Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex

Cyril Reboul, Grischa R Meyer, Benjamin Porebski, Natalie A Borg, Ashley M Buckle

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35 Citations (Scopus)

Abstract

The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent snapshots and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on alpha2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into scanning mechanism of SB27 that extends the role of the germline encoded CDR2alpha and CDR2beta loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.
Original languageEnglish
Pages (from-to)1 - 11
Number of pages11
JournalPLoS Computational Biology
Volume8
Issue number3 (Art. ID: e1002404)
DOIs
Publication statusPublished - 2012

Cite this

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title = "Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex",
abstract = "The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent snapshots and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on alpha2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into scanning mechanism of SB27 that extends the role of the germline encoded CDR2alpha and CDR2beta loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.",
author = "Cyril Reboul and Meyer, {Grischa R} and Benjamin Porebski and Borg, {Natalie A} and Buckle, {Ashley M}",
year = "2012",
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Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex. / Reboul, Cyril; Meyer, Grischa R; Porebski, Benjamin; Borg, Natalie A; Buckle, Ashley M.

In: PLoS Computational Biology, Vol. 8, No. 3 (Art. ID: e1002404), 2012, p. 1 - 11.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex

AU - Reboul, Cyril

AU - Meyer, Grischa R

AU - Porebski, Benjamin

AU - Borg, Natalie A

AU - Buckle, Ashley M

PY - 2012

Y1 - 2012

N2 - The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent snapshots and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on alpha2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into scanning mechanism of SB27 that extends the role of the germline encoded CDR2alpha and CDR2beta loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.

AB - The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent snapshots and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on alpha2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into scanning mechanism of SB27 that extends the role of the germline encoded CDR2alpha and CDR2beta loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.

UR - http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002404

U2 - 10.1371/journal.pcbi.1002404

DO - 10.1371/journal.pcbi.1002404

M3 - Article

VL - 8

SP - 1

EP - 11

JO - PLoS Computational Biology

JF - PLoS Computational Biology

SN - 1553-7358

IS - 3 (Art. ID: e1002404)

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