Structural Basis of Functional Mimicry between Carbohydrate and Peptide Ligands of Con A

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Biochemical and Biophysical Research Communications 272, 843–849 (2000)

doi:10.1006/bbrc.2000.2871, available online at http://www.idealibrary.com on

tructural Basis of Functional Mimicry betweenarbohydrate and Peptide Ligands of Con A

eepti Jain, Kanwal J. Kaur, Manisha Goel, and Dinakar M. Salunke1

tructural Biology Unit, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110 067, India

eceived May 8, 2000

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Crystallographic studies have shown independentinding sites for sugar and peptide ligands of con-anavalin A, although they were considered func-ional mimics based on biochemical experiments. Theopological correlation of 12-residue peptide with dif-erent carbohydrate ligands of concanavalin A showedimilarity between trimannose and the YPY region ofhe peptide establishing structural mimicry. Molecu-ar docking of trimannose and the YPY motif on theeciprocal binding sites revealed equivalent interac-ions and energetics implying that the peptide-inding sites may constitute additional sugar-bindingubsites of concanavalin A. The binding of a mannose-ich neoglycoprotein with significantly higher affinityompared with that of the methyl a-D-mannopyrano-ide is consistent with this interpretation. © 2000

cademic Press

Key Words: molecular docking; carbohydrate-imicking peptide; receptor-binding site; molecular

ecognition.

Concanavalin A (Con A), a lectin from Canavaliansiformis, has been exploited for addressing struc-ural basis of molecular mimicry (1, 2). Several smalleptides showing consensus sequence motif YPYave been identified to bind Con A, which is other-ise known to be a mannose-specific agglutinin (2–). It was shown earlier that binding of these pep-ides could be competitively inhibited by a-D-annopyranoside suggesting that the peptides and

ugars could share the binding site on Con A. Also,he polyclonal antibodies raised against a-D-annopyranoside showed cross-reactivity with the

eptides and the polyclonal antibodies raised against2mer peptide (DVWYPYPYASGS) showed cross-eactivity with a-D-mannopyranoside (2).We have recently determined the crystal structure ofon A-12mer complex (1). The peptide binds to Con A

1 To whom correspondence should be addressed. Fax: (91) 11 616125. E-mail: [email protected].

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ions resulting in a primary peptide-binding site (P1)nd a secondary peptide-binding site (P2) close to P1,enerated as a result of symmetry-related interactions.he P1 and P2 together form a continuous groove onon A. Three-dimensional structure of Con A has beeneported in complex with mannopyranoside (5), diman-ose (6), trimannose (7, 8), and a pentasaccharide (9).omparison of the binding sites of these sugars with

hose of the peptide, shows that although located verylose, neither P1 nor P2 overlap with either mono-, di-r trimannose. However, a terminal sugar of the pen-asaccharide extends slightly in to the P2 site.

Con A is shown to induce proliferation of T lym-hocytes (10). It induces mitogenicity by binding topecific receptors on T lymphocytes (11, 12). Theannose-rich complex carbohydrates constitute Con-specific receptors on lymphocytic surface. We havearlier shown that Con A-induced T cell proliferationan be inhibited by the 12mer implying that the P1nd P2 sites are indeed functionally relevant (1).hus, the cell surface carbohydrate-binding site ofon A could be much larger than that identifiedased on earlier crystallographic studies. Here, weave analyzed the structural relationship of the2mer peptide with the carbohydrate ligands inerms of surface topology of the ligands and theirnteractions with Con A. Based on this analysis, weypothesize that mannose-rich complex carbohy-rates on cell surface recognize an extended func-ional site on Con A. The binding experiments usingffinity sensor and involving a model receptor neo-lycoprotein corroborate this hypothesis.

ATERIALS AND METHODS

Molecular docking. Molecular docking was carried out using MSIoftware (Molecular Simulations Inc., USA) on Octane work stationSilicon Graphics, USA). All the residues of the protein were con-trained, except the contacting residues after docking. The ligandas left flexible in all the cases. The atomic coordinates of Con A in

omplex with peptide were available in this laboratory (1) and thoseith mannose (5cna), dimannose (1qdc) and trimannose (1cvn) werebtained from Protein Data Bank (13). The program CONTACT of

0006-291X/00 $35.00Copyright © 2000 by Academic PressAll rights of reproduction in any form reserved.

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Vol. 272, No. 3, 2000 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

CP4 suite (14) was used for identifying protein-ligand contacts. Theocked structures were energy minimized to convergence using theISCOVER module of MSI software. The crystal structures of Con Aound to sugar and peptide were also energy minimized beforeomparison.

Affinity measurements. Binding kinetics were determined bysing IAsys Auto1 (Affinity Sensor, England). The mannosylated-SA was prepared by conjugation of mannose with bovine serumlbumin (BSA) by a two step reaction as described earlier (2). Conwas covalently immobilized onto a carboxylate surface at con-

entration of 1 mg/ml in 10 mM Bis Tris containing 5 mM MnCl2

FIG. 1. Topological similarities of the peptide and the carbohrimannose by optimization of atomic overlap. (B) Comparison of tecorated with the hydropathy features.

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nd 50 mM CaCl2, 150 mM NaCl, pH 6.5, using amine-coupling kitAffinity Sensor, England). The unreacted activated carboxylroups were blocked with BSA. All measurements were carried in0 mM Bis Tris buffer containing 5 mM MnCl2 and 50 mM CaCl2,50 mM NaCl, pH 7.0. For the determination of association rateonstants, mannosylated-BSA (178 mM–11 mM) in the same bufferas used. Dissociation rate constants were measured by passing

he buffer only. Following analyte binding, surface was regener-ted with 20 mM HCl. Kinetics of the interaction of theannosylated-BSA was analyzed by non-linear regression using

he FASTfit software.

ate moiety. (A) Structural superimposition of 12mer peptide andvan der Waals surfaces of the peptide and the trimannose moiety

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ESULTS AND DISCUSSION

omparison of the van der Waals Surfaces of thePeptide and the Carbohydrate Ligands

The peptide and sugar ligands bind to Con A at twoifferent sites. However, an independent comparison of

FIG. 2. Comparison of molecular interactions of different ligands1 site, (C) YPY motif at P2 site, and (D) trimannose moiety at P2 sity thick sticks.

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heir structures was imperative since cross-reactivityf the polyclonal antibodies suggested topological mim-cry between them (2). Superimposition of differentugar ligands with various parts of the 12mer peptideas carried out. The results indicated that, trimannoseoiety (7) could be superimposed on the peptide resi-

P1 and P2 sites. (A) YPY motif at P1 site, (B) trimannose moiety athe Con A residues are shown by thin sticks and the ligand is shown

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ues 6 to 8 constituting the YPY motif (Fig. 1A). Theerminal sugar rings in trisaccharide overlap on theyrosines such that two of the hydroxyl groups of sugaroincide with those of the tyrosine residues. The cen-ral sugar moiety overlaps with the proline ring. Theuitable juxtaposition of the ring structures of the ar-matic residues and the proline through appropriateackbone conformation appears to be critical for mim-cry.

There is adequate evidence to suggest that the hy-rophobic interactions contribute to the specific recog-ition of carbohydrate moieties (15–17). But, only hy-rogen bonding has been extensively studied in thisontext. Even though carbohydrates are polar mole-ules, the steric disposition of hydroxyl groups is suchhat it creates hydrophobic patches on sugar surfaces,hich form contacts with the hydrophobic regionshile binding to proteins (17). The comparison of hy-ropathy features showed excellent correspondence ofPY region of 12mer with trimannose. Figure 1Bhows the van der Waals surfaces of 12mer and tri-annose where the molecules are coloured on the basis

f a hydropathy index. The hydropathy features ofrimannose are closest to those of the YPY motif asgainst any other part of the peptide.Thus, all the structural features of sugar as well as

eptide involved in Con A binding are similar. This isonsistent with experiments involving cross-reactivityf anti-sugar polyclonal antibodies with the designednalogs of the 12mer. Either of the tyrosines of thePY motif when replaced with another hydrophobicesidue, phenylalanine, shows similar cross-reactivityignal, but when replaced with serine, a hydrophilicesidue, the cross-reactivity signal was considerablyower (data not shown). Similar substitutions in0mer, another peptide which functionally mimicsugar, also showed identical results (1).

olecular Docking of Trimannose at Peptide BindingSites and Vice Versa

Molecular docking of the trimannose moiety at thewo peptide-binding sites reveals similarities ineptide-Con A and sugar-Con A interactions. Figure 2

Buried Surface Area and Intermolecular Eat Primary and Seconda

Ligand of Con ABuried surface area

of Con A (Å2)Buried s

of liga

PY motif at P1 site 282.2 45PY motif at P2 217.313 35rimannose docked at P1 site 273.82 40rimannose docked at P2 site 211.92 33

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hows the residues of Con A interacting with the YPYotif of P1 and P2 and the trimannose moiety docked

n both these peptide-binding sites, using above super-mposition. The results indicate that the shape of theeptide-binding crevice is complementary to triman-ose as much as it is to YPY at both these sites.omparison of the van der Waals contacts of theocked trisaccharide with those of the YPY motif in P1ite results in identical contact residues as those in-olved in the YPY-Con A interaction. The buried sur-ace area of trimannose is comparable to that of thePY motif corroborating the existence of structuralimicry. On the other hand, docking of trimannose at2 site shows difference of one residue with respect toPY-Con A interaction. The YPY motif has contactsith Thr15, but in case of trisaccharide the contactsre with Leu99. At P2 site also, the buried surfacereas of both the ligands is comparable. Since P2 isenerated by symmetry-related interactions, the bur-ed surface area of either of the ligands at this site isess than that at P1 (Table 1). However, comparison ofhe intermolecular interaction energies shows that theon A-trimannose interaction is equally favorable atoth P1 and P2 whereas Con A-YPY interaction isore favourable at P1 than at P2. This is primarily due

o the favourable electrostatic energy in case of dockedugar at P2 site. This may imply that P1 and P2 sitesre, in fact, designed for carbohydrate ligands.Analysis of the available crystal structures shows

hat the sugar binding sites of Con A are in the form ofshallow cavity with oligomers occupying a continuous

xtended cleft on the protein. The YPY motifs from P1nd P2 site were docked in the trimannose-binding siten Con A. Figure 3 shows the residues of Con A at therimannose-binding site interacting with trimannosetself, the YPY motif of P1 and that of P2 site. Theesults indicate that the same residues are involved inan der Waals contacts in all the three cases. Table 2hows the burried surface areas and the intermolecu-ar energies of various ligands at the sugar bindingite. The buried surface areas of the three ligands, therimannose, the docked YPY motif of P1 and of P2 areomparable. It may be noted that the buried surfacereas of Con A and of various carbohydrate ligands

rgy Calculations of Trisaccharide DockedPeptide Binding Sites

ce area(Å2)

vdW Energy(kcal/mol)

Electrostatic energy(kcal/mol)

Total energy(kcal/mol)

247.7299 241.922 289.65196 239.1893 25.4749 244.66420 238.9325 222.4003 261.3322 226.9173 225.4333 252.3505

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ncrease with increase in the number of sugar moietiesTable 2). The comparison of the intermolecular ener-ies shows that the Con A-trisaccharide binding isbout 30 kCal/mol. more favourable than either of thePY motifs at the sugar binding site. This difference isntirely due to contribution from the electrostatic in-eractions and not the van der Waals interactions.

A network of hydrogen bonding interactions facili-ates sugar-Con A binding. These interactions areormed involving the hydroxyl groups of the sugar andhe oxygen atoms of the protein. It was observed that

FIG. 3. Comparison of molecular interactions of different ligandsC) YPY from P2. The Con A residues are shown by thin sticks and

TAB

Buried Surface Area and Intermolecular Energy Calculatio

Ligand of Con ABuried surface area

of Con A (Å2)Buried su

of liga

annose 128.36 27imannose 179.94 34rimannose 259.66 42PY of P1 at trimannose site 256.79 38PY of P2 at trimannose site 245.05 38

847

he Con A-trisaccharide interactions are more favour-ble than Con A-YPY interactions at all the sites. Thiss expected because there are 8 hydroxyl groups inrisaccharide that are available for hydrogen bondingo Con A whereas there are only 2 in case of YPY motif.n spite of this difference in the number of hydroxylroups between the two, at least 6 electrostatic con-acts could be matched between trimannose and YPYotif of P1 and trimannose and YPY motif of P2 (Table

). However, similar correspondence was not forthcom-ng when trimannose was docked at P1 or P2.

the trimannose binding site. (A) trimannose, (B) YPY from P1, andligand is shown by thick sticks.

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of YPY of P1 and P2 Docked at Trisaccaride Binding Site

ce area(Å2)

vdW energy(kcal/mol)

Electrostatic energy(kcal/mol)

Total energy(kcal/mol)

7 224.6614 224.6103 249.27173 229.7924 238.4361 268.22845 234.3425 268.4887 2102.8312 240.2033 231.754 271.95734 239.9921 230.0167 270.0088

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inding of Mannose-Rich Neoglycoprotein to Con A

The similarity in the nature of interactions at theeptide and sugar-binding sites with either of the li-ands may lead to the inference that the peptide-inding sites mapped on the Con A surface are alsodditional sugar binding sub-sites. These sites are con-iguous to the crystallographically characterizedarbohydrate-binding sites and, topologically, give anppearance of a common extended receptor-bindingite. It has been suggested that the natural ligands ofon A are the mannose-rich complex carbohydrates on

he cell surface (18). A mannose-rich neoglycoproteinrepared by chemical conjugation of a-D-mannopyrano-ide to bovine serum albumin (mannosylated-BSA) haseen used as an excellent model for the mannose-richligosaccharides on cell surface, e.g. in the context ofperm-zona interaction (19). We have used this modeleoglycoprotein for investigating the extended carbo-ydrate binding site of Con A.The binding of varying concentrations of manno-

ylated-BSA to Con A was analyzed by using Affinityensor (Fig. 4). The analysis of the data gives associa-ion rate constant and dissociation rate constant forhe interaction of mannosylated-BSA with Con A as18 M21 s21 and 0.00173352 s21 respectively with a KD

f 14.69 3 1026 M, representing the affinity ofannose-rich neoglycoprotein towards Con A. The

inding affinities of the natural mannose-rich oligosac-harides to Con A would be significantly higher thanheir monomeric counterparts. Although Con A bindso monomers such as methyl a-D-mannopyranosideith high specificity, the binding affinity is weak withissociation constant in the millimolar range (KD 55.0 3 1025 M) (20). The artificially prepared mannose-ich neoglycoprotein shows significantly higher affinityhan that of monosaccharide corroborating the possi-

Complementarity of E

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on A-trimannose and Con A-YPY Tyr 12 OHof P1 docked at trimannose site Pro 13 O

Thr 15 NThr 15 OG1Arg 228 NArg 228 NE

on A-trimannose and Con A-YPY Tyr 12 OHof P2 docked at trimannose site Thr 15 N

Thr 15 OG1Asp 16 NAsp 208 OD1Arg 228 N

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ility of several different sub-sites for mannose onon A.

ONCLUSIONS

The YPY region of the 12mer peptide shows directtructural correspondence with trimannose. Although,he binding sites of the two ligands were found to beon-overlapping, the nature of interactions of Con Aith the YPY region of the peptide are similar to thosebserved for carbohydrate moieties. The correlation ofhe YPY-Con A and sugar-Con A interactions and theeptide-carbohydrate mimicry, described here, high-ights the role of hydrophobic interaction in the mim-

trostatic Interactions

sidue ofeptide

Distance(Å)

Residue ofsugar

Distance(Å)

r 1 O 2.76 Man 2 O4 2.55r 1 OH 2.50 Man 3 O3 3.01r 1 OH 2.85 Man 3 O3 2.95r 1 OH 2.70 Man 3 O3 2.95r 2 OH 3.02 Man 1 O3 2.82r 2 OH 2.75 Man 1 O3 2.77r 2 O 3.50 Man 2 O4 2.55r 2 OH 3.29 Man 3 O3 3.01r 2 OH 2.52 Man 3 O4 2.53r 1 OH 3.10 Man 3 O4 3.22r 1 OH 2.57 Man 1 O4 3.40r 1 OH 3.18 Man 1 O3 2.82r 2 OH 2.87 Man 3 O6 3.29

FIG. 4. The association phases of different concentrations ofannosylated-BSA with immobilized Con A. An enhancement in the

esponse (in arc seconds) on the association of sugar–BSA to the Conwith time reflects the accompanying changes in the mass during

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interactions. The structural comparison of the car-ohydrate mimicking 12mer peptide and trisaccharideas enabled mapping the additional functional sub-ites of Con A. Comparison of the binding affinities ofhe monomeric sugar with a mannosylated-BSA, cor-aborated possibility of such an extended carbohy-rate-binding site of Con A.

CKNOWLEDGMENTS

This work is supported by the DBT (Govt. of India) with fundsrovided to the National Institute of Immunology. D.J. is a recipientf the fellowship from the CSIR (India).

EFERENCES

1. Jain, D., Kaur, K. J., Sundaravadivel, B., and Salunke, D. M.(2000) Structural and functional consequences of peptide-carbohydrate mimicry. J. Biol. Chem. 275, 16098–16102.

2. Kaur, K. J., Khurana, S., and Salunke, D. M. (1997) Topologicalanalysis of the functional mimicry between a peptide and acarbohydrate moiety. J. Biol. Chem. 272, 5539–5543.

3. Oldenberg, K. R., Loganathan, D., Goldstein, I. J., Schultz, P. G.,and Gallop, M. A. (1992) Peptide ligands for a sugar-bindingprotein isolated from a random peptide library. Proc. Natl. Acad.Sci. USA 89, 5393–5397.

4. Scott, J. K., Loganathan, D., Easly, R. B., Gong, X., and Gold-stein, I. J. (1992) A family of concanavalin A-binding peptidesfrom a hexapeptide epitope library. Proc. Natl. Acad. Sci. USA89, 5398–5402.

5. Derewenda, Z., Yariv, J., Helliwell, J. R., Kalb (Gilboa), A. J.,Dodson, E. J., Papiz, M. Z., Wan, T., and Campbell, J. (1989) Thestructure of the saccharide-binding site of concanavalin A.EMBO J. 8, 2189–2193.

6. Bouckaert, J., Hamelryck, T. W., Wyns, L., and Loris, R. (1999)The crystal structures of Man(a1 3 3)Man(a1 3 O)Me andMan(a1 3 6)Man(a1 3 O)Me in complex with concanavalin A.J. Biol. Chem. 274, 29188–29195.

7. Naismith, J. H., and Field, R. A. (1996) Structural basis oftrimannoside recognition by concanavalin A. J. Biol. Chem. 271,972–976.

8. Loris, R., Maes, D., Poortmans, F., Wyns, L., and Bouckaert, J.

849

methyl-3,6-di-O-(a-D-mannopyranosyl)-a-D-mannopyranosidereveals two binding modes. J. Biol. Chem. 271, 30614–30618.

9. Moothoo, D. N., and Naismith, J. H. (1998) Concanavalin Adistorts the b-GlcNAc-(1 3 2)-Man linkage of b-GlcNAc-(1 32)-a-Man-(1 3 3)-[b-GlcNAc-(1 3 2)-a-Man-(1 3 6)]-Man uponbinding. Glycobiology 8, 173–181.

0. Yahora, I., and Edelman, G. M. (1972) Restriction of the mobilityof lymphocyte immunoglobulin receptors by concanavalin A.Proc. Natl. Acad. Sci. USA 69, 608–612.

1. Zanetta, J. P., Badache, A., Maschke, S., Marschal, P., andKuchler, S. (1994) Carbohydrates and soluble lectins in the reg-ulation of cell adhesion and proliferation. Histol. Histopathol. 9,385–412.

2. Ni, Y., and Tizard, I. (1996) Lectin-carbohydrate interaction inthe immune system. Vet. Immunol. Immunopathol. 55, 205–223.

3. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F.,Brice, M. D., Rogers, J. R., Kennard, O., Shimanouchi, T., andTasumi, M. (1977) The protein data bank: A computer basedarchival file for macromolecular structures. J. Mol. Biol. 112,535–542.

4. SERC Daresbury Laboratory (1979) CCP4. A Suite of Programsfor Protein Crystallography, SERC Daresbury Laboratory, War-rington WA4 4AD, England.

5. Elgavish, S., and Shaanan, B. (1997) Lectin-carbohydrate inter-actions: Different folds, common recognition principles. TrendsBiochem. Sci. 22, 462–467.

6. Lis, H., and Sharon, N. (1998) Lectins: Carbohydrate-specificproteins that mediate cellular recognition. Chem. Rev. 98, 637–674.

7. Sundari, C. S., and Balasubramanian, D. (1997) Hydrophobicsurfaces in saccharide chains. Prog. Biophys. Mol. Biol. 67, 183.

8. Gupta, D., Oscarson, S., Raju, T. S., Stanley, P., Toone, E. J., andBrewer, C. F. (1996) A comparison of the fine saccharide-bindingspecificity of Dioclea grandiflora lectin and concanavalin A. Eur.J. Biochem. 242, 320–326.

9. Youssef, H. M., Doncel, G. F., Bassiouni, B. A., and Acosta, A. A.(1996) Mannose-binding sites on human spermatozoa and spermmorphology. Fertility and Sterility 66, 640–645.

0. Van landschoot, A., Loontiens, F. G., and de Bruyne, C. K. (1980)Binding of mannooligosaccharides to concanavalin A, substitu-tion titration with a fluorescent-indicator ligand. Eur. J. Bio-chem. 103, 307–312.

Structural Basis of Functional Mimicry between Carbohydrate and Peptide Ligands of Con A

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