the deletion or introduction of key residues such as
His, Glu, and Cys residues at appropriate positions on protein
(29) The Suzuki coupling reactions were carried out in an aqueous solution of
0
.15 M NaCl containing 4-iodoaniline (2.5 mM), phenylboronic acid (5.2
mM), NaOH (4.5 mM), and Pd(allyl)· apo-Frs (0.025 µM). The reactions
were allowed to proceed for 12 h at 50 °C.
(
30) Viciu, M. S.; Germaneau, R. F.; Navarro-Fernandez, O.; Stevens, E. D.;
Nolan, S. P. Organometallics 2002, 21, 5470–5472.
(31) The values of TOF per Pd atom of Pd(allyl)· apo-Fr and [Pd(allyl)Cl]
were 34 ( 4 and 76 ( 1, respectively.
2
JA802463A
1
0514 J. AM. CHEM. SOC. 9 VOL. 130, NO. 32, 2008