Minute Time Scale Prolyl Isomerization Governs Antibody Recognition of an Intrinsically Disordered Immunodominant Epitope

Overview

Journal J Biol Chem

Specialty Biochemistry

Date 2013 Mar 19

PMID 23504368

Citations 9

Authors

Marisol Fassolari

Lucia B Chemes

Mariana Gallo

Clara Smal

Ignacio E Sanchez

Gonzalo de Prat-Gay

Affiliations

Soon will be listed here.

Abstract

Conformational rearrangements in antibody·antigen recognition are essential events where kinetic discrimination of isomers expands the universe of combinations. We investigated the interaction mechanism of a monoclonal antibody, M1, raised against E7 from human papillomavirus, a prototypic viral oncoprotein and a model intrinsically disordered protein. The mapped 12-amino acid immunodominant epitope lies within a "hinge" region between the N-terminal intrinsically disordered and the C-terminal globular domains. Kinetic experiments show that despite being within an intrinsically disordered region, the hinge E7 epitope has at least two populations separated by a high energy barrier. Nuclear magnetic resonance traced the origin of this barrier to a very slow (t(1/2)∼4 min) trans-cis prolyl isomerization event involving changes in secondary structure. The less populated (10%) cis isomer is the binding-competent species, thus requiring the 90% of molecules in the trans configuration to isomerize before binding. The association rate for the cis isomer approaches 6 × 10(7) M(-1) s(-1), a ceiling for antigen-antibody interactions. Mutagenesis experiments showed that Pro-41 in E7Ep was required for both binding and isomerization. After a slow postbinding unimolecular rearrangement, a consolidated complex with K(D) = 1.2 × 10(-7) M is reached. Our results suggest that presentation of this viral epitope by the antigen-presenting cells would have to be "locked" in the cis conformation, in opposition to the most populated trans isomer, in order to select the specific antibody clone that goes through affinity and kinetic maturation.

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References

Boehr D, Nussinov R, Wright P . The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol. 2009; 5(11):789-96. PMC: 2916928. DOI: 10.1038/nchembio.232. View

Batista F, Neuberger M . Affinity dependence of the B cell response to antigen: a threshold, a ceiling, and the importance of off-rate. Immunity. 1998; 8(6):751-9. DOI: 10.1016/s1074-7613(00)80580-4. View

Krchnak V, Vagner J, SUCHANKOVA A, Krcmar M, Ritterova L, Vonka V . Synthetic peptides derived from E7 region of human papillomavirus type 16 used as antigens in ELISA. J Gen Virol. 1990; 71 ( Pt 11):2719-24. DOI: 10.1099/0022-1317-71-11-2719. View

Chemes L, Sanchez I, de Prat-Gay G . Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target. J Mol Biol. 2011; 412(2):267-84. DOI: 10.1016/j.jmb.2011.07.015. View

Vogt A, Di Cera E . Conformational selection or induced fit? A critical appraisal of the kinetic mechanism. Biochemistry. 2012; 51(30):5894-902. PMC: 3550001. DOI: 10.1021/bi3006913. View

Tindle R, Smith J, Geysen H, Selvey L, Frazer I . Identification of B epitopes in human papillomavirus type 16 E7 open reading frame protein. J Gen Virol. 1990; 71 ( Pt 6):1347-54. DOI: 10.1099/0022-1317-71-6-1347. View

Sibille N, Huvent I, Fauquant C, Verdegem D, Amniai L, Leroy A . Structural characterization by nuclear magnetic resonance of the impact of phosphorylation in the proline-rich region of the disordered Tau protein. Proteins. 2011; 80(2):454-62. DOI: 10.1002/prot.23210. View

Dantur K, Alonso L, Castano E, Morelli L, Centeno-Crowley J, Vighi S . Cytosolic accumulation of HPV16 E7 oligomers supports different transformation routes for the prototypic viral oncoprotein: the amyloid-cancer connection. Int J Cancer. 2009; 125(8):1902-11. DOI: 10.1002/ijc.24579. View

Zeng Q, Peng S, Monie A, Yang M, Pang X, Hung C . Control of cervicovaginal HPV-16 E7-expressing tumors by the combination of therapeutic HPV vaccination and vascular disrupting agents. Hum Gene Ther. 2010; 22(7):809-19. PMC: 3135274. DOI: 10.1089/hum.2010.071. View

10.

de Prat Gay G, Fersht A . Generation of a family of protein fragments for structure-folding studies. 1. Folding complementation of two fragments of chymotrypsin inhibitor-2 formed by cleavage at its unique methionine residue. Biochemistry. 1994; 33(25):7957-63. DOI: 10.1021/bi00191a024. View

11.

Allcorn L, Martin A . SACS--self-maintaining database of antibody crystal structure information. Bioinformatics. 2002; 18(1):175-81. DOI: 10.1093/bioinformatics/18.1.175. View

12.

Uversky V, Roman A, Oldfield C, Dunker A . Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. J Proteome Res. 2006; 5(8):1829-42. DOI: 10.1021/pr0602388. View

13.

Smal C, Wetzler D, Dantur K, Chemes L, Garcia-Alai M, Dellarole M . The human papillomavirus E7-E2 interaction mechanism in vitro reveals a finely tuned system for modulating available E7 and E2 proteins. Biochemistry. 2009; 48(50):11939-49. DOI: 10.1021/bi901415k. View

14.

Rajbhandari P, Finn G, Solodin N, Singarapu K, Sahu S, Markley J . Regulation of estrogen receptor α N-terminus conformation and function by peptidyl prolyl isomerase Pin1. Mol Cell Biol. 2011; 32(2):445-57. PMC: 3255769. DOI: 10.1128/MCB.06073-11. View

15.

Cerutti M, Ferreiro D, Sanguineti S, Goldbaum F, de Prat-Gay G . Antibody recognition of a flexible epitope at the DNA binding site of the human papillomavirus transcriptional regulator E2. Biochemistry. 2006; 45(51):15520-8. DOI: 10.1021/bi0615184. View

16.

Chemes L, Glavina J, Alonso L, Marino-Buslje C, de Prat-Gay G, Sanchez I . Sequence evolution of the intrinsically disordered and globular domains of a model viral oncoprotein. PLoS One. 2012; 7(10):e47661. PMC: 3485249. DOI: 10.1371/journal.pone.0047661. View

17.

Leder L, Berger C, BORNHAUSER S, Wendt H, ACKERMANN F, Jelesarov I . Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry. 1995; 34(50):16509-18. DOI: 10.1021/bi00050a035. View

18.

Sugase K, Dyson H, Wright P . Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature. 2007; 447(7147):1021-5. DOI: 10.1038/nature05858. View

19.

Davey N, Van Roey K, Weatheritt R, Toedt G, Uyar B, Altenberg B . Attributes of short linear motifs. Mol Biosyst. 2011; 8(1):268-81. DOI: 10.1039/c1mb05231d. View

20.

James L, Tawfik D . Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proc Natl Acad Sci U S A. 2005; 102(36):12730-5. PMC: 1200256. DOI: 10.1073/pnas.0500909102. View