Skip to main content
Top
Published in: Immunologic Research 1-3/2010

01-07-2010

Conformational heterogeneity of MHC class II induced upon binding to different peptides is a key regulator in antigen presentation and epitope selection

Authors: Scheherazade Sadegh-Nasseri, Sateesh Natarajan, Chih-Ling Chou, Isamu Z. Hartman, Kedar Narayan, AeRyon Kim

Published in: Immunologic Research | Issue 1-3/2010

Login to get access

Abstract

T cells bearing αβ receptors recognize antigenic peptides bound to class I and class II glycoproteins encoded in the major histocompatibility complex (MHC). Cytotoxic and helper T cells respond respectively to peptide antigens derived from endogenous sources presented by MHC class I, and exogenous sources presented by MHC II, on antigen presenting cells. Differences in the MHC class I and class II structures and their maturation pathways have evolved to optimize antigen presentation to their respective T cells. A main focus of our laboratory is on efforts to understand molecular events in processing of antigen for presentation by MHC class II. The different stages of MHC class II—interactions with molecular chaperons involved in folding and traffic from the ER through the antigen-loading compartments, peptide exchange, and transport to the cell surface have been investigated. Through intense research on biophysical and biochemical properties of MHC class II molecules, we have learned that the conformational heterogeneity of MHC class II induced upon binding to different peptides is a key regulator in antigen presentation and epitope selection, and a determinant of the ability of MHC class II to participate in peptide association or dissociation and interaction with the peptide editor HLA-DM.
Literature
1.
go back to reference Germain RN, Margulies DH. The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol. 1993;11:403–50.CrossRefPubMed Germain RN, Margulies DH. The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol. 1993;11:403–50.CrossRefPubMed
2.
go back to reference Sadegh-Nasseri S, Germain RN. How MHC class II molecules work: peptide-dependent completion of protein folding. Immunol Today. 1992;13(2):43–6.CrossRefPubMed Sadegh-Nasseri S, Germain RN. How MHC class II molecules work: peptide-dependent completion of protein folding. Immunol Today. 1992;13(2):43–6.CrossRefPubMed
3.
go back to reference Sadegh-Nasseri S, Germain RN. A role for peptide in determining MHC class II structure. Nature. 1991;353(6340):167–70.CrossRefPubMed Sadegh-Nasseri S, Germain RN. A role for peptide in determining MHC class II structure. Nature. 1991;353(6340):167–70.CrossRefPubMed
4.
go back to reference Sadegh-Nasseri S, McConnell HM. A kinetic intermediate in the reaction of an antigenic peptide and I-Ek. Nature. 1989;337(6204):274–6.CrossRefPubMed Sadegh-Nasseri S, McConnell HM. A kinetic intermediate in the reaction of an antigenic peptide and I-Ek. Nature. 1989;337(6204):274–6.CrossRefPubMed
5.
go back to reference Sadegh-Nasseri S, Stern LJ, Wiley DC, Germain RN. MHC class II function preserved by low-affinity peptide interactions preceding stable binding. Nature. 1994;370(6491):647–50.CrossRefPubMed Sadegh-Nasseri S, Stern LJ, Wiley DC, Germain RN. MHC class II function preserved by low-affinity peptide interactions preceding stable binding. Nature. 1994;370(6491):647–50.CrossRefPubMed
6.
go back to reference Sato AK, Zarutskie JA, Rushe MM, Lomakin A, Natarajan SK, Sadegh-Nasseri S, et al. Determinants of the peptide-induced conformational change in the human class II major histocompatibility complex protein HLA-DR1. J Biol Chem. 2000;275(3):2165–73.CrossRefPubMed Sato AK, Zarutskie JA, Rushe MM, Lomakin A, Natarajan SK, Sadegh-Nasseri S, et al. Determinants of the peptide-induced conformational change in the human class II major histocompatibility complex protein HLA-DR1. J Biol Chem. 2000;275(3):2165–73.CrossRefPubMed
7.
go back to reference Carven GJ, Stern LJ. Probing the ligand-induced conformational change in HLA-DR1 by selective chemical modification and mass spectrometric mapping. Biochemistry. 2005;44(42):13625–37.CrossRefPubMed Carven GJ, Stern LJ. Probing the ligand-induced conformational change in HLA-DR1 by selective chemical modification and mass spectrometric mapping. Biochemistry. 2005;44(42):13625–37.CrossRefPubMed
8.
go back to reference Dornmair K, Rothenhausler B, McConnell HM. Structural intermediates in the reactions of antigenic peptides with MHC molecules. Cold Spring Harb Symp Quant Biol. 1989;54(Pt 1):409–16.PubMed Dornmair K, Rothenhausler B, McConnell HM. Structural intermediates in the reactions of antigenic peptides with MHC molecules. Cold Spring Harb Symp Quant Biol. 1989;54(Pt 1):409–16.PubMed
9.
go back to reference Witt SN, McConnell HM. Formation and dissociation of short-lived class II MHC-peptide complexes. Biochemistry. 1994;33(7):1861–8.CrossRefPubMed Witt SN, McConnell HM. Formation and dissociation of short-lived class II MHC-peptide complexes. Biochemistry. 1994;33(7):1861–8.CrossRefPubMed
10.
go back to reference Schmitt L, Boniface JJ, Davis MM, McConnell HM. Conformational isomers of a class II MHC-peptide complex in solution. J Mol Biol. 1999;286(1):207–18.CrossRefPubMed Schmitt L, Boniface JJ, Davis MM, McConnell HM. Conformational isomers of a class II MHC-peptide complex in solution. J Mol Biol. 1999;286(1):207–18.CrossRefPubMed
11.
go back to reference Natarajan SK, Assadi M, Sadegh-Nasseri S. Stable peptide binding to MHC class II molecule is rapid and is determined by a receptive conformation shaped by prior association with low affinity peptides. J Immunol. 1999;162(7):4030–6.PubMed Natarajan SK, Assadi M, Sadegh-Nasseri S. Stable peptide binding to MHC class II molecule is rapid and is determined by a receptive conformation shaped by prior association with low affinity peptides. J Immunol. 1999;162(7):4030–6.PubMed
12.
go back to reference Rabinowitz JD, Vrljic M, Kasson PM, Liang MN, Busch R, Boniface JJ, et al. Formation of a highly peptide-receptive state of class II MHC. Immunity. 1998;9(5):699–709.CrossRefPubMed Rabinowitz JD, Vrljic M, Kasson PM, Liang MN, Busch R, Boniface JJ, et al. Formation of a highly peptide-receptive state of class II MHC. Immunity. 1998;9(5):699–709.CrossRefPubMed
13.
go back to reference Zarutskie JA, Busch R, Zavala-Ruiz Z, Rushe M, Mellins ED, Stern LJ. The kinetic basis of peptide exchange catalysis by HLA-dm. Proc Natl Acad Sci USA. 2001;98(22):12450–5.CrossRefPubMed Zarutskie JA, Busch R, Zavala-Ruiz Z, Rushe M, Mellins ED, Stern LJ. The kinetic basis of peptide exchange catalysis by HLA-dm. Proc Natl Acad Sci USA. 2001;98(22):12450–5.CrossRefPubMed
14.
go back to reference Watts TH, Brian AA, Kappler JW, Marrack P, McConnell HM. Antigen presentation by supported planar membranes containing affinity-purified I-Ad. Proc Natl Acad Sci USA. 1984;81(23):7564–8.CrossRefPubMed Watts TH, Brian AA, Kappler JW, Marrack P, McConnell HM. Antigen presentation by supported planar membranes containing affinity-purified I-Ad. Proc Natl Acad Sci USA. 1984;81(23):7564–8.CrossRefPubMed
15.
go back to reference Buus S, Sette A, Colon SM, Jenis DM, Grey HM. Isolation and characterization of antigen-IA complexes involved in T cell recognition. Cell. 1986;47(6):1071–7.CrossRefPubMed Buus S, Sette A, Colon SM, Jenis DM, Grey HM. Isolation and characterization of antigen-IA complexes involved in T cell recognition. Cell. 1986;47(6):1071–7.CrossRefPubMed
16.
go back to reference Dornmair K, McConnell HM. Refolding and reassembly of separate alpha and beta chains of class II molecules of the major histocompatibility complex leads to increased peptide-binding capacity. Proc Natl Acad Sci USA. 1990;87(11):4134–8.CrossRefPubMed Dornmair K, McConnell HM. Refolding and reassembly of separate alpha and beta chains of class II molecules of the major histocompatibility complex leads to increased peptide-binding capacity. Proc Natl Acad Sci USA. 1990;87(11):4134–8.CrossRefPubMed
17.
go back to reference Germain RN, Hendrix LR. MHC class II structure, occupancy and surface expression determined by post-endoplasmic reticulum antigen binding. Nature. 1991;353(6340):134–9.CrossRefPubMed Germain RN, Hendrix LR. MHC class II structure, occupancy and surface expression determined by post-endoplasmic reticulum antigen binding. Nature. 1991;353(6340):134–9.CrossRefPubMed
18.
go back to reference Davidson HW, Reid PA, Lanzavecchia A, Watts C. Processed antigen binds to newly synthesized MHC class II molecules in antigen-specific b lymphocytes. Cell. 1991;67(1):105–16.CrossRefPubMed Davidson HW, Reid PA, Lanzavecchia A, Watts C. Processed antigen binds to newly synthesized MHC class II molecules in antigen-specific b lymphocytes. Cell. 1991;67(1):105–16.CrossRefPubMed
19.
go back to reference Sadegh-Nasseri S. Peptide, invariant chain, or molecular aggregation preserves class II from functional inactivation. In: Humphreys RE, Pierce SK, editors. Antigen processing and presentation, vol. 1. San Diego: Academic Press; 1994. p. 170–87. Sadegh-Nasseri S. Peptide, invariant chain, or molecular aggregation preserves class II from functional inactivation. In: Humphreys RE, Pierce SK, editors. Antigen processing and presentation, vol. 1. San Diego: Academic Press; 1994. p. 170–87.
20.
go back to reference Park SJ, Sadegh-Nasseri S, Wiley DC. Invariant chain made in Escherichia coli has an exposed n-terminal segment that blocks antigen binding to HLA-DR1 and a trimeric c-terminal segment that binds empty HLA-DR1. Proc Natl Acad Sci USA. 1995;92(24):11289–93.CrossRefPubMed Park SJ, Sadegh-Nasseri S, Wiley DC. Invariant chain made in Escherichia coli has an exposed n-terminal segment that blocks antigen binding to HLA-DR1 and a trimeric c-terminal segment that binds empty HLA-DR1. Proc Natl Acad Sci USA. 1995;92(24):11289–93.CrossRefPubMed
21.
go back to reference Jardetzky TS, Gorga JC, Busch R, Rothbard J, Strominger JL, Wiley DC. Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 1990;9(6):1797–803.PubMed Jardetzky TS, Gorga JC, Busch R, Rothbard J, Strominger JL, Wiley DC. Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 1990;9(6):1797–803.PubMed
22.
go back to reference Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature. 1994;368(6468):215–21.CrossRefPubMed Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature. 1994;368(6468):215–21.CrossRefPubMed
23.
go back to reference Murthy VL, Stern LJ. The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding. Structure. 1997;5(10):1385–96.CrossRefPubMed Murthy VL, Stern LJ. The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding. Structure. 1997;5(10):1385–96.CrossRefPubMed
24.
go back to reference Hammer J, Valsasnini P, Tolba K, Bolin D, Higelin J, Takacs B, et al. Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell. 1993;74(1):197–203.CrossRefPubMed Hammer J, Valsasnini P, Tolba K, Bolin D, Higelin J, Takacs B, et al. Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell. 1993;74(1):197–203.CrossRefPubMed
25.
go back to reference Wu S, Gorski J, Eckels DD, Newton-Nash DK. T cell recognition of MHC class II-associated peptides is independent of peptide affinity for MHC and sodium dodecyl sulfate stability of the peptide/MHC complex. Effects of conservative amino acid substitutions at anchor position 1 of influenza matrix protein19–31. J Immunol. 1996;156(10):3815–20.PubMed Wu S, Gorski J, Eckels DD, Newton-Nash DK. T cell recognition of MHC class II-associated peptides is independent of peptide affinity for MHC and sodium dodecyl sulfate stability of the peptide/MHC complex. Effects of conservative amino acid substitutions at anchor position 1 of influenza matrix protein19–31. J Immunol. 1996;156(10):3815–20.PubMed
26.
go back to reference Verreck FA, Vermeulen C, Poel AV, Jorritsma P, Amons R, Coligan JE, et al. The generation of SDS-stable HLA DR dimers is independent of efficient peptide binding. Int Immunol. 1996;8(3):397–404.CrossRefPubMed Verreck FA, Vermeulen C, Poel AV, Jorritsma P, Amons R, Coligan JE, et al. The generation of SDS-stable HLA DR dimers is independent of efficient peptide binding. Int Immunol. 1996;8(3):397–404.CrossRefPubMed
27.
go back to reference Chicz RM, Urban RG, Lane WS, Gorga JC, Stern LJ, Vignali DA, et al. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature. 1992;358(6389):764–8.CrossRefPubMed Chicz RM, Urban RG, Lane WS, Gorga JC, Stern LJ, Vignali DA, et al. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature. 1992;358(6389):764–8.CrossRefPubMed
28.
go back to reference Natarajan SK, Stern LJ, Sadegh-Nasseri S. Sodium dodecyl sulfate stability of HLA-DR1 complexes correlates with burial of hydrophobic residues in pocket 1. J Immunol. 1999;162(6):3463–70.PubMed Natarajan SK, Stern LJ, Sadegh-Nasseri S. Sodium dodecyl sulfate stability of HLA-DR1 complexes correlates with burial of hydrophobic residues in pocket 1. J Immunol. 1999;162(6):3463–70.PubMed
29.
go back to reference Stern LJ, Wiley DC. The human class II MHC protein HLA-DR1 assembles as empty alpha beta heterodimers in the absence of antigenic peptide. Cell. 1992;68(3):465–77.CrossRefPubMed Stern LJ, Wiley DC. The human class II MHC protein HLA-DR1 assembles as empty alpha beta heterodimers in the absence of antigenic peptide. Cell. 1992;68(3):465–77.CrossRefPubMed
30.
go back to reference Germain RN, Rinker AG Jr. Peptide binding inhibits protein aggregation of invariant-chain free class II dimers and promotes surface expression of occupied molecules. Nature. 1993;363(6431):725–8.CrossRefPubMed Germain RN, Rinker AG Jr. Peptide binding inhibits protein aggregation of invariant-chain free class II dimers and promotes surface expression of occupied molecules. Nature. 1993;363(6431):725–8.CrossRefPubMed
31.
go back to reference Romagnoli P, Germain RN. The clip region of invariant chain plays a critical role in regulating major histocompatibility complex class II folding, transport, and peptide occupancy. J Exp Med. 1994;180(3):1107–13.CrossRefPubMed Romagnoli P, Germain RN. The clip region of invariant chain plays a critical role in regulating major histocompatibility complex class II folding, transport, and peptide occupancy. J Exp Med. 1994;180(3):1107–13.CrossRefPubMed
32.
go back to reference Chou CL, Sadegh-Nasseri S. HLA-dm recognizes the flexible conformation of major histocompatibility complex class II. J Exp Med. 2000;192(12):1697–706.CrossRefPubMed Chou CL, Sadegh-Nasseri S. HLA-dm recognizes the flexible conformation of major histocompatibility complex class II. J Exp Med. 2000;192(12):1697–706.CrossRefPubMed
33.
go back to reference Pu Z, Lovitch SB, Bikoff EK, Unanue ER. T cells distinguish MHC-peptide complexes formed in separate vesicles and edited by H2-DM. Immunity. 2004;20(4):467–76.CrossRefPubMed Pu Z, Lovitch SB, Bikoff EK, Unanue ER. T cells distinguish MHC-peptide complexes formed in separate vesicles and edited by H2-DM. Immunity. 2004;20(4):467–76.CrossRefPubMed
34.
go back to reference Marin-Esteban V, Falk K, Rotzschke O. “Chemical analogues” Of HLA-DM can induce a peptide-receptive state in HLA-DR molecules. J Biol Chem. 2004;279(49):50684–90.CrossRefPubMed Marin-Esteban V, Falk K, Rotzschke O. “Chemical analogues” Of HLA-DM can induce a peptide-receptive state in HLA-DR molecules. J Biol Chem. 2004;279(49):50684–90.CrossRefPubMed
35.
go back to reference Pashine A, Busch R, Belmares MP, Munning JN, Doebele RC, Buckingham M, et al. Interaction of HLA-DR with an acidic face of HLA-DM disrupts sequence-dependent interactions with peptides. Immunity. 2003;19(2):183–92.CrossRefPubMed Pashine A, Busch R, Belmares MP, Munning JN, Doebele RC, Buckingham M, et al. Interaction of HLA-DR with an acidic face of HLA-DM disrupts sequence-dependent interactions with peptides. Immunity. 2003;19(2):183–92.CrossRefPubMed
36.
go back to reference Belmares MP, Busch R, Mellins ED, McConnell HM. Formation of two peptide/MHC II isomers is catalyzed differentially by HLA-DM. Biochemistry. 2003;42(3):838–47.CrossRefPubMed Belmares MP, Busch R, Mellins ED, McConnell HM. Formation of two peptide/MHC II isomers is catalyzed differentially by HLA-DM. Biochemistry. 2003;42(3):838–47.CrossRefPubMed
37.
go back to reference Stratikos E, Mosyak L, Zaller DM, Wiley DC. Identification of the lateral interaction surfaces of human histocompatibility leukocyte antigen (HLA)-DM with HLA-DR1 by formation of tethered complexes that present enhanced HLA-dm catalysis. J Exp Med. 2002;196(2):173–83.CrossRefPubMed Stratikos E, Mosyak L, Zaller DM, Wiley DC. Identification of the lateral interaction surfaces of human histocompatibility leukocyte antigen (HLA)-DM with HLA-DR1 by formation of tethered complexes that present enhanced HLA-dm catalysis. J Exp Med. 2002;196(2):173–83.CrossRefPubMed
38.
go back to reference Doebele RC, Busch R, Scott HM, Pashine A, Mellins ED. Determination of the HLA-DM interaction site on HLA-DR molecules. Immunity. 2000;13(4):517–27.CrossRefPubMed Doebele RC, Busch R, Scott HM, Pashine A, Mellins ED. Determination of the HLA-DM interaction site on HLA-DR molecules. Immunity. 2000;13(4):517–27.CrossRefPubMed
39.
go back to reference Narayan K, Chou CL, Kim A, Hartman IZ, Dalai S, Khoruzhenko S, et al. HLA-DM targets the hydrogen bond between the histidine at position beta81 and peptide to dissociate HLA-DR-peptide complexes. Nat Immunol. 2007;8(1):92–100.CrossRefPubMed Narayan K, Chou CL, Kim A, Hartman IZ, Dalai S, Khoruzhenko S, et al. HLA-DM targets the hydrogen bond between the histidine at position beta81 and peptide to dissociate HLA-DR-peptide complexes. Nat Immunol. 2007;8(1):92–100.CrossRefPubMed
40.
go back to reference Fremont DH, HenDRickson WA, Marrack P, Kappler J. Structures of an MHC class II molecule with covalently bound single peptides. Science. 1996;272(5264):1001–4.CrossRefPubMed Fremont DH, HenDRickson WA, Marrack P, Kappler J. Structures of an MHC class II molecule with covalently bound single peptides. Science. 1996;272(5264):1001–4.CrossRefPubMed
41.
go back to reference Fremont DH, Monnaie D, Nelson CA, HenDRickson WA, Unanue ER. Crystal structure of I-Ak in complex with a dominant epitope of lysozyme. Immunity. 1998;8(3):305–17.CrossRefPubMed Fremont DH, Monnaie D, Nelson CA, HenDRickson WA, Unanue ER. Crystal structure of I-Ak in complex with a dominant epitope of lysozyme. Immunity. 1998;8(3):305–17.CrossRefPubMed
42.
go back to reference Wilson N, Fremont D, Marrack P, Kappler J. Mutations changing the kinetics of class II MHC peptide exchange. Immunity. 2001;14(5):513–22.CrossRefPubMed Wilson N, Fremont D, Marrack P, Kappler J. Mutations changing the kinetics of class II MHC peptide exchange. Immunity. 2001;14(5):513–22.CrossRefPubMed
43.
go back to reference McFarland BJ, Beeson C, Sant AJ. Cutting edge: a single, essential hydrogen bond controls the stability of peptide-MHC class II complexes. J Immunol. 1999;163(7):3567–71.PubMed McFarland BJ, Beeson C, Sant AJ. Cutting edge: a single, essential hydrogen bond controls the stability of peptide-MHC class II complexes. J Immunol. 1999;163(7):3567–71.PubMed
44.
go back to reference Saito K, Oda M, Sarai A, Azuma T, Kozono H. Contribution of a single hydrogen bond between betahis81 of MHC class II I-E(k) and the bound peptide to the PH-dependent thermal stability. Microbiol Immunol. 2004;48(1):53–7.PubMed Saito K, Oda M, Sarai A, Azuma T, Kozono H. Contribution of a single hydrogen bond between betahis81 of MHC class II I-E(k) and the bound peptide to the PH-dependent thermal stability. Microbiol Immunol. 2004;48(1):53–7.PubMed
45.
go back to reference Sadegh-Nasseri S, Chen M, Narayan K, Bouvier M. The convergent roles of tapasin and HLA-DM in antigen presentation. Trends Immunol. 2008;29(3):141–7.CrossRefPubMed Sadegh-Nasseri S, Chen M, Narayan K, Bouvier M. The convergent roles of tapasin and HLA-DM in antigen presentation. Trends Immunol. 2008;29(3):141–7.CrossRefPubMed
46.
go back to reference Narayan K, Su KW, Chou CL, Khoruzhenko S, Sadegh-Nasseri S. HLA-DM mediates peptide exchange by interacting transiently and repeatedly with HLA-DR1. Mol Immunol. 2009;46(15):3157–62.CrossRefPubMed Narayan K, Su KW, Chou CL, Khoruzhenko S, Sadegh-Nasseri S. HLA-DM mediates peptide exchange by interacting transiently and repeatedly with HLA-DR1. Mol Immunol. 2009;46(15):3157–62.CrossRefPubMed
47.
go back to reference Chen M, Bouvier M. Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J. 2007;26(6):1681–90.CrossRefPubMed Chen M, Bouvier M. Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J. 2007;26(6):1681–90.CrossRefPubMed
Metadata
Title
Conformational heterogeneity of MHC class II induced upon binding to different peptides is a key regulator in antigen presentation and epitope selection
Authors
Scheherazade Sadegh-Nasseri
Sateesh Natarajan
Chih-Ling Chou
Isamu Z. Hartman
Kedar Narayan
AeRyon Kim
Publication date
01-07-2010
Publisher
Humana Press Inc
Published in
Immunologic Research / Issue 1-3/2010
Print ISSN: 0257-277X
Electronic ISSN: 1559-0755
DOI
https://doi.org/10.1007/s12026-009-8138-1

Other articles of this Issue 1-3/2010

Immunologic Research 1-3/2010 Go to the issue