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J. Biol. Chem., Vol. 276, Issue 52, 49359-49364, December 28, 2001
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From the
Received for publication, September 6, 2001, and in revised form, October 4, 2001
UreE is proposed to be a metallochaperone that
delivers nickel ions to urease during activation of this bacterial
virulence factor. Wild-type Klebsiella aerogenes UreE binds
approximately six nickel ions per homodimer, whereas H144*UreE (a
functional C-terminal truncated variant) was previously reported to
bind two. We determined the structure of H144*UreE by multi-wavelength anomalous diffraction and refined it to 1.5 Å resolution. The present
structure reveals an Hsp40-like peptide-binding domain, an Atx1-like
metal-binding domain, and a flexible C terminus. Three metal-binding
sites per dimer, defined by structural analysis of Cu-H144*UreE, are on
the opposite face of the Atx1-like domain than observed in the copper
metallochaperone. One metal bridges the two subunits via the pair of
His-96 residues, whereas the other two sites involve metal coordination
by His-110 and His-112 within each subunit. In contrast to the copper
metallochaperone mechanism involving thiol ligand exchanges between
structurally similar chaperones and target proteins, we propose that
the Hsp40-like module interacts with urease apoprotein and/or other
urease accessory proteins, while the Atx1-like domain delivers
histidyl-bound nickel to the urease active site.
Urease (EC 3.5.1.5) is a nickel-containing enzyme that catalyzes
the hydrolysis of urea to produce ammonia and carbamate (1). Increased
pH arising from this reaction is critical to the virulence of several
human and animal pathogens (2). The crystal structure of urease from
Klebsiella aerogenes provided the first three-dimensional
model of the protein and revealed a unique dinuclear active site with
the metal ions bridged by a carbamylated lysine residue (3, 4).
Subsequent investigations of ureases from Bacillus pasteurii
(5) and Helicobacter pylori (6) show essentially identical
active site structures. Proper assembly of this metallocenter is a key
step for maturation of urease and, in K. aerogenes, involves
the products of the ureD, ureE, ureF,
and ureG accessory genes located adjacent to the structural genes (ureA, ureB, and ureC) (7).
UreD, UreF, and UreG are known to form a series of complexes with
urease apoprotein (8-11) and are suggested to act as a molecular
chaperone for activation (7). In vitro activation and
mutagenesis studies of the largest of these complexes,
UreD-UreF-UreG-urease apoprotein (UreDFG-apourease), reveal that UreG
functions as a GTPase during activation (12). Urease within the
UreDFG-apourease complex can be fully activated in the presence of
nickel, bicarbonate (for lysine carbamylation), GTP, and UreE (13). The
latter protein is proposed to function as a "metallochaperone" by
delivering nickel ions to UreDFG-apourease (14).
The metal-binding properties of wild-type UreE and H144*UreE, which has
15 residues truncated C-terminally, have been extensively characterized
(15-18). The wild-type protein binds approximately six nickel ions per
homodimer in distorted octahedral geometry with an average of
three-five histidine donors per metal ion (14, 16). Most of these
ligands are presumed to derive from the C-terminal fragment that
contains 10 histidines within the last 15 residues. H144*UreE lacking
the His-rich region is competent for activating urease in
vivo (15) but was reported to bind only two nickel ions per dimer;
thus, internal ligands, not the histidine residues at the C terminus,
are necessary for UreE to assist in K. aerogenes urease
activation (15). Based on extensive mutagenesis and spectroscopic studies of H144*UreE, a model for the critical nickel-binding sites was
proposed (17). Structural information of UreE is desired to test the
validity of this model and to identify potential residues involved in
interaction with urease.
Major advances have been made in understanding the structure and
function of copper metallochaperones in recent years (19, 20); however,
structural information on chaperones for other metals is lacking. Here
we provide the first view of a suspected metallochaperone for nickel
incorporation. The H144*UreE structure reveals a unique two-domain
architecture with one domain structurally related to a heat shock
protein and the second to the Atx1 copper metallochaperone.
Significantly, the metal-binding sites in UreE and Atx1 are distinct in
location and types of residues despite the relationship between these
proteins. In contrast to the thiol ligand exchange mechanism used by
the copper metallochaperones (21, 22), we propose a distinct mechanism
for UreE activation of urease.
Purification, Crystallization, and Data
Collection--
Recombinant H144*UreE and two of its variants (H91A
and H110A) were purified as described previously (17), except that the host cells used were Escherichia coli B834(DE3). Protein was
dialyzed against 20 mM Tris-HCl buffer, pH 7.5, containing
20 mM imidazole, 2 mM EDTA, and 2 mM dithiothreitol and then concentrated to 15 mg/ml.
Crystallization was performed by the hanging-drop vapor diffusion
method at 22 °C. The reservoir solution for crystallization of the
H91A mutant (native and
Se-Met1 substituted)
consisted of 100 mM sodium cacodylate, pH 6.5, containing 18-19% (w/v) polyethylene glycol 8000 and 200 mM
calcium acetate. For cryo-cooling, a crystal was transferred to
reservoir solution containing 20% (v/v) glycerol before flash-freezing
in a nitrogen stream at 100 K. The H91A mutant crystallized in the
P21 space group with unit cell parameters of a = 43.88, b = 129.36, c = 56.79 Å, and Structure Determination and Refinement--
Fifteen of 16 possible selenium sites (including four N-terminal methionine) in the
H91A asymmetric unit were located with SOLVE (24). The phases were
improved and extended to 1.5 Å with DM (25). The initial model
was built using the warpNtrace option of the program ARP/warp (26) with
the DM phase set as input. The model was rebuilt with the program O
(27) using an electron density map based on the combination of the
multi-wavelength anomalous diffraction and model phases. The protein
model was refined with CNS (28), including the bulk solvent
correction. The 4-fold noncrystallographic symmetry was maintained with
tight restraint during the early stages of refinement but was relaxed
in the final rounds. The model of the H144*UreE (H91A) mutant (Se-Met
substituted) accounts for 138 residues in three molecules and 140 residues in one molecule. No electron density was observed for the
C-terminal segments (139). Solvent molecules were added using
model-phased difference Fourier maps by using CNS (28).
Statistics for the refined model are described in Table I.
Subsequently, the structure of H144*UreE (H91A) complexed with
Cu2+ ions was also refined (Table I). The positions of the
metals were clearly determined by using model-phased difference Fourier map at 8 Overall Structure of UreE--
The H144*UreE homodimer has an
elongated shape with approximate dimensions of 90 × 43 × 32 Å (Fig. 1a). Each monomer
folds into two discrete domains with approximate dimensions of 58 × 32 × 30 Å (Fig. 1b). The first domain (termed the
peptide-binding domain; residues 1-70) consists of two Peptide-binding Domain--
Comparison to proteins in the DALI
data base (33) indicated structural similarity (Z = 2.8) between
the first domain of H144*UreE (residues 1-70) and the peptide-binding
domain (domain I; residues 180-255) of yeast Hsp40 or Sis1 (34) (Fig.
2, c and d). A
superposition of structurally equivalent residues in several secondary
structural elements of UreE and the corresponding residues in Sis1
(PDB ID 1C3G) yields an r.m.s. deviation of 2.7 Å for 51 matching C Metal-binding Domain--
When the complete three-dimensional
structure of H144*UreE was compared with proteins in the DALI data base
(33), a notable structural similarity (Z score > 2.0) was found
in 89 proteins. Representatives showing the highest structural
similarity are the pro-(activation) domain of procarboxypeptidase A2
(Z = 5.5), copper metallochaperone Atx1 (Z = 5.4), elongation
factor G (Z = 5.2), the fourth metal-binding domain of Menkes
copper-transporting ATPase (Z = 5.1), and domain 1 of the copper
chaperone for superoxide dismutase (Z = 4.5). The Atx1-like
folding unit of these proteins shares an identical topology with the
metal-binding domain of UreE (Fig. 2, a and b).
The putative nickel metallochaperone metal-binding domain is very
similar in overall structure to Atx1 despite a lack of overall sequence
similarity (37). Superpositioning of structurally equivalent residues
in several secondary structural elements of UreE and Atx1 (PDB
ID 1CC8) yields an r.m.s. deviation of 1.9 Å for 50 matching C Metal-binding Sites--
Efforts to crystallize H144*UreE in the
presence of nickel ions were not successful and addition of nickel ions
to preformed crystals led to their dissolution. These results parallel
the reported inability to crystallize full-length wild-type UreE with nickel and the fracturing of wild-type apoprotein crystals upon nickel
addition (14). As an alternative to obtaining the nickel-bound structure, we solved the copper-bound form of H144*UreE for which the
metal binding properties are well characterized (17, 18). After soaking
50 mM CuSO4 solution into pre-grown UreE
crystals for 2 h, the copper-binding sites were readily located in
the (Fo
Spectroscopic studies had earlier revealed a
thiolate-to-Cu2+ charge-transfer transition in
Cu2+-bound H144*UreE that was absent in the C79A variant
(17). Based on these results, some of us had concluded that one
Cu2+ site must bind Cys-79. In contrast, we detect no
additional electron density near residue Cys-79 in the structure, and
this position is quite distant from the experimentally determined
Cu2+-sites (Fig. 3d). We suggest that the
apparent discrepancy arises from comparison of solution studies
versus investigation of Cu2+ addition to
crystals. Specifically, we propose that in solution Cys-79 of one dimer
interacts with a copper site in another dimer, whereas crystal packing
prevents this interaction in the solid state. Perhaps related to
such a proposed aggregation event, we observe transient turbidity
upon adding copper ions to H144*UreE solutions. Selective binding
of Hg2+ to Cys-79 (along with Met-84) supports the proposal
that this residue is accessible for metal binding (data not shown).
Intriguingly, Cys-79 of UreE is structurally equivalent to the
metal-binding Cys-15 of Atx1; thus, further highlighting the
relationship between these proteins (Fig. 2, a and
b). While the Atx1 thiol is one of two cysteines essential
to its copper metallochaperone role, Cys-79 is not important to
function of UreE (17, 18). Cys-89, located in helix H2, has no
counterpart in Atx1 and is not available to bind metals because it is
involved in subunit dimerization.
Proposed Mechanism--
While the structures of ureases from
different sources (3, 5, 6) have provided details of the nickel-binding
site and possible mechanisms of urea hydrolysis (1), our understanding of how nickel is incorporated into the enzyme is very limited. Assembly
of the dinuclear nickel center requires that the pre-organized apoprotein structure (38) be partially opened up to expose the deeply
buried metal-binding sites. This process, along with carbamylation of a
specific lysine residue, appears to be carried out by a
GTP-dependent molecular chaperone comprised of UreD, UreF,
and UreG that forms the UreDFG-apourease complex (7). The role of
nucleotide hydrolysis in urease activation remains unclear, but we
speculate that it provides energy for conformational transitions like
in the classical chaperone action (35, 36). The putative
metallochaperone UreE participates in urease activation by delivering
nickel ions but may also function in the molecular chaperone process.
In particular, the putative peptide-binding domain of UreE that shares
very similar architecture to Sis1 domain I may bind to urease
apoprotein or an accessory protein to control specific conformational
changes needed for activation. Conformational changes within UreE or
the UreDFG-apourease may be coupled to nickel transfer from the
proposed metallochaperone to the urease apoprotein, perhaps via His-96. We speculate that nickel ions are delivered one at a time to form the
dinuclear site in urease, perhaps with the His-110/His-112 sites acting
as a nickel reservoir to facilitate that process. Notably, this
mechanism is unrelated to the thiol ligand exchange reactions that
occur during copper delivery by copper metallochaperones (21, 22). It
is also unrelated to the mechanism of iron sulfur cluster assembly
mediated by NifS (39).
UreE has counterparts involved in the activation of two other
nickel-containing enzymes (40), carbon monoxide dehydrogenase (41) and
hydrogenase (42). CooJ of Rhodospirillum rubrum
contains a C-terminal His-rich region and binds ~4 Ni2+
per monomer for incorporation into CO dehydrogenase (43). HypB from
Bradyrhizobium japonicum possesses a His-rich sequence at the N terminus, binds 18 Ni2+ per dimer, and is proposed to
have a dual role of both storing and delivering the metal to
apohydrogenase (44). It is reasonable to suspect that CooJ and HypB
perform similar roles with their target enzymes as UreE does in urease
activation. Therefore, this structural study of UreE may provide more
general insight into mechanisms of nickel enzyme activation.
We thank G. Bourenkov and H. Bartunik for
help with data collection at BW6 beamline of Deutsches
Elektronen Synchrotron, Hamburg, Germany. In addition, we thank Stefano
Ciurli for sharing information on the crystal structure of B. pasteurii UreE prior to publication.
*
These studies were supported by the National Institutes of
Health Grant DK45686 (to R. P. H.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
The atomic coordinates and the structure factors (code 1gmu, 1gmw, and 1gmv) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).
§
Current address and to whom correspondence may be addressed: Dept.
of Cancer Biology, Dana-Farber Cancer Inst. and Dept. of Molecular
Pharmacology, Harvard Medical School, 44 Binney St., Boston, MA 02115;
E-mail: hksong@red.dfci.harvard.edu.
Published, JBC Papers in Press, October 8, 2001, DOI 10.1074/jbc.M108619200
The abbreviation used is:
Se-Met, selenomethionine.
Crystal Structure of Klebsiella aerogenes
UreE, a Nickel-binding Metallochaperone for Urease Activation*
§,
, and
Abteilung Strukturforschung,
Max-Planck-Institut für Biochemie, Am Klopferspitz 18a,
D-82152, Planegg-Martinsried, Germany and the ¶ Departments of
Microbiology & Molecular Genetics and Biochemistry & Molecular Biology,
Michigan State University, East Lansing, Michigan 48824
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ABSTRACT
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES
![]()
INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES
![]()
EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES
= 93.72°. The
asymmetric unit contains four molecules of the polypeptide. The H110A
mutant crystallized in a different form using slightly different
crystallization conditions (100 mM sodium cacodylate, pH
6.5, 19-20% (w/v) polyethylene glycol 8000 and 200 mM
magnesium acetate). The crystal belongs to the P212121 space group with unit cell
parameters of a = 40.11, b = 80.42, and c = 99.85 Å.
The asymmetric unit contains a dimer. Due to a lack of reproducibility
of the native crystals, the structure was determined by using
multi-wavelength anomalous diffraction data collected from a
crystal of the Se-Met-substituted H91A variant (Table
I). Data were collected on a
charge-coupled device detector at the BW6 beamline of the Deutsche
Elektronen Synchrotron Center, Hamburg, Germany. Diffraction data were
processed and scaled using the HKL software package (23).
Data collection and refinement statistics for H144*UreE variants
and confirmed by the anomalous difference Fourier map. The
initial phases of the H144*UreE (H110A) crystal were determined by the
molecular replacement method using AmoRe (29). Refinement of the model
was performed as above. The geometry of the models was assessed by the
program PROCHECK (30), and the secondary structure elements were
assigned by the program PROMOTIF (31). Coordinates of the
Se-Met-substituted H144*UreE (H91A), this protein complexed with
Cu2+, and H144*UreE (H110A) have been deposited in the
Protein Data Bank under ID codes 1gmu, 1gmw, and 1gmv, respectively.
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RESULTS AND DISCUSSION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES
-sheets (A1,
Leu-2-Leu-4; A2, Arg-29-Thr-33; A3, Asp-39-Leu-43; and B1,
Gln-6-Arg-7; B2, Ala-16-Leu-20; B3, Val-55-Ser-57; B4, Phe-64-Ala-69)
and a short
-helix (H1, Ile-22-Arg-25), while the second domain
(termed the metal-binding domain; residues 71-133) consists of an
anti-parallel
-sheet (C1, Asp-71-Arg-78; C2, Gln-100-Met-102; C3,
Glu-105-His-109; C4, Val-125-Pro-131) and two
-helices (H2,
Pro-82-Asn-94; and H3, His-112-Arg-119). The C-terminal tail is
flexible and would be followed by a characteristic histidine-rich
segment (10 of the last 15 residues) in the wild-type UreE protein
(15). A superposition of the four refined models (two crystal forms
with dimers in the asymmetric unit) shows that the peptide-binding domain and the C terminus are flexible (Fig. 1c), consistent
with the dramatic B-factor distribution of a monomer in the H110A
structure (Fig. 1d). The average B-factors of the N- and
C-domains in a monomer of this protein are 91.5 and 37.9 Å2. A long
-helix (H2), a short
-strand (C2), their
connecting loop, and a portion of C-terminal tail are involved in
dimerization (Fig. 1a). For both crystal forms the dimer
interface is composed of the following residues: Pro-82, Phe-83,
Leu-85, Ala-86, Lys-87, Cys-89, Tyr-90, His-91, Gly-93, Asn-94, His-96,
Val-97, Pro-98, Leu-99, Ile-101, Met-102, Pro-103, Glu-135, and
Gly-137. The interface accessible surface area is ~810
Å2 per monomer (biochem.ucl.ac.uk/bsm/PP/server).
This value is within the frequently observed range of the minimal
buried surface area required for stable dimer association (32). This
dimer interface is the most rigid part in the structure as shown in Fig. 1, c and d.

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Fig. 1.
Structure of the K. aerogenes H144*UreE nickel metallochaperone.
a, ribbon diagram indicating the two-domain dimeric
structure (the putative peptide-binding domain and the metal-binding
domain are shown in purple and green,
respectively) and Cu2+-binding sites. b, stereo
ribbon diagram showing the secondary structure elements of the
metal-free monomer. Domains are colored as in a. Essential
histidine residues (His-96, His-110, and His-112) for metal binding are
shown and labeled. Approximately every tenth residue is also labeled
and marked by a black dot. c, domain movement of
the UreE monomer. C
traces of UreE structures are drawn by
overlapping their metal-binding domains (residues 71-132).
d, temperature factor distribution of the UreE monomer. High
temperature factors (flexible region) are red and low
temperature factors (rigid region) are blue, ranging from
105.0 to 18.6 Å2. Panels a and b
were drawn with MOLSCRIPT (45) and rendered with RASTER 3D (46). Panels
c and d were prepared with GRASP (47).
atoms (UreE residues 15-32, 39-43, and 48-74). Many
molecular chaperone/unfoldase proteins, including Hsp40, are known to
utilize hydrophobic patches to form transient complexes with
hydrophobic residues exposed in non-native peptides (35, 36). For
example, domain I of Sis1 has a hydrophobic depression formed by
residues Val-184, Leu-186, Ile-203, and Phe-251, and this was proposed
as a binding site for interaction with non-native peptides (34).
Intriguingly, UreE possesses a long hydrophobic canyon beginning in the
putative peptide-binding domain (albeit at a different location that
the hydrophobic region of Sis1) and extending into the metal-binding
domain and C-terminal tail (Fig. 3a). In addition, many
hydrophobic residues are located on the opposite surface of the
suggested UreE peptide-binding domain (Fig. 3c). We presume
that several of these residues are crucial for transient interaction of
UreE with urease and/or the other accessory proteins, UreD, UreF, and
UreG. The UreE variants examined thus far (Fig. 3, b and
d) have focused on potential metal ligands (16, 17) and
provide no insight into possible functions associated with these
hydrophobic regions. As described above, the peptide-binding domain is
not well ordered possibly as a consequence of lack of crystal packing.
It may also be an intrinsic structural property (Fig. 1d) as
expected for a module involved in transient protein-protein interactions. The illustrated conformation of UreE may differ from that
when UreE interacts with its partners. Further biochemical and
mutagenesis studies on this domain are needed to see whether this
module has a peptide-binding role during urease activation.

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Fig. 2.
Structural homology of UreE domains to
Atx1 and Sis1. Ribbon diagrams are shown comparing the overall
structures of the metal-binding domain of UreE (a), Atx1
copper chaperone (b), putative peptide-binding domain of
UreE (c), and domain I of Sis1 (d). Metal-binding
residues and bound metal ions are indicated (His-96, His-110, His-112,
and Cu2+ in UreE; Cys-15, Cys-18, and Hg2+ in
Atx1). Residues 1-13 and 130-138 in the UreE structure are not
included for clarity.

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Fig. 3.
Surface representations of
H144*UreE. a and c, residues forming the
hydrophobic surfaces of UreE are colored green and labeled.
Bound-copper ions are shown as red balls. b and
d, residues that have previously been subjected to
mutagenesis are colored magenta and labeled in one subunit,
and those in the other are colored blue and labeled with a
prime ('). Bound-copper ions are shown as green balls. The
view in a and b is the same as that in Fig.
1a, and the view in c and d is
obtained by a 180° rotation around a vertical axis. Figs. were drawn
with GRASP (47).
atoms (UreE residues 75-96, 98-109, 111-122, and 126-129, excluding
parts that show large deviations). Despite sharing a common folding
pattern, a significant structural difference exists between the
metal-binding domain of UreE and Atx1. Specifically, Atx1 is known to
be a monomer in solution (21), whereas UreE is a dimer in the presence
or absence of nickel ions (14). The human homologue of Atx1 is a
homodimer, but the intersubunit contacts for Hah1 (22) differ from that observed in UreE. Further studies involving mutagenesis and biophysical analysis are necessary to better understand the possible role of
subunit interactions in the catalytic function of the UreE urease
accessory protein.
Fc) difference Fourier and
anomalous difference maps (Fig. 4). The
UreE dimer binds three copper ions (Fig. 1a), consistent with the reported three sequential Cu2+ binding steps
observed by kinetics (18). The pair of His-96 residues binds one copper
atom between the subunits, whereas the other two copper sites involve
His-110 and His-112 from within each subunit (Fig. 4). These are the
same three pairs of residues implicated by mutagenesis studies in
nickel ion binding (17); however, equilibrium dialysis measurements
have consistently shown only two nickel ions bound per H144*UreE (15,
17). We suggest that aberrant reactivity of UreE with protein assay
reagents may have resulted in an underestimation of nickel binding by
this protein. Significantly, only His-96 is conserved in all reported UreE sequences (17). As shown in Fig. 4, there is little conformational change in the main-chain between free and copper-complexed states (an
r.m.s. deviation of less than 1.0 Å including the C-terminal tail)
except for a dramatic side chain movement of His-112. Several water
molecules (one or two for each binding site) also coordinate Cu2+, but their relative positions differ as shown in Fig.
4.

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Fig. 4.
Fo
Fc
electron density map of the metal-binding sites in His144*UreE.
a, the copper-binding site involving the pair of His-96
residues. b, the copper-binding sites involving His-110 and
His-112. The maps were calculated using 17-2.5 Å data and contoured
at 6
. The blue and green copper atoms and the
different colored ribbons represent the superimposed molecules in the
asymmetric unit. The distances indicated are an average value for the
superimposed molecules in the crystallographic asymmetric unit.
Green and white side-chains represent
Cu2+-complexed and free UreE, respectively. The positions
of water molecules (red balls) differ in the four molecules.
The figure was drawn with BOBSCRIPT (48) and rendered with RASTER 3D
(46).
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ACKNOWLEDGEMENTS
![]()
FOOTNOTES
To whom correspondence may be addressed: Tel.: 517-353-9675;
Fax: 517-353-8957; E-mail: hausinge@msu.edu.
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ABBREVIATIONS
![]()
REFERENCES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
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