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J Biol Chem, Vol. 275, Issue 6, 4066-4071, February 11, 2000
From the The substrate specificity of the catalytic domain
of SHP-1, an important regulator in the proliferation and development
of hematopoietic cells, is critical for understanding the physiological functions of SHP-1. Here we report the crystal structures of the catalytic domain of SHP-1 complexed with two peptide substrates derived
from SIRP Protein-tyrosine phosphatases
(PTPs)1 consist of a diverse
family of enzymes that play crucial roles in cell growth,
differentiation, and transformation (1-3). They can be broadly divided
into membrane-bound, receptor-like PTPs, and cytosolic PTPs. The
cytosolic PTPs contain only one catalytic domain, whereas the
membrane-bound receptor-like PTPs usually contain two tandem catalytic
domains. The catalytic domains of PTPs are highly conserved in their
three-dimensional structures (4-7). However, they have remarkably
different substrate specificity (3, 8-10), which is still not well
understood. Previous studies using various synthetic phosphotyrosyl
peptides failed to identify a shared by PTP substrate because the
peptides studied were not derived from physiological substrates of
PTPs. In the present study, we have addressed the structural basis for the substrate specificity of PTPs using SHP-1 and its physiological substrate SIRP SHP-1 is expressed primarily in hematopoietic cells, and contains two
Src homology 2 (SH2) domains, a neighboring catalytic domain, and a
C-terminal tail. Its phosphatase activity is inhibited by both the SH2
domains and the C-terminal tail (11, 12). SHP-1 is activated upon the
binding of its tandem SH2 domains to immunoreceptor tyrosine-based
inhibitory motifs. Domain-swapping studies on SHP-1 and its analogue,
SHP-2, have shown that the catalytic domains of SHP-1 and SHP-2 have
distinct substrate specificity (9, 10), and therefore illustrate that
the dissection of the structural basis for the substrate specificity of
SHP-1 is fundamental to the understanding of its physiological
functions. The identification of the substrates of SHP-1
(i.e. SIRP Crystallization and Data Collection--
The C455S mutant of the
SHP-1 catalytic domain (245-532) was cloned, expressed, and purified
as described elsewhere (16). The phosphotyrosyl decapeptides were
synthesized and purified to 90% purity by SynPep Inc. (Dublin, CA).
Crystals of the native enzyme were obtained by vapor diffusion method
with 5 mg/ml protein drops equilibrating over reservoir solution
containing 1.9 M
(NH4)2SO4, 0.1 M
Tris-HCl, pH 8.5. The Tyr(P)469 complex crystals were
obtained by co-crystallization method with the protein and the peptide
at a 1:1 molar ratio. The Tyr(P)495 complex crystals were
grown by soaking native crystals in cryosolvent (30% sucrose, 1.9 M (NH4)2SO4, 0.1 M Tris-HCl, pH 8.5) containing 0.5 mM peptide
Tyr(P)495 for 2-3 days. A data set of the
Tyr(P)469 complex diffracted up to 2.5 Å was collected at
Structure Determination--
Crystal structures of both
complexes were solved by molecular replacement method with program
AMoRe (18), using coordinates of the native enzyme (Protein Data Bank
code 1GWZ) as the search model. The molecular replacement solution for
each complex structure was refined by rigid body and positional
protocols in X-PLOR (19). The peptide positions were identified from
the initial electron density difference map (Fo Identification of in Vitro Substrates for SHP-1--
SIRP Structures of the Two Complexes--
Crystal structures of the
catalytic domain of SHP-1 (with C455S mutation) complexed with peptides
Tyr(P)469 and Tyr(P)495 were determined at 2.5 and 2.3 Å resolution, respectively (Table I). The final electron
density maps around the Tyr(P) peptides in both complex structures are
shown in Fig. 1 (A and
B). The average B factor for peptide Tyr(P)495
was higher than the average B factors for peptide Tyr(P)469
and the SHP-1 catalytic domain, indicating that peptide
Tyr(P)495 was very flexible.
Both peptides bound to the catalytic domain of SHP-1 in extended
conformations (Fig. 1, C and D). Backbones of the
peptides were approximately 45 degrees to the central twist The P-2 Subpocket--
P-2 was the most distinct subpocket at the
N-terminal side of the Tyr(P) subpocket. It was formed by hydrocarbons
from the side chains of Lys362 and Arg277 and
by side chain of Tyr278. In the Tyr(P)469
complex, the P-2 subpocket was occupied by LeuP-2 (Fig. 1,
C and E). Surprisingly, it was occupied by
PheP-3 in the Tyr(P)495 complex structure,
indicating a likely residue shift at the N-terminal side of residue
Tyr(P) in the Tyr(P)495 complex relative to the
Tyr(P)469 complex. Because of this novel residue shift, the
conformations of residue Tyr(P) were also different between the two
complex structures. By shifting into the P-2 subpocket,
PheP-3 pushed SerP-2 of peptide
Tyr(P)495 into the P-1 subpocket, which was occupied by
ThrP-1 in the Tyr(P)469 complex structure. At
the same time, it pushed GlnP-1 of peptide
Tyr(P)495 toward the solvent (Fig. 1D).
The Subpockets N-terminal to the P-2 Subpocket--
The kinetic
studies showed that the substrate specificity of SHP-1 catalytic domain
was determined mainly by residues N-terminal to residue Tyr(P) in the
peptides. Between the Tyr(P)469 and Tyr(P)495
complexes, significant conformational differences were observed for
peptide residues N-terminal to the P-2 subpocket (Fig. 1E). These N-terminal residues interacted mainly with the The Tyr(P)-binding Subpocket--
Like other PTPs, the signature
motif of SHP-1, i.e. HCXAGXGR(S/T), formed the
base for the Tyr(P) subpocket and interacted with the phosphate group
of residue Tyr(P) by extensive hydrogen bonds in both complex
structures (Fig. 2). Because of different binding at the P-2 subpocket,
the Tyr(P)469 and Tyr(P)495 complexes had
different conformations for residue Tyr(P) at the active site and
therefore had different hydrogen bond networks. The O Substrate Specificity of SHP-1--
We have determined that the
The catalytic domain swapping studies on SHP-1 and SHP-2 have
demonstrated the different substrate specificity of the catalytic domains of SHP-1 and SHP-2 (9, 10). Among the six identified substrate-binding subpockets other than the Tyr(P) subpocket, only the
P-4 subpocket differs between SHP-1 and SHP-2 (see Fig. 4). Residue
360, which is located at the Comparison with PTP1B-Hexapeptide Complex--
Comparison of the
Tyr(P)469 and Tyr(P)495 complex structures with
the PTP1B-hexapeptide structure (21) (Fig.
3) indicates significant conformational
differences for residues on the N-terminal side of residue Tyr(P)
between the Tyr(P)469 and Tyr(P)495 complex
structures and the PTP1B-hexapeptide structure. The N terminus of the
hexapeptide was positioned away from the PTP1B enzyme molecule and
extended into the solvent, whereas the N termini of peptides
Tyr(P)469 and Tyr(P)495 bound much closer to
the catalytic domain of SHP-1. Based on the PTP1B-hexapeptide
structure, Arg47 of PTP1B (equivalent to Arg279
of SHP-1) was proposed to recognize and stabilize the hexapeptide through two hydrogen bonds (34). However, we propose that the different
substrate specificity of PTPs is not determined by Arg47,
because it is highly conserved among PTPs (Fig.
4). In contrast to PTP1B, which shows
indiscriminate low Km and high kcat/Km toward phosphotysosyl
peptides (22, 23), SHP-1 exhibits much higher
kcat/Km toward peptides
Tyr(P)469 and Tyr(P)495 than other
phosphotyrosyl peptides (24). The high Km values of SHP-1 toward peptide Tyr(P)469 and
Tyr(P)495 are due to the fact that the substrate
specificity of SHP-1 is conferred by both the catalytic domain and the
two tandem SH2 domains. Subcellular relocation of SHP-1 by its SH2
domains would significantly increase the local substrate
concentrations. Therefore, the SHP-1-peptide complex structures are
better representations of the in vivo PTP-substrate
interactions than the PTP1B-hexapeptide structure.
Comparison with Other PTPs--
Residues forming the six
substrate-binding subpockets other than the Tyr(P) subpocket were
distributed around loop
Residues forming the P-2 subpocket are highly conserved among PTPs,
except for Yersinia PTP, suggesting that the observed residue shift at the P-2 subpocket is also present in other PTPs. Therefore, the P-2 subpocket contributes to the binding affinity of
PTPs toward their substrates, without necessarily determining their
substrate specificity. Residue 360, the P-4 subpocket-forming residue
located in the hyper-variable We thank Drs. Neal Brown, Michael Czech,
Roger Davis, and Michael Green for critical reading of the manuscript.
*
This work was supported by a Career Development Award from
the American Diabetes Association (to G. W. Z.), the Pilot
project from the DERC Program of the University of Massachusetts
Medical School (to G. W. Z.), and National Institutes of
Health Grants AL45858 (to G. W. Z.) and HL57393 (to Z. J. Z.).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.
§
Fellow of the H. Arthur Smith Foundation.
The abbreviations used are:
PTP, protein-tyrosine phosphatase;
SH2, Src homology 2;
r.m.s., root mean
square.
Structural Basis for Substrate Specificity of Protein-tyrosine
Phosphatase SHP-1*
§,
,
,
,
Program in Molecular Medicine, University of
Massachusetts Medical School, Worcester, Massachusetts 01605 and the
¶ Department of Medicine, Vanderbilt University,
Nashville, Tennessee 37232
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ABSTRACT
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
, a member of the signal-regulatory proteins. We show that
the variable
5-loop-
6 motif confers SHP-1 substrate specificity
at the P-4 and further N-terminal subpockets. We also observe a novel
residue shift at P-2, the highly conserved subpocket in protein-
tyrosine phosphatases. Our observations provide new insight into the
substrate specificity of SHP-1.
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REFERENCES
/SHPS-1 as a model. SIRP
is a transmembrane protein of the signal-regulatory protein
family. Its extracellular domain contains three immunoglobulin domains,
and its cytoplasmic domain contains four phosphotyrosine sites
(Tyr(P)427, Tyr(P)452, Tyr(P)469,
and Tyr(P)495).
, CD22, and CD72; Refs. 13-15) has made it
possible for us to probe this structural basis. The results of this
probe are presented below.
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188 °C using an ADSC cryosystem and MAR imaging plate (Area
Detector System Corp., Poway, CA); the x-ray source was generated from
a Rigaku (Japan) RU-300 operating at 50 kV and 100 mA. A data set
diffracted to 2.3 Å resolution for Tyr(P)495 complex was
collected at
180 °C on F1 beamline at CHESS (Cornell University).
Both data sets were processed with DENZO and SCALEPACK (17). The
crystal statistics are summarized in Table
I.
Crystal data and refinement results
Fc). However, the electron densities for the
peptides were not quite continuous. After several cycles of model
rebuilding and refinements, the electron densities for the peptides
became clearer, and the peptides were added to the models. The complex
models were then subjected to X-PLOR refinement, using the slow cool
and positional refinement protocols with the 2
cutoff data between
6 Å and the highest resolution. The R-free value was also
calculated from the beginning to the penultimate cycle by randomly
selecting 10% data as the test set. The model building interspersed
with X-PLOR refinement was done by the program TURBO-FRODO (20). In the
penultimate cycle, the R-free values were 30.3% and 27.2%
for the Tyr(P)469 and Tyr(P)495 complexes,
respectively. The final crystallographic R-values for the
Tyr(P)469 and Tyr(P)495 complexes were 19.9 and
20.5%, respectively, with all reflections used in the refinement.
Fifty-three water molecules were added in the final
Tyr(P)495 complex model; however, no water molecules were
added in the final Tyr(P)469 complex model. The final
refinement results and geometry analyses for each complex are also
summarized in Table I.
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has
been identified as a potential physiological substrate of SHP-1 in
macrophages (13). However, the dephosphorylation sites of SHP-1 on
SIRP
are still unknown. To identify these sites, we synthesized four
phosphotyrosyl decapeptides corresponding to the four phosphotyrosine
sites in the cytoplasmic domain of SIRP
and measured the kinetic
parameters of the catalytic domain of SHP-1 toward each of them (Table
II). The results demonstrated that
peptides Tyr(P)469 and Tyr(P)495 were effective
in vitro substrates for SHP-1. With respect to amino acid
sequence, the four synthetic peptides fall into two groups:
Tyr(P)427 and Tyr(P)469, and
Tyr(P)452 and Tyr(P)495. The two peptides in
each group have very similar sequences for the residues on the
C-terminal side of residue Tyr(P). However, only one peptide in each
group (Tyr(P)469 and Tyr(P)495, respectively)
is the in vitro substrate of SHP-1. Therefore, substrate
specificity of the catalytic domain of SHP-1 is determined primarily by
residues N-terminal to residue Tyr(P) in the peptide substrates.
Kinetic parameters for the catalytic domains of SHP-1 against the four
synthetic phosphotyrosyl peptides

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Fig. 1.
A and B, the electron density
maps (2Fo
Fc) for the
phosphotyrosyl peptide sites in both Tyr(P)469
(A) and Tyr(P)495 (B) complexes. The
maps are contoured at 1.0
to 2.5 (A) and 2.3 Å (B), respectively, with the refined models of the
decapeptides in yellow. The amino acids are labeled.
C and D, ribbon representations of the
Tyr(P)469 (C) and the Tyr(P)495
(D) complex structures. The peptides are shown in the
stick model. The catalytic domain of SHP-1 is shown in
green. Structures of the catalytic domain in the two
complexes were almost identical, with an r.m.s deviation of 0.5 Å.
They were also similar to the native catalytic domain structure (7),
with an r.m.s deviation of 0.8 Å. This Fig. was prepared by SETOR
(25). E, comparison of peptides Tyr(P)469 and
Tyr(P)495 after superimposing two complexes on their
catalytic domains. Peptides Tyr(P)469 and
Tyr(P)495 are shown in yellow and
blue, respectively.
-sheet
that formed the core of the catalytic domain of SHP-1. Binding peptides Tyr(P)469 and Tyr(P)495 to the catalytic domain
of SHP-1 buried 800 and 660 Å2 solvent-accessible surface,
respectively. The binding of peptides Tyr(P)469 and
Tyr(P)495 to the catalytic domain of SHP-1 did not bring
the WPD loop (Trp419-Pro428) into the closed
conformation. In contrast, the WPD loop moved from the
half-open/half-closed conformation observed in the native enzyme
structure (7) to the open conformation in the complex structures. In
addition to the Tyr(P) subpocket, six substrate-binding subpockets were
well defined (Fig. 2). Unlike the Tyr(P)
subpocket that protruded into the center of the catalytic domain, these subpockets were relatively shallow and open to the solvent. For the
convenience of discussion, we name each subpocket according to the
residue numbers within the structure of the Tyr(P)469
complex. In both peptides, residues at the C-terminal side of residue
Tyr(P) bound to the same binding subpockets of SHP-1 with similar
orientations and conformations, except for a slight difference at the
P+4 subpocket. The C-terminal residues of the peptides interacted
mainly with loop
1/
1 and the
5-loop-
6 motif of SHP-1
(defined in Fig. 2).

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Fig. 2.
Schematic representation of the hydrogen
bonds formed between the catalytic domain of SHP-1 and peptides
Tyr(P)469 (A) and Tyr(P)495
(B) in the Tyr(P)469 and
Tyr(P)495 complex structures, respectively. Residues
labeled with asterisks are from symmetry-related molecules.
In addition to the hydrogen bonds, peptides Tyr(P)469 and
Tyr(P)495 also interacted with the catalytic domain of
SHP-1 by van der Waals' interactions. Besides the Tyr(P) subpocket, we
also identified six well defined substrate-binding subpockets (P-4,
P-2, P+1, P+2, P+3, and P+4). The P-4 subpocket was formed mainly by
residue Arg360 from the
5-loop-
6 motif. The P-2
subpocket was formed by residue Lys362 from the
5-loop-
6 motif and residues Arg277 and
Tyr278 from loop
1/
1. The Tyr(P) subpocket was formed mainly by the PTP signature motif
(HCXAGXGR(S/T)) and residue Tyr278
from loop
1/
1. The P+1 subpocket was formed by residues
Tyr278, Asn280, and Ile281 from
loop
1/
1. The P+2 subpocket was formed by residue
Gln502 from the
5-loop-
6 motif. The P+3 subpocket was
formed by residue Ser498 from the
5-loop-
6 motif,
residue Ile281 from loop
1/
1, and residue
Lys259. The P+4 subpocket was formed mainly by residues
Gln491 and Arg494 from the
5-loop-
6
motif.
5-loop-
6 motif of SHP-1. Therefore, the
5-loop-
6 motif determines, at least in part, the substrate specificity of SHP-1. In both complex structures, the
5-loop-
6 motif moved approximately 6.5 Å toward the N termini of the peptides and formed different interactions with
the substrates. In the Tyr(P)469 complex,
AspP-4 formed a salt bridge with residue Arg360
of the
5-loop-
6 motif. This salt bridge was further stabilized by
two hydrogen bonds between Arg360 and Asn361
(Fig. 2A). These suggest that either an aspartate or a
glutamate will be preferred for the P-4 position of the peptide
substrates of SHP-1. In the Tyr(P)495 complex structure,
ProP-5 was the corresponding residue to AspP-4.
Because of the repulsion between the guanidine group of residue Arg360 and the hydrocarbons of residue ProP-5,
ProP-5 swept away from the SHP-1 molecule into the solvent.
Residue Arg360 also underwent a conformational change and
formed weak van der Waals' interactions with residue
ProP-5. Other N-terminal residues, such as
ThrP-3 and GluP-5 of peptide
Tyr(P)469 and SerP-4 in peptide
Tyr(P)495, were exposed to the solvent.
atom of Ser455 was 2.6 Å from the phosphorus atom of
residue Tyr(P) in the Tyr(P)469 complex structure and 2.3 Å from the phosphorus atom of residue Tyr(P) in the
Tyr(P)495 complex structure. The walls of the Tyr(P)
subpocket were formed by residues Tyr278,
Ser456, Ile459, Lys362,
Gln502, and Gln506. The most prominent residue
was Tyr278 in loop
1/
1, which formed a stable


interaction between its phenyl ring and the side chain of
residue Tyr(P) in the Tyr(P)469 complex structure. However,
this 

interaction was much weaker in the Tyr(P)495
complex structure because of the different conformations of
Tyr278 and Tyr(P). The results indicated that peptide
Tyr(P)469 had stronger binding affinity and was a more
favorable in vitro substrate for SHP-1, which is consistent
with the kinetic study results (Table II). In addition,
Tyr278 of the enzyme was involved in defining the depth of
the Tyr(P) subpocket, making the subpocket too deep to bind either
phosphoserine or phosphothreonine residue.
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5-loop-
6 motif and loop
1/
1 determined the substrate
specificity of SHP-1. We also observed the novel residue shift at the
P-2 subpocket. The P-2 subpocket can bind either the P-2 or the P-3
residue of phosphotyrosyl substrates, provided that they are
hydrophobic residues. To our knowledge, this is the first time that a
residue shift has been observed in protein-protein recognition. This
novel residue shift suggests peptides containing the sequence
(L/I/V)XnpYXX(L/I/V) (n = 1 or 2) be potential substrates for SHP-1. The formation of the salt
bridge between residue Arg360 of SHP-1 and residue
AspP-4 of peptide Tyr(P)469 in the
Tyr(P)469 complex structure suggests that peptides having
the consensus sequence
(D/E)X(L/I/V)XnpYXX(L/I/V)
(n = 1 or 2) are favored as substrates of SHP-1. This
consensus sequence explains why peptides Tyr(P)427 and
Tyr(P)452 are not in vitro substrates for SHP-1.
Recently, signal transduction co-receptors CD22 and CD72 were
identified as both the activators and substrates of SHP-1 (14, 15).
Using the consensus sequence, we predict that sites Tyr777,
Tyr837, and Tyr857 of CD22 and sites
Tyr7 and Tyr39 of CD72 are the
dephosphorylation sites of SHP-1.
5-loop-
6 motif, is an arginine in
SHP-1 and a lysine in SHP-2. This residue difference is one of the main
reasons for the different substrate specificity of SHP-1 and SHP-2. In
addition to residue 360, several other residues in the
5-loop-
6
motif also differ between SHP-1 and SHP-2. These residues confer
specific recognition for P-4 and further N-terminal residues of the substrates.

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Fig. 3.
Superimposition of the Tyr(P)469
and Tyr(P)495 complex structures with the PTP1B-hexapeptide
complex structure. The peptides are shown as stick
models, and the catalytic domains are shown as ribbons.
The Tyr(P)469, Tyr(P)495, and PTP1B complex
structures are shown in yellow, blue, and
gray, respectively. The only similarity between the
SHP-1-peptide complex structures and PTP1B-hexapeptide structure was
that residue Tyr(P) fit into the Tyr(P)-binding subpocket, and the
phosphate group of residue Tyr(P) made extensive hydrogen bonds with
the PTP signature motif. In the PTP1B-hexapeptide structure, the side
chain of residue LeuP+1 pointed in the direction of the
main chain of peptides Tyr(P)469 and Tyr(P)495
in the SHP-1 complex structures. This directional change may have been
caused by the end effects (i.e. LeuP+1 is the
C-terminal residue). However, at the N terminus the peptide was
positioned away from the PTP1B molecule and extended into the
solvent.

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Fig. 4.
Comparison of the sequences of 21 PTPs around
the
5-loop-
6 motif,
loop
1/
1, and
the
5-loop-
6
motif. The amino acid sequences of the PTPs were obtained from the
SWISS-PROT protein sequence data base and aligned by the program
CLUSTALW Version 1.5. Conserved residues are shown in red,
and the homologous residues are shown in green.
1/
1, the
5-loop-
6 motif, and the
5-loop-
6 motif. Because the catalytic domains of PTPs share a
highly conserved three-dimensional structure, we aligned the amino acid
sequences of 21 different PTPs around these three substrate-binding
regions (Fig. 4). In addition to the hyper-variable
5-loop-
6
motif, the P+3 and P+4 subpocket-forming residues in the
5-loop-
6
motif were also variable in PTPs. This finding strongly suggests that
P+3 and P+4 residues in the substrates also can be the specific
recognition sites for PTPs and that the recognition is conferred by the
5-loop-
6 motif of PTPs.
5-loop-
6 motif, is either an
arginine or a lysine in most PTPs. Therefore, those PTPs will prefer
either an aspartate or a glutamate residue at the P-4 position of the
peptide substrates. Other residues within the
5-loop-
6 motif are
highly variable among PTPs. These residues likely are involved in the
formation of the P-4 subpocket and its interaction with further
N-terminal residues of the peptide substrates. The above analyses
indicate that PTP substrate specificity comes from two regions: the P-4
and further N-terminal sites and the P+3 and P+4 sites of the
substrates. The recognition of these two regions was conferred by the
5-loop-
6 and
5-loop-
6 motifs, respectively.
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ACKNOWLEDGEMENTS
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FOOTNOTES
To whom correspondence should be addressed. Tel.:
508-856-6869; Fax: 508-856-4289; E-mail: G.Zhou@ummed.edu.
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ABBREVIATIONS
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REFERENCES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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