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J Biol Chem, Vol. 275, Issue 6, 4066-4071, February 11, 2000


Structural Basis for Substrate Specificity of Protein-tyrosine Phosphatase SHP-1*

Jian YangDagger §, Zhiliang ChengDagger , Tianqi NiuDagger , Xiaoshan LiangDagger , Zhizhuang Joe Zhao, and G. Wayne ZhouDagger ||

From the Dagger  Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and the  Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232

    ABSTRACT
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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 SIRPalpha , a member of the signal-regulatory proteins. We show that the variable beta 5-loop-beta 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.

    INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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 SIRPalpha /SHPS-1 as a model. SIRPalpha 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).

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. SIRPalpha , 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.

    EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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 -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.

                              
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Table I
Crystal data and refinement results

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 - 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 sigma  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.

    RESULTS
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

Identification of in Vitro Substrates for SHP-1-- SIRPalpha has been identified as a potential physiological substrate of SHP-1 in macrophages (13). However, the dephosphorylation sites of SHP-1 on SIRPalpha are still unknown. To identify these sites, we synthesized four phosphotyrosyl decapeptides corresponding to the four phosphotyrosine sites in the cytoplasmic domain of SIRPalpha 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.

                              
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Table II
Kinetic parameters for the catalytic domains of SHP-1 against the four synthetic phosphotyrosyl peptides

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.


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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 sigma  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.

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 beta -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 alpha 1/beta 1 and the alpha 5-loop-alpha 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 beta 5-loop-beta 6 motif. The P-2 subpocket was formed by residue Lys362 from the beta 5-loop-beta 6 motif and residues Arg277 and Tyr278 from loop alpha 1/beta 1. The Tyr(P) subpocket was formed mainly by the PTP signature motif (HCXAGXGR(S/T)) and residue Tyr278 from loop alpha 1/beta 1. The P+1 subpocket was formed by residues Tyr278, Asn280, and Ile281 from loop alpha 1/beta 1. The P+2 subpocket was formed by residue Gln502 from the alpha 5-loop-alpha 6 motif. The P+3 subpocket was formed by residue Ser498 from the alpha 5-loop-alpha 6 motif, residue Ile281 from loop alpha 1/beta 1, and residue Lys259. The P+4 subpocket was formed mainly by residues Gln491 and Arg494 from the alpha 5-loop-alpha 6 motif.

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 beta 5-loop-beta 6 motif of SHP-1. Therefore, the beta 5-loop-beta 6 motif determines, at least in part, the substrate specificity of SHP-1. In both complex structures, the beta 5-loop-beta 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 beta 5-loop-beta 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.

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 Ogamma 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 alpha 1/beta 1, which formed a stable pi -pi interaction between its phenyl ring and the side chain of residue Tyr(P) in the Tyr(P)469 complex structure. However, this pi -pi 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.

    DISCUSSION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

Substrate Specificity of SHP-1-- We have determined that the beta 5-loop-beta 6 motif and loop alpha 1/beta 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.

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 beta 5-loop-beta 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 beta 5-loop-beta 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.

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.


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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 beta 5-loop-beta 6 motif, loop alpha 1/beta 1, and the alpha 5-loop-alpha 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.

Comparison with Other PTPs-- Residues forming the six substrate-binding subpockets other than the Tyr(P) subpocket were distributed around loop alpha 1/beta 1, the beta 5-loop-beta 6 motif, and the alpha 5-loop-alpha 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 beta 5-loop-beta 6 motif, the P+3 and P+4 subpocket-forming residues in the alpha 5-loop-alpha 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 alpha 5-loop-alpha 6 motif of PTPs.

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 beta 5-loop-beta 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 beta 5-loop-beta 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 beta 5-loop-beta 6 and alpha 5-loop-alpha 6 motifs, respectively.

    ACKNOWLEDGEMENTS

We thank Drs. Neal Brown, Michael Czech, Roger Davis, and Michael Green for critical reading of the manuscript.

    FOOTNOTES

* 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.

|| To whom correspondence should be addressed. Tel.: 508-856-6869; Fax: 508-856-4289; E-mail: G.Zhou@ummed.edu.

    ABBREVIATIONS

The abbreviations used are: PTP, protein-tyrosine phosphatase; SH2, Src homology 2; r.m.s., root mean square.

    REFERENCES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
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