Mapping epitopes and antigenicityby site-directed maskingDidrik Paus* and Greg Winter†

Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom

Edited by Michael Sela, Weizmann Institute of Science, Rehovot, Israel, and approved May 8, 2006 (received for review February 1, 2006)

Here we describe a method for mapping the binding of antibodiesto the surface of a folded antigen. We first created a panel ofmutant antigens (�-lactamase) in which single surface-exposedresidues were mutated to cysteine. We then chemically tetheredthe cysteine residues to a solid phase, thereby masking a surfacepatch centered on each cysteine residue and blocking the bindingof antibodies to this region of the surface. By these means wemapped the epitopes of several mAbs directed to �-lactamase.Furthermore, by depleting samples of polyclonal antisera to themasked antigens and measuring the binding of each depletedsample of antisera to unmasked antigen, we mapped the antige-nicity of 23 different epitopes. After immunization of mice andrabbits with �-lactamase in Freund’s adjuvant, we found that theantisera reacted with both native and denatured antigen and thatthe antibody response was mainly directed to an exposed andflexible loop region of the native antigen. By contrast, afterimmunization in PBS, we found that the antisera reacted onlyweakly with denatured antigen and that the antibody responsewas more evenly distributed over the antigenic surface. We sug-gest that denatured antigen (created during emulsification inFreund’s adjuvant) elicits antibodies that bind mainly to the flex-ible regions of the native protein and that this explains thecorrelation between antigenicity and backbone flexibility. Dena-turation of antigen during vaccination or natural infections wouldtherefore be expected to focus the antibody response to theflexible loops.

backbone flexibility � Freund’s adjuvant � conformational epitope �antisera

The antigenic epitopes of a protein for antibodies are locatedon the surface of a protein (1, 2) and in early work were

generally located by use of soluble peptide fragments of theantigen. This approach led to the classification of epitopes as‘‘sequential’’ or as ‘‘conformational’’ (3), corresponding respec-tively to residues from the same section of the polypeptide chain(and capable of being mimicked by a peptide) or to those fromdifferent sections brought together in the folded protein. Later,the three-dimensional crystal structures of several antibodyantigen complexes revealed interactions of the antibody withmultiple polypeptide segments of the antigen (4–6), proving theexistence of both sequential and conformational elements in thesame antigen-binding site.

For the design of vaccines, adjuvants, and the clinical use oftherapeutic proteins, it is important to understand the determi-nants of protein antigenicity. Antisera has been analyzed bybinding to small synthetic peptides; in particular, the use of‘‘overlapping’’ peptides on arrays of pins has provided a system-atic means of mapping the antigenicity of sequential epitopesalong the entire span of a polypeptide chain (7–10). This andearlier work have indicated that the sequential epitopes correlatewith regions of major flexibility in the folded polypeptide chain(11, 12). However it proved more difficult to map conforma-tional epitopes in antisera, and it is not clear whether they alsocorrelate with regions of flexibility and�or other features of theprotein surface (13).

One promising approach for analysis of antisera for confor-mational epitopes has involved the use of mutants of the antigen(14, 15) or natural homologues (16). However, the binding ofantisera depended not only on the location of the mutation butalso on the exact sequence of the mutation(s) (15, 17). Here wehave used mutants of the antigen but in a different manner; wetethered the antigen at the site of mutation to solid phase andthereby blocked the corresponding surface patch to binding ofantisera. With a panel of mutants, we mapped the epitopes of apanel of monoclonal antibodies to a model antigen and alsoidentified those epitopes contributing to its antigenity in anti-sera. Many of the classic model antigens used in studies ofantigenicity, for example, cytochrome c (16), serum albumin(18), myoglobin (19), and lysozyme (20) have homologues in theimmunized species. Because their use may bias the antigenicitytoward regions of the antigen that most differ from the hosthomologue (16), we used the bacterial enzyme (�-lactamase) asour model antigen because it has no natural homologue inrabbits or mice.

ResultsMapping of mAbs. The solvent accessible surface of �-lactamaseis �11,200 Å2, which approximates to the binding sites of 13mutually exclusive antibodies, assuming an average bindinginterface of 850 Å2 (21). For our studies we distributed thetethering sites around the surface at a density greater than thetheoretical antibody footprint. Single cysteine mutants of �-lac-tamase were created at 23 sites scattered over the surface andmasked by biotinylation and capture on a streptavidin-coatedsurface (ELISA plates or polystyrene beads) (Fig. 1A). Thetethered mutants were similarly active in catalysis, as shown byhydrolysis of the chromogenic �-lactamase substrate nitrocefin.However, a few of the tethered mutants (C34, C55, C146, C175,and C215) bound to mAb P64.1 (specific to denatured protein;data not shown), consistent with the presence of some denaturedprotein in these mutants.

The panel of tethered mutants was mapped for binding of ninemonoclonal antibodies. The results for two representative anti-bodies, P50.2 and P51.1 (which bind to native but not denatured�-lactamase), are shown in Fig. 2. Binding of P50.2 (Fig. 2 A) tothree tethered mutants (C100, C114, and C140) was greatlydiminished as was binding to P51.1 (Fig. 2B) for four tetheredmutants (C227, C254, C281, and C288). These sites cluster on thethree-dimensional surface of �-lactamase (Fig. 2C). The methodalso distinguishes between sites such as C100, C110, and C114 (orC227, C240, and C254) that are sequential in the primarystructure but do not cluster together in the three-dimensionalstructure. This finding indicates that our method is able toidentify the surfaces comprising the conformational epitopes ofthese mAbs.

Conflict of interest statement: No conflicts declared.

This paper was submitted directly (Track II) to the PNAS office.

*Present address: Affitech AS, Gaustadalleen 21, N-0349 Oslo, Norway.

†To whom correspondence should be addressed. E-mail: winter@mrc-lmb.cam.ac.uk.

© 2006 by The National Academy of Sciences of the USA

9172–9177 � PNAS � June 13, 2006 � vol. 103 � no. 24 www.pnas.org�cgi�doi�10.1073�pnas.0600263103

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020

Mapping of Antisera. In principle, having localized the bindingof the mAbs to the surface of the antigen, we could have analyzedthe binding of polyclonal antisera by competition with eachof the mAbs. However, we used a simpler and more directapproach. Separate aliquots of antisera were depleted on eachtethered mutant according to the scheme of Fig. 1B. The bindingof each depleted antiserum was analyzed by ELISA on a mutant(C308) tethered at the C terminus (‘‘unmasked’’) (Fig. 1C) andon the tethered mutant used for the depletion (‘‘masked’’). Thedifference between the two signals represents the antibodies tonative folded antigen that are specific for each masked site.

The resulting pattern for all of the tethered mutants isillustrated for rabbit 1 immunized with �-lactamase inFreund’s adjuvant (Fig. 3A) and shows enhanced antigenicitymainly between residues 90 and 140. This finding was con-firmed by the use of an alternative format for the assay: thedepleted antisera was captured on anti-IgG-coated ELISAplates and then assayed for binding to �-lactamase (via thecatalytic activity of the �-lactamase because this detects onlythe native folded enzyme) (Fig. 3B). This assay gave a similarpattern as in Fig. 3A, confirming the enhanced antigenicity ofthe region 90–140. Sera from another rabbit (Fig. 3C) and fourmice (Fig. 3D) immunized with �-lactamase in Freund’sadjuvant (Table 1) all showed enhanced antigenicity betweenresidues 90 and 140. These residues cluster together on theantigen surface, indicating a major surface epitope (Fig. 4A).

Immunization Regime. We also immunized two rabbits in theabsence of Freund’s adjuvant (rabbits 3 and 4). In contrast to

rabbits 1 and 2 (Fig. 3 A and C), the sera from rabbits 3 and4 revealed a more even pattern of reactivity (Fig. 3 E and F).Rabbit sera were also tested for binding to native and tochemically denatured (carboxymethylated) �-lactamase (Fig.3G). Whereas the sera from rabbits 1 and 2 bound both formsof the antigen, those from rabbits 3 and 4 bound well to nativebut poorly to denatured �-lactamase.

This finding raised the question of whether the majorantigenic epitope evident in rabbits 1 and 2 (and the mice) wasdue to antibodies to denatured antigen that crossreacted withnative. We therefore purified each portion of depleted anti-serum from rabbit 1 by affinity purification on native �-lac-tamase (mutant C308) and then analyzed its binding todenatured �-lactamase (Fig. 3H). This experiment indicatedthat crossreactive antibodies were indeed present and focusedto the major epitope (residues 90–140) noted above.

The possible role of denatured antigen in generating cross-reactive antibodies was confirmed by immunizing anotherrabbit (rabbit 5) with chemically denatured �-lactamase inFreund’s adjuvant (Fig. 3I). This experiment generated anextreme pattern, with little binding to most portions of thesurface of the native antigen but with significant reactivity tothe major epitope (90–114) and also to another epitope atresidues 197–202.

Action of Freund’s Adjuvant. By emulsifying the enzyme inFreund’s adjuvant and then breaking the emulsion by additionof ether, we found that the catalytic activity of the enzymedecayed exponentially in the adjuvant (t1/2 � 20 min; data not

Fig. 1. Mapping method. (A) mAbs. Antigen (cube) tethered to a solid surface at cysteine residues sites through a bifunctional biotin linker to astreptavidin-coated surface (disk). Binding of mAb to the ‘‘white’’ epitope is masked (shown in the center of A). (B and C) Serum antibodies. Antibodies weredepleted from the serum by binding to masked antigen (B), and those remaining were analyzed by binding to unmasked antigen and detected withenzyme-conjugated secondary antibodies (C).

Fig. 2. Mapping of mAbs. Shown is the assay as summarized in Fig. 1A. Binding of mAb to masked �-lactamase tethered at each of the 23 sites indicated. (A)mAb P50.2. (B) mAb P51.1. Dashed line indicates 20% of maximum signal. (C) Location of each cysteine tether on �-lactamase marked as a colored circle of 7 Å.Epitopes for mAbs (�20% signal) are marked green after replotting data from A (upper left side of C) and B (lower right side of C).

Paus and Winter PNAS � June 13, 2006 � vol. 103 � no. 24 � 9173

IMM

UN

OLO

GY

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020

shown). Native �-lactamase also resisted digestion with trypsin(1�100 wt�wt) in PBS but not when coemulsified with trypsinin Freund’s adjuvant (data not shown), indicating that �-lactamase becomes denatured in Freund’s adjuvant, as re-ported for lysozyme (22).

DiscussionOur method provides a systematic means of masking patchesof the antigen surface, thereby blocking the binding of anti-bodies to the patch. By these means we mapped the epitopesof several mAbs to the surface of �-lactamase. Our method

Fig. 3. Mapping of serum antibodies and immunization regime. Shown is the assay as summarized in Fig. 1B. Binding of antisera (generally depleted on �-lactamasetethered at each of the 23 sites) to unmasked �-lactamase. Signals were generally detected by anti-IgG ELISA except for in B, in which the assay was inverted as describedin the text (capture of depleted serum with anti-IgG and detection by �-lactamase activity). Animals were immunized with �-lactamase: (A and B) rabbit 1 in Freund’sadjuvant; (C) rabbit 2 in Freund’s adjuvant; (D) mice 1–4 in Freund’s adjuvant; (E and F) rabbits 3 and 4, respectively, in PBS; (G) total antisera from the individual rabbitsto native (black bars) or denatured (gray bars) �-lactamase (sera dilutions 1:25,000); (H) rabbit 1 in Freund’s adjuvant after affinity purification of the depleted antiseraon native antigen and with binding to denatured antigen; and (I) rabbit 5 but after immunization with chemically denatured (carboxymethylated) �-lactamase. Thedata from animals were normalized to an average value of 1.0 (dashed line). White bars, signal on ‘‘unmasked.’’ Black bars, signal on ‘‘masked’’ subtracted from‘‘unmasked.’’ These data correspond to ELISA signals (for ‘‘unmasked’’ antigen) in the ranges 0.10–0.62, 0.06–0.67, 0.02–0.40, 0.07–0.29, and 0.01–0.30 for panels A,C, D, E, and F, respectively.

9174 � www.pnas.org�cgi�doi�10.1073�pnas.0600263103 Paus and Winter

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020

benefits from the three-dimensional structure of antigen todesign the tethering sites and for interpretation of the results.However, where the structure is available, it should be moredefinitive for mapping conformational determinants than theuse of peptides on pins (7–10) or peptide libraries displayed onphage (23), both of which have to assume the presence of asignificant sequential component within the conformationaldeterminant.

We further developed our method for analysis of antisera byselectively isolating pools of antibodies binding to each‘‘masked’’ patch. By these means, we measured the antigenicityof different regions of the surface and also compared immuni-zation regimes. With immunization in PBS, the antibody re-sponse was directed mainly to native protein (Fig. 3G) and witha fairly uniform distribution over the entire surface (Fig. 3 E andF). This observation contrasts with interaction ‘‘hot-spots’’ notedfor other protein–protein interactions (24, 25).

However, with immunization in Freund’s adjuvant, theresponse was directed to both native and to denatured protein(Fig. 3G); this appears to be due to the (partial) denaturationof antigen by Freund’s adjuvant. Furthermore, a major anti-genic determinant appeared between residues 90 and 140 (Fig.3 A–C), ref lecting the presence of antibodies crossreactive toboth native and denatured protein (Fig. 3H). Immunizationwith chemically denatured protein also elicited a response tothe native antigen directed to the major antigenic region(Fig. 3I).

Thus, the antibody response to native antigen after immuni-zation in Freund’s adjuvant (Fig. 3 A and C) can be representedqualitatively as a superposition of the responses to separateimmunizations with native antigen (Fig. 3 E and F) and withdenatured protein (Fig. 3I). However, the presence of native and

denatured antigen together in the same immunization may beexpected to promote the development of the crossreactiveantibodies.

The region 90–140 corresponds to a flexible loop region of�-lactamase (Fig. 4C), and there is a striking correlation of themajor peaks of antigenicity with backbone flexibility along thelinear protein sequence (Fig. 4B). Such correlations, also basedon the analysis of sera from immunizations using Freund’sadjuvant, have been previously reported for the sequentialepitopes of several antigens (11, 12), and it had been suggestedby Stanworth that denaturation of the antigen might be an issue(26). Our work suggests that the enhanced antigenicity of someconformational epitopes (Fig. 4B) is due to the presence ofantibodies raised against denatured antigen that crossreact withexposed and flexible segments. It is well established that immu-nization with peptide segments comprising flexible loop regionsof the antigen can elicit antibodies reactive to the native state ofthe antigen (27).

In conclusion, we describe a method for mapping the epitopesof mAbs and also for measuring the antigenicity of differentregions of the antigenic surface. Our use of the method suggeststhat the presence of denatured antigen can have a major role indirecting the antibody response to flexible loops of the nativeantigen. This finding is relevant to the development of vaccines,adjuvants, and therapeutic proteins and also to understandingnatural infections. For example, antibodies to denatured antigendo arise during viral infections; indeed, a recent analysis of thehuman antibody response to SARS virus (28) showed that mostof the antibodies were directed toward denatured viral antigen.We suggest that denaturation of a viral antigen during infectionmay direct antibodies to the flexible loops, regions more tolerantof mutation (29), and perhaps at the expense of a neutralizingresponse. By mutation of the loops, the virus is thereby able topresent a moving antigenic target to the immune system. De-naturation of the antigen, before or during presentation to theimmune system, may therefore facilitate viral escape fromantibody selection pressure.

Materials and MethodsExpression of �-Lactamase. The �-lactamase gene, ampC, wasamplified from pBR322 by PCR with the primers 5�-CCC AAGCTT GGG ATG CTT CAA TAA TAT TG-3� and 5�-CCT CACTGA TTA AGC ATT GGG CTC TAG ATT ACA AGG ATGACG ATG ACA AGC ATC ATC ATC ACC ATC ACT AAGAAT TCC GG-3�, thereby adding C-terminal FLAG and His (6)

Table 1. Immunizations

Animal Antigen

Rabbits 1 and 2 �-Lactamase in CFA�IFARabbits 3 and 4* �-Lactamase in PBSRabbit 5 CM-�-lactamase in CFA�IFAMice 1–4 �-Lactamase in CFA�IFA

CFA, complete Freund’s adjuvant; IFA, incomplete Freund’s adjuvant; CM,carboxymethylated.*Barstar in CFA�IFA injected into a separate site in rabitt 4. (Immunizationregimes are detailed in the supporting information.)

Fig. 4. Antigenicity of �-lactamase. (A) Location of each cysteine tether was marked as a colored circle of 7 Å on the surface of �-lactamase, with major antigenicepitope (�150% of average signal of data from Fig. 3 A and C) marked red. (B) Backbone flexibility of �-lactamase (crystallographic B values) averaged over awindow of seven residues, and major epitopes marked; rabbits 1 and 2 (■ ), rabbit 5 (Œ), and mice (F). (C) Cartoon of main chain �-lactamase with regions of highbackbone flexibility (�150% of average) (residues 84–115 and 196–200 marked in red).

Paus and Winter PNAS � June 13, 2006 � vol. 103 � no. 24 � 9175

IMM

UN

OLO

GY

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020

tags to the protein sequence, and ligated into pRooster (gift fromPeter Wang) between the HindIII and EcoRI sites. The latterprimer was replaced by 5�-GAA TTC TTA ACA TCC GTGATG GTG ATG ATG ATG CTT GTC ATC GTC ATC CTTGTA ATC TAG A-3� to extend the C terminus of the aboveaffinity tags with Gly-Cys in mutant C308. Other cysteineresidues were introduced by site-specific mutagenesis (30). DNAwas sequenced by the dideoxy method (31). The recombinant�-lactamase was expressed in E. coli HB2151, purified, andbiotinylated as described in the supporting information, which ispublished on the PNAS web site.

Production of Monoclonal Antibodies (mAbs). The production ofmAbs was carried out in collaboration with Elisabeth Paus andTone Varaas at the Central Laboratory of the NorwegianRadium Hospital (Montebello, N-0310 Oslo, Norway) by usingstandard methods (see supporting information).

Production of Antisera. For details, see supporting information.The rabbits, of 4–4.5 kg, were Murex Bioservices (Dartford,U.K.) Lop (hybrid of English Full Lop and New Zealand crossedfor several generations). �-lactamase (500 �l of 1 mg�ml) wasinjected s.c. into four sites on the back of the rabbits in PBS aloneor emulsified in 500 �l of Freund’s adjuvant (Difco). Chemicallydenatured (carboxymethylated) �-lactamase used in immuniza-tion was prepared as described in the supporting information.Sera were taken 10 days after injection and stored at �20°C with0.02% sodium azide. The mice were all female BALB�c mice 6weeks old. �-lactamase (100 �l of 1 mg�ml) was injected s.c. intofour sites on the back of the mice in PBS alone or emulsified in100 �l of Freund’s adjuvant. Sera were taken 7 days afterinjection and stored as described above. (Sera taken before thefirst injection showed no antibodies specific for �-lactamase inELISA for any of the animals.)

Preparation of ELISA Plates. Biotinylated �-lactamase was immo-bilized on streptavidin-coated plates (details in the supportinginformation). Plates with denatured �-lactamase were preparedby in situ carboxymethylation of internal cysteine disulfides or bycoating �-lactamase directly on the plates and drying for 1 hour.The absence of native �-lactamase was verified with the enzymesubstrate Nitrocefin (Calbiochem) The presence of �-lactamasewas detected with antiserum to �-lactamase or anti-FLAG-tagantibody.

Mapping of mAbs. The mapping method is illustrated in Fig. 1 A.ELISA plates were prepared with �-lactamase mutants as de-scribed. We added 0.5 �g�ml mAbs in 100 �l 0.1% bovine serum

albumin in PBS and allowed binding for 1 hour with shaking atroom temperature before detection with horseradish peroxi-dase-conjugated secondary antibodies (Sigma) with 3�,3�,5�,5�-tetramethylbenzidine and hydrogen peroxide as substrate. Re-actions were stopped with 50 �l of 1 M H2SO4 and recorded asthe difference between OD650 nm and OD450 nm.

Mapping of Serum Antibodies. The mapping method is illustratedin Fig. 1B. Depletion of sera was carried out with �-lactamaseimmobilized on streptavidin-coated beads (see supporting in-formation) or plates. For the depletion step, biotinylated �-lactamase was loaded on streptavidin-coated ELISA plates(StreptaWell High Bind; Roche Diagnostics) as described. Eachserum aliquot, diluted in 120 �l of 0.1% Tween 20 in PBS, wasadded to an ELISA plate well with one of 23 biotinylated�-lactamase mutants. This was incubated shaking for 15 min andtransferred to a second well with the same �-lactamase mutant.The process was repeated over 11 wells. For the detection step,depleted samples were diluted 1:2 in 0.1% TPBS and were addedto ELISA plate wells with mutant C308 or the same mutant asused for depletion. Bound serum antibodies were detected withsecondary antibodies conjugated to horseradish peroxide asabove. Sera concentrations were 1:20,000, 1:50,000, 1:30,000,1:30,000, and 1:30,000 for rabbits 1, 2, 3, 4, and 5, respectively,and 1:5,000 for the mice.

Extraction of �-Lactamase from Freund’s Adjuvant. Twenty volumesof mineral oil (Sigma) or 2 vol of ether were added to emulsionof antigen in Freund’s adjuvant. This mixture was vortexed andcentrifuged followed by pipetting of the nonaqueous phase. Thisstep was repeated until the emulsion was completely brokendown. Vortexing �-lactamase in PBS with mineral oil or etheralone did not reduce the enzyme activity of the �-lactamase(data not shown).

Antigen Structure. The atomic coordinates and the crystallo-graphic B-values, used for calculations of the backbone flexibil-ity, were attained from the crystallographic structure reported(32) and by using the CCP4-supported software BAVERAGE(www.ccp4.ac.uk). The surface and backbone structure repre-sentations of �-lactamase were created with GRASP (33) andMOLSCRIPT (34).

We thank Elisabeth Paus and Tone Varaas for help in making mono-clonal antibodies; Michael Neuberger, Aaron Klug, Robert Raison, LutzRiechmann, and Leo James for their comments at various stages of themanuscript; and Peter Jones for help with software. D.P. was supportedby the Research Council of Norway.

1. Benjamin, D. C., Berzofsky, J. A., East, I. J., Gurd, F. R., Hannum, C., Leach,S. J., Margoliash, E., Michael, J. G., Miller, A., Prager, E. M., et al. (1984) Annu.Rev. Immunol. 2, 67–101.

2. Harper, M., Lema, F., Boulot, G. & Poljak, R. J. (1987) Mol. Immunol. 24,97–108.

3. Sela, M., Schechter, B., Schechter, I. & Borek, F. (1967) Cold Spring HarborSymp. Quant. Biol. 32, 537–545.

4. Amit, A. G., Mariuzza, R. A., Phillips, S. E. & Poljak, R. J. (1986) Science 233,747–753.

5. Fields, B. A., Goldbaum, F. A., Ysern, X., Poljak, R. J. & Mariuzza, R. A.(1995) Nature 374, 739–742.

6. Lescar, J., Pellegrini, M., Souchon, H., Tello, D., Poljak, R. J., Peterson, N.,Greene, M. & Alzari, P. M. (1995) J. Biol. Chem. 270, 18067–18076.

7. Geysen, H. M., Rodda, S. J., Mason, T. J., Tribbick, G. & Schoofs, P. G. (1987)J. Immunol. Methods 102, 259–274.

8. Radford, A. J., Wood, P. R., Billman-Jacobe, H., Geysen, H. M., Mason, T. J.& Tribbick, G. (1990) J. Gen. Microbiol. 136, 265–272.

9. Tribbick, G., Triantafyllou, B., Lauricella, R., Rodda, S. J., Mason, T. J. &Geysen, H. M. (1991) J. Immunol. Methods 139, 155–166.

10. Reineke, U., Kramer, A. & Schneider-Mergener, J. (1999) Curr. Top. Microbiol.Immunol. 243, 23–36.

11. Westhof, E., Altschuh, D., Moras, D., Bloomer, A. C., Mondragon, A., Klug,A. & Van Regenmortel, M. H. (1984) Nature 311, 123–126.

12. Tainer, J. A., Getzoff, E. D., Paterson, Y., Olson, A. J. & Lerner, R. A. (1985)Annu. Rev. Immunol. 3, 501–535.

13. MacCallum, R. M., Martin, C. R. & Thornton, J. M. (1996) J. Mol. Biol. 262,732–745.

14. Cunningham, B. C., Jhurani, P., Ng, P. & Wells, J. A. (1989) Science 243, 1330–1336.15. Weber, J. R., Nelson, C., Cunningham, B. C., Wells, J. A. & Fong, S. (1992)

Mol. Immunol. 29, 1081–1088.16. Urbanski, G. J. & Margoliash, E. (1977) J. Immunol. 118, 1170–1180.17. Jemmerson, R. & Margoliash, E. (1979) Nature 282, 468–471.18. Benjamin, D. C. & Teale, J. M. (1978) J. Biol. Chem. 253, 8087–8092.19. East, I. J., Hurrell, J. G., Todd, P. E. & Leach, S. J. (1982) J. Biol. Chem. 257,

3199–3202.20. Metzger, D. W., Ch’ng, L. K., Miller, A. & Sercarz, E. E. (1984) Eur.

J. Immunol. 14, 87–93.21. Lo Conte, L., Chothia, C. & Janin, J. (1999) J. Mol. Biol. 285, 2177–2198.22. Scibienski, R. J. (1973) J. Immunol. 111, 114–120.23. Stephen, C. W. & Lane, D. P. (1992) J. Mol. Biol. 225, 577–583.24. Clackson, T. & Wells, J. A. (1995) Science 267, 383–386.25. Bogan, A. A. & Thorn, K. S. (1998) J. Mol. Biol. 280, 1–9.

9176 � www.pnas.org�cgi�doi�10.1073�pnas.0600263103 Paus and Winter

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020

26. Van Regenmortel, M. H. V., Altschuh, D. & Klug, A. (1986) in SyntheticPeptides as Antigens, Ciba Foundation Symposium, eds. Porter, R. & Whelan,J. (Wiley, New York), Vol. 119, pp. 76–84.

27. Arnon, R., Maron, E., Sela, M. & Anfinsen, C. B. (1971) Proc. Natl. Acad. Sci.USA 68, 1450–1455.

28. Traggiai, E., Becker, S., Subbarao, K., Kolesnikova, L., Uematsu, Y., Gis-mondo, M. R., Murphy, B. R., Rappuoli, R. & Lanzavecchia, A. (2004) Nat.Med. 10, 871–875.

29. Skehel, J. J. & Wiley, D. C. (2000) Annu. Rev. Biochem. 69, 531–569.30. Kunkel, T. A. (1985) Proc. Natl. Acad. Sci. USA 82, 488–492.31. Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci. USA 74,

5463–5467.32. Jelsch, C., Mourey, L., Masson, J. M. & Samama, J. P. (1993) Proteins 16,

364–383.33. Nicholls, A., Sharp, K. A. & Honig, B. (1991) Proteins 11, 281–296.34. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946–950.

Paus and Winter PNAS � June 13, 2006 � vol. 103 � no. 24 � 9177

IMM

UN

OLO

GY

Dow

nloa

ded

by g

uest

on

Janu

ary

18, 2

020